Contacts of the helix formed by residues 84 - 102 (chain B) in PDB entry 4EA3
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 THR 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LYS 5.7 0.7 - - - +
82B MET* 2.9 16.7 + - + +
83B LYS* 1.3 76.4 - - - +
85B ALA* 1.3 66.8 + - - +
86B THR* 3.9 5.0 + - - -
87B ASN* 2.9 36.9 + - - +
88B ILE* 3.0 14.4 + - - +
162B ARG* 5.4 4.5 - - - -
164B SER* 4.7 0.7 - - - +
325B ASN* 6.2 2.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
84B THR* 1.3 74.9 - - - +
86B THR* 1.3 61.7 + - - +
88B ILE 3.4 0.7 + - - -
89B TYR* 2.9 29.3 + - + -
147B ASP* 3.4 24.7 - - - +
162B ARG* 3.4 42.8 + - + +
163B THR 4.7 1.1 - - - -
164B SER* 4.7 2.0 - - - +
167B ALA* 3.7 20.3 - - + +
1502B OLC 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.2 5.0 + - - -
85B ALA* 1.3 77.3 - - - +
87B ASN* 1.3 63.6 + - - +
89B TYR* 3.1 13.1 + - - +
90B ILE* 2.9 35.7 + - + +
144B MET* 4.0 22.1 + - + +
147B ASP* 3.5 7.6 + - - -
148B ARG* 3.8 10.0 + - - -
162B ARG* 3.5 17.3 + - - +
261B ILE* 3.9 23.2 - - + +
264B LEU* 5.3 4.3 - - + -
265B VAL* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.5 18.7 - - + +
82B MET* 2.9 54.6 + - - +
84B THR* 2.9 19.1 + - - +
86B THR* 1.3 80.5 - - - +
88B ILE* 1.3 57.3 + - - +
90B ILE* 3.9 10.5 - - - +
91B PHE* 2.7 32.6 + - - +
323B ASP* 4.5 5.1 + - - +
325B ASN* 5.3 3.0 - - - +
326B PHE* 4.0 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 4.3 10.5 - - + -
83B LYS* 3.9 32.3 - - + -
84B THR 3.0 12.5 + - - +
85B ALA 3.7 7.0 - - - +
87B ASN* 1.3 78.9 - - - +
89B TYR* 1.3 60.8 + - - +
91B PHE* 3.5 9.3 - - + +
92B ASN 3.3 9.5 + - - -
164B SER* 3.8 23.1 - - - -
167B ALA* 3.9 5.4 - - + -
168B GLN* 3.8 38.4 - - + +
171B ASN* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA 2.9 24.0 + - - -
86B THR* 3.1 7.3 + - - +
88B ILE* 1.3 77.2 - - - +
90B ILE* 1.3 64.9 + - - +
91B PHE 3.2 0.2 - - - -
92B ASN* 3.0 14.0 + - - +
93B LEU* 3.1 10.2 + - - +
140B THR* 3.3 13.1 - - + +
143B ALA* 4.1 16.4 - - + -
144B MET* 3.2 35.4 - - + -
147B ASP* 4.0 24.2 - - + -
167B ALA* 3.4 39.2 - - + -
170B VAL* 3.5 30.4 - - + +
171B ASN* 3.4 14.1 - - - -
174B ILE* 5.1 0.4 - - + -
1502B OLC 3.5 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.9 16.6 - - + -
76B ILE* 4.2 5.2 - - + -
86B THR* 2.9 24.3 + - + +
87B ASN* 3.5 18.6 - - - +
89B TYR* 1.3 75.8 - - - +
91B PHE* 1.3 62.7 + - - +
93B LEU* 3.1 10.8 + - - +
94B ALA* 2.9 21.5 + - - +
144B MET* 4.0 16.1 - - + -
264B LEU* 4.4 10.5 - - + -
319B TYR* 3.5 47.3 + - + +
326B PHE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 5.4 0.2 - - - -
73B MET* 3.6 65.9 - - + +
76B ILE* 4.4 19.3 - - + -
77B LEU* 4.2 25.8 - - + -
87B ASN 2.7 20.5 + - - +
88B ILE* 3.5 15.0 - - + +
90B ILE* 1.3 73.6 - - - +
92B ASN* 1.3 60.1 + - - +
94B ALA* 3.2 6.5 + - - +
95B LEU* 2.9 39.5 + - + +
171B ASN* 5.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE 3.3 2.2 + - - -
89B TYR 3.0 11.7 + - - +
91B PHE* 1.3 82.3 - - - +
93B LEU* 1.3 62.2 + - - +
95B LEU* 3.5 9.6 + - - +
96B ALA* 3.1 22.3 + - - +
136B THR* 4.7 2.4 + - - -
140B THR* 2.9 24.3 + - - +
171B ASN* 3.0 41.4 + - - +
174B ILE* 3.9 14.1 - - - +
175B TRP* 2.7 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR 3.1 14.6 + - - +
90B ILE* 3.1 8.5 + - - +
92B ASN* 1.3 73.6 - - - +
94B ALA* 1.3 61.0 + - - +
96B ALA* 3.1 6.8 + - - +
97B ASP* 2.8 40.2 + - - +
136B THR 5.1 0.2 - - - -
137B SER* 3.8 29.4 - - - +
140B THR* 3.7 24.9 - - + +
141B LEU* 4.1 16.2 - - + -
144B MET* 3.9 23.1 - - + -
268B VAL* 4.4 8.7 - - + -
272B PHE* 6.6 0.2 - - + -
315B ASN* 4.5 6.3 - - - +
319B TYR* 3.7 20.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
69B ASN* 3.3 32.4 - - + +
72B VAL* 4.4 11.4 - - + -
73B MET* 3.6 20.9 - - + