Contacts of the helix formed by residues 83 - 110 (chain B) in PDB entry 5HJS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 83 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 1.4 70.3 - - - +
84B GLU* 1.4 57.0 + - - +
86B ARG* 3.7 34.0 - - - +
87B GLN* 2.9 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 3.1 10.3 + - - +
83B ARG* 1.4 78.6 - - - +
85B ALA* 1.4 56.5 + - - +
87B GLN* 3.7 7.9 - - - +
88B GLN* 3.0 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 3.4 18.8 - - + +
82B SER* 3.0 25.7 + - - +
84B GLU* 1.4 72.5 + - - +
86B ARG* 1.4 60.9 + - - +
88B GLN* 3.4 2.4 + - - +
89B ARG* 3.1 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 3.0 18.6 + - - +
83B ARG* 3.7 47.9 - - - +
85B ALA* 1.4 75.0 - - - +
87B GLN* 1.4 60.1 + - + +
89B ARG* 3.5 13.9 + - - +
90B PHE* 3.3 23.4 + - - +
164B LYS 4.6 9.1 - - - +
165B ALA 5.5 0.5 - - - -
166B GLY* 6.6 0.2 - - - -
269B LYS* 5.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 2.9 63.9 + - + +
84B GLU* 3.7 7.4 - - - +
86B ARG* 1.4 75.1 - - + +
88B GLN* 1.3 56.8 + - - +
90B PHE* 3.6 7.5 + - - +
91B ALA* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.7 21.4 - - + +
73B PRO* 3.2 26.8 - - - +
74B TRP 4.6 0.2 - - - -
75B PRO* 3.8 26.0 - - + +
84B GLU* 3.0 38.8 + - - +
85B ALA* 3.7 5.7 - - - +
86B ARG 3.3 0.2 - - - -
87B GLN* 1.3 74.7 - - - +
89B ARG* 1.4 59.3 + - - +
91B ALA* 3.5 6.7 + - - +
92B HIS* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.5 39.5 - - + +
75B PRO* 3.5 29.7 - - + +
85B ALA* 3.1 47.4 + - - +
86B ARG* 3.8 8.1 - - - +
87B GLN 3.4 0.2 - - - -
88B GLN* 1.4 72.6 - - - +
90B PHE* 1.3 63.8 + - - +
92B HIS* 3.2 4.9 + - - +
93B PHE* 3.1 21.7 + - - +
164B LYS* 3.3 57.2 + - - +
165B ALA* 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG 3.3 14.2 + - - +
87B GLN* 3.7 8.1 - - - +
89B ARG* 1.3 75.1 - - - +
91B ALA* 1.4 61.0 + - - +
93B PHE* 3.3 4.2 + - - +
94B THR* 2.9 49.2 + - + +
165B ALA 3.3 27.5 + - - +
166B GLY* 4.6 1.3 - - - -
264B LEU* 4.1 23.3 - - + -
269B LYS* 3.7 44.0 - - + +
270B LYS 3.6 25.6 - - - -
271B LEU* 4.5 3.1 - - + -
272B PRO* 5.3 0.4 - - + -
301B 668 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 4.3 10.8 - - + +
87B GLN 3.0 20.1 + - - +
88B GLN* 3.7 6.1 - - - +
89B ARG 3.4 0.2 - - - -
90B PHE* 1.4 75.2 - - + +
92B HIS* 1.4 59.7 + - - +
94B THR* 2.9 9.5 + - - -
95B GLU* 2.8 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.8 15.0 - - + +
72B THR* 2.7 30.8 + - - +
73B PRO* 4.5 3.1 - - + +
74B TRP* 3.5 28.9 + + + -
88B GLN 2.9 14.9 + - - +
89B ARG 3.2 9.6 + - - +
91B ALA* 1.4 75.5 - - - +
93B PHE* 1.3 57.8 + + - +
95B GLU* 3.3 4.0 + - - +
96B LEU* 3.0 51.6 + - + +
155B PHE* 3.8 29.0 - + - -
157B TYR* 2.7 33.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 3.6 28.3 - + - -
89B ARG 3.1 7.2 + - - +
90B PHE 3.8 6.5 - - - +
92B HIS* 1.3 79.1 - + - +
94B THR* 1.4 58.8 + - - +
96B LEU* 3.5 8.9 + - + +
97B ALA* 3.0 27.0 + - - +
151B PHE* 4.3 8.1 - + - -
157B TYR* 4.0 27.4 - + + -
161B ASP 4.4 0.7 - - - -
162B PHE* 3.8 52.3 - + - -
165B ALA* 3.6 27.1 - - + -
167B LEU* 3.9 12.1 - - + -
301B 668 3.7 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 2.9 43.6 + - + +
91B ALA* 2.9 19.2 + - - -
93B PHE* 1.4 72.7 - - - +
95B GLU* 1.3 61.7 + - - +
97B ALA* 3.4 2.8 + - - +
98B ILE* 3.0 32.6 + - - +
271B LEU* 4.4 1.6 - - + -
272B PRO* 3.7 30.1 - - + +
275B LEU* 3.6 3.8 - - + +
301B 668 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG 4.0 5.0 - - - +
71B VAL* 3.7 17.3 - - + -
72B THR* 2.8 46.2 + - - -
91B ALA* 2.8 30.4 + - - +
92B HIS 3.7 3.6 - - - +
94B THR* 1.3 79.4 + - - +
96B LEU* 1.4 62.1 + - - +
98B ILE* 3.3 16.3 + - + +
99B VAL* 3.1 27.9 + - - +
272B PRO* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.3 9.8 - - + +
92B HIS* 3.0 45.4 + - + +
93B PHE* 3.8 10.5 - - + +
94B THR 3.4 0.2 - - - -
95B GLU* 1.4 74.0 - - - +
97B ALA* 1.3 57.9 + - - +
99B VAL* 3.3 6.2 + - - +
100B SER 3.0 22.5 + - - -
151B PHE* 3.7 33.4 - - + -
152B LEU* 3.8 21.1 - - + -
155B PHE* 4.0 14.8 - - + -
157B TYR* 4.4 2.2 - - + -
301B 668 3.4 40.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE 3.0 16.6 + - - +
94B THR 3.5 5.8 - - - +
95B GLU 3.3 0.2 - - - -
96B LEU* 1.3 77.0 - - - +
98B ILE* 1.4 56.6 + - - +
100B SER* 3.3 3.9 + - - -
101B VAL* 3.0 32.4 + - - +
134B MET* 3.7 24.5 - - + +
275B LEU* 3.8 20.6 - - + -
279B TRP* 4.7 0.7 - - + -
301B 668 4.0 19.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR 3.0 16.3 + - - +
95B GLU* 3.3 17.5 + - + +
97B ALA* 1.4 71.4 - - - +
99B VAL* 1.4 64.8 + - + +
101B VAL* 3.3 5.2 + - - +
102B GLN* 3.1 45.6 + - - +
272B PRO* 3.6 33.0 - - + -
273B PRO* 5.6 0.4 - - + -
274B LEU* 4.5 20.6 - - + +
275B LEU* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.9 39.0 - - + -
71B VAL* 4.4 9.6 - - + -
95B GLU 3.1 17.2 + - - +
96B LEU* 3.3 9.4 + - - +
98B ILE* 1.4 75.1 - - + +
100B SER* 1.4 57.7 + - - +
102B GLN* 3.3 14.5 + - - +
103B GLU* 3.0 45.4 + - + +
152B LEU* 4.5 9.0 - - + -
301B 668 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU 3.0 13.4 + - - -
97B ALA* 3.3 11.4 + - - -
99B VAL* 1.4 72.9 - - - +
101B VAL* 1.4 63.9 + - - +
103B GLU* 3.2 4.4 + - - +
104B ILE* 3.0 32.5 + - - +
134B MET* 3.4 27.4 - - - +
137B GLU* 5.0 3.8 - - - +
301B 668 3.9 39.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA 3.0 19.7 + - - +
98B ILE 3.8 5.8 - - - +
100B SER* 1.4 72.3 - - - +
102B GLN* 1.3 64.1 + - - +
104B ILE* 3.1 10.8 + - + +
105B VAL* 3.0 35.3 + - + +
130B ALA* 4.8 7.6 - - + -
134B MET* 4.1 16.2 - - - -
274B LEU* 3.8 27.8 - - + -
275B LEU* 4.1 12.3 - - + -
278B ILE* 4.0 28.3 - - + -
