Contacts of the helix formed by residues 85 - 104 (chain B) in PDB entry 2HXO
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 SER 85 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 1.3 78.7 - - - +
86B PRO* 1.3 76.6 - - - +
87B GLN* 3.5 14.8 + - - +
88B ASP* 3.1 28.2 + - - +
89B ALA* 2.9 21.2 + - - +
91B ARG* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP 4.4 1.6 - - - +
85B SER* 1.3 88.9 - - - +
87B GLN* 1.3 61.4 + - - +
89B ALA* 3.3 2.4 + - - +
90B VAL* 3.0 34.1 + - - +
134B GLN* 3.3 28.1 - - + +
137B ALA* 3.8 30.1 - - + +
138B MSE 3.6 26.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
85B SER* 3.1 11.7 - - - +
86B PRO* 1.3 92.9 - - - +
88B ASP* 1.3 59.9 + - - +
90B VAL* 3.3 4.7 + - - +
91B ARG* 3.1 41.6 + - - +
138B MSE 3.6 24.2 - - + +
225B LEU* 3.7 30.4 - - + +
229B THR* 3.6 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 3.9 23.7 - - + +
85B SER* 3.1 23.1 + - - +
87B GLN* 1.3 74.4 - - - +
89B ALA* 1.3 61.6 + - - +
91B ARG* 2.9 33.2 + - - +
92B ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 4.8 13.4 + - - +
85B SER 2.9 13.2 + - - +
86B PRO 3.5 8.7 - - - +
88B ASP* 1.3 77.8 - - - +
90B VAL* 1.3 61.5 + - - +
92B ALA* 3.2 9.2 + - - +
93B VAL* 3.0 28.7 + - + +
134B GLN* 3.6 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO 3.0 17.8 + - - +
87B GLN 3.6 8.1 - - - +
89B ALA* 1.3 75.7 - - - +
91B ARG* 1.3 58.4 + - - +
93B VAL* 3.2 9.9 + - - +
94B ALA* 2.9 26.8 + - + +
131B LEU* 4.2 14.3 - - + +
134B GLN* 3.6 22.7 - - + -
135B VAL* 5.8 0.2 - - + -
138B MSE 5.2 2.0 - - - -
152B LEU* 4.0 36.8 - - + -
156B ILE* 6.0 0.9 - - + -
221B ILE* 4.4 9.2 - - + -
225B LEU* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 5.2 0.2 + - - -
87B GLN* 3.1 32.4 + - - +
88B ASP* 2.9 35.0 + - - +
90B VAL* 1.3 75.7 - - - +
92B ALA* 1.3 59.8 + - - +
94B ALA* 3.8 6.3 - - - +
95B LEU* 2.8 39.9 + - + +
218B LEU* 4.5 18.8 + - + +
221B ILE* 4.0 17.3 - - + +
222B THR* 3.1 40.4 + - - +
225B LEU* 4.3 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA 5.1 0.5 - - - +
75B VAL 4.7 11.3 - - - +
84B ASP* 5.7 3.6 - - - +
88B ASP 2.9 11.4 + - - +
89B ALA* 3.2 12.1 + - - +
91B ARG* 1.3 73.2 - - - +
93B VAL* 1.3 62.4 + - + +
95B LEU* 4.1 6.8 - - - +
96B GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.9 24.9 - - + +
89B ALA* 3.0 17.6 + - + +
90B VAL* 3.2 9.2 + - - +
92B ALA* 1.3 78.6 - - + +
94B ALA* 1.3 61.3 + - - +
96B GLY* 3.3 2.3 + - - -
97B LEU* 3.1 36.4 + - + +
127B ILE* 5.0 4.3 - - + -
130B SER* 4.1 29.6 - - - +
131B LEU* 3.7 28.3 - - + -
134B GLN* 5.9 0.4 - - + -
156B ILE* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 2.9 16.0 + - + +
91B ARG* 3.8 5.6 - - - +
93B VAL* 1.3 75.4 - - - +
95B LEU* 1.3 53.7 + - - +
97B LEU* 3.2 7.1 + - - +
98B TRP* 2.7 34.7 + - - +
131B LEU* 5.5 0.9 - - + +
156B ILE* 3.4 33.7 - - + -
217B PHE* 3.6 17.1 - - + -
218B LEU* 5.6 0.4 - - + -
221B ILE* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 2.8 29.1 + - + +
92B ALA* 4.1 6.1 - - - +
94B ALA* 1.3 69.4 - - - +
96B GLY* 1.3 58.8 + - - +
98B TRP* 3.9 5.2 - - + -