5D LEU* 5.3 3.8 - - + -
8D LEU* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 3.1 34.0 + - - +
99B VAL* 3.5 16.2 - - - +
101B VAL* 1.3 76.6 - - - +
103B GLU* 1.3 56.3 + - + +
105B VAL* 3.5 7.1 + - - +
106B ASP* 3.1 35.5 + - - +
274B LEU* 4.6 5.2 - - + +
4D ILE* 6.2 1.0 - - - +
8D LEU* 4.0 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN 5.1 6.1 - - - +
99B VAL* 3.0 26.2 + - + +
100B SER 3.2 8.5 + - - +
102B GLN* 1.3 73.5 - - + +
104B ILE* 1.3 61.2 + - + +
106B ASP* 3.5 9.9 + - - +
107B PHE* 2.9 30.0 + - - +
141B ARG* 5.4 0.3 + - - -
152B LEU* 4.9 3.3 - - - +
301B 668 3.5 41.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B SER* 3.0 24.5 + - - +
101B VAL* 3.1 11.4 + - + +
103B GLU* 1.3 73.9 - - + +
105B VAL* 1.4 55.6 + - + +
107B PHE* 3.3 7.6 + - + +
108B ALA* 2.8 36.7 + - - +
126B LEU* 4.2 18.8 - - + -
129B SER* 5.5 0.4 - - - +
130B ALA* 3.6 22.4 - - + +
133B VAL* 3.6 34.3 - - + +
134B MET* 3.6 31.4 - - + +
137B GLU* 5.4 4.3 - - + +
196B ILE* 5.9 0.4 - - + -
200B ILE* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.0 29.5 + - + +
102B GLN 3.7 5.8 - - - +
104B ILE* 1.4 74.1 - - + +
106B ASP* 1.3 64.9 + - - +
108B ALA* 3.4 6.6 + - - +
109B LYS* 3.0 32.4 + - + +
126B LEU* 4.1 10.1 - - + -
5D LEU* 3.7 26.5 - - + -
8D LEU* 3.8 43.7 - - + +
9D LEU* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 3.1 22.5 + - - +
103B GLU* 3.6 8.9 - - - +
104B ILE 3.3 0.2 - - - -
105B VAL* 1.3 81.3 - - - +
107B PHE* 1.4 61.0 + - - +
109B LYS* 3.6 21.1 + - - +
110B GLN* 3.3 19.8 + - - +
8D LEU* 5.2 1.4 - - - +
11D GLU* 5.0 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.4 35.7 - - + -
56B ALA* 4.2 16.2 - - + +
57B GLN* 3.4 32.5 - - + +
103B GLU 2.9 18.4 + - - +
104B ILE* 3.7 6.3 - - - +
106B ASP* 1.4 73.3 - - - +
108B ALA* 1.4 62.7 + - - +
110B GLN* 3.0 24.2 + - - +
111B LEU* 3.4 34.4 + - + +
133B VAL* 6.0 0.4 - - + -
193B ALA* 4.0 24.2 - - + -
196B ILE* 3.5 33.4 - - + -
197B ALA 4.7 0.2 - - - -
200B ILE* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE 2.8 22.1 + - - +
105B VAL* 3.6 5.8 - - - +
107B PHE* 1.4 70.9 - - - +
109B LYS* 1.3 64.1 + - - +
111B LEU* 3.0 25.2 + - - +
114B PHE* 3.1 37.3 - - + +
126B LEU* 3.7 25.4 - - + -
200B ILE* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.0 32.7 + - + +
106B ASP* 3.9 16.0 + - - +
107B PHE 3.2 0.6 - - - -
108B ALA* 1.3 78.1 - - - +
110B GLN* 1.4 60.4 + - + +
111B LEU 3.7 3.3 + - - +
114B PHE* 4.1 6.5 - - + +
115B LEU* 3.4 38.9 - - + +
8D LEU 3.1 19.0 + - - -
9D LEU* 3.4 37.3 + - + +
11D GLU* 3.9 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.5 6.0 - - + +
56B ALA* 3.7 36.6 + - + +
106B ASP 3.3 18.6 - - - +
107B PHE* 3.0 11.8 + - + +
109B LYS* 1.4 78.5 - - + +
111B LEU* 1.3 63.7 + - - +
112B PRO* 3.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il