99B ASP* 2.6 45.3 + - - +
214B ARG* 3.6 34.3 - - + +
217B PHE* 4.2 10.5 - - + -
218B LEU* 3.8 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 3.2 40.6 - - - +
75B VAL* 4.2 3.4 - - - -
92B ALA 2.9 18.3 + - - -
93B VAL 3.7 2.5 - - - -
94B ALA 3.2 0.2 - - - -
95B LEU* 1.3 77.2 - - - +
97B LEU* 1.3 56.3 + - - +
99B ASP* 4.0 3.2 - - - +
100B ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.0 37.0 - - + -
74B ALA* 5.4 0.2 - - - -
75B VAL* 4.4 6.3 - - + -
93B VAL* 3.1 24.4 + - + +
94B ALA* 3.5 7.4 - - - +
95B LEU 3.2 0.2 - - - -
96B GLY* 1.3 73.9 - - - +
98B TRP* 1.3 64.9 + - - +
100B ALA* 3.4 2.8 + - + +
101B THR* 3.0 34.6 + - + +
107B LEU* 5.5 0.9 - - + -
111B LEU* 4.4 14.8 - - + -
127B ILE* 4.1 35.7 - - + -
131B LEU* 5.9 0.7 - - + -
153B MSE 6.3 0.2 - - + -
156B ILE* 3.9 28.5 - - + -
157B LEU* 5.4 4.9 - - + -
160B ALA* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA 2.7 20.7 + - - +
95B LEU* 3.6 5.8 - - + +
97B LEU* 1.3 72.9 - - - +
99B ASP* 1.3 78.5 + - - +
101B THR* 3.2 17.7 + - - -
102B GLU* 3.3 25.1 + - - +
159B ALA* 3.6 14.4 - - + -
160B ALA* 3.8 19.2 - - - +
163B ASN* 3.2 48.6 + - + -
213B ASP* 3.8 20.4 - - + -
214B ARG* 3.7 47.5 - - + +
217B PHE* 3.5 43.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 5.8 1.8 - - + -
95B LEU* 2.6 25.0 + - - +
96B GLY* 4.2 3.5 - - - +
98B TRP* 1.3 73.9 - - - +
100B ALA* 1.3 60.2 + - - +
102B GLU* 3.1 17.4 + - - +
103B ALA* 2.9 29.9 + - - +
214B ARG* 2.9 43.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.9 13.5 - - + +
71B VAL* 5.1 2.2 - - + -
74B ALA* 3.6 18.8 - - + +
96B GLY 3.0 19.7 + - - +
97B LEU* 3.8 5.2 - - - +
98B TRP 3.3 0.2 - - - -
99B ASP* 1.3 77.6 - - - +
101B THR* 1.3 57.2 + - - +
102B GLU 3.0 0.2 - - - -
103B ALA* 3.2 5.2 + - - +
104B HIS* 2.8 35.8 + - - +
107B LEU* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.0 16.4 + - + +
98B TRP 3.2 11.4 + - - -
100B ALA* 1.3 74.1 - - - +
102B GLU* 1.3 59.1 + - - +
104B HIS 3.5 21.4 - - - +
105B PRO* 3.8 7.8 - - - +
107B LEU* 3.6 24.7 - - + -
108B ALA* 4.3 12.1 - - + +
111B LEU* 4.3 15.5 - - + -
160B ALA* 3.7 32.6 + - + +
163B ASN* 5.1 2.1 + - - -
164B ALA* 3.9 14.6 - - - +
167B SER* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.3 22.3 + - - +
99B ASP* 3.2 28.9 - - - +
100B ALA 3.0 0.4 - - - -
101B THR* 1.3 79.5 - - - +
103B ALA* 1.3 62.5 + - - +
104B HIS 3.3 0.2 - - - -
105B PRO* 4.5 5.9 - - - +
163B ASN* 3.4 26.3 + - - +
164B ALA* 5.8 0.2 - - - +
167B SER* 4.8 19.7 + - - +
214B ARG* 4.4 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 4.1 4.5 - - - +
99B ASP 2.9 14.5 + - - +
100B ALA* 3.2 5.6 + - - +
102B GLU* 1.3 79.3 - - - +
104B HIS* 1.3 80.0 + - + +
105B PRO* 3.6 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.8 14.6 - - + -
29B ASP* 2.7 37.5 + - - -
70B VAL* 3.3 33.0 - - + +
100B ALA* 2.8 13.8 + - - +
101B THR* 3.5 7.5 - - - +
103B ALA* 1.3 93.3 + - + +
105B PRO* 1.3 63.2 - - - +
106B TRP* 3.2 26.9 + + + +
107B LEU* 2.8 29.0 + - + +
----------------------------------------------------------
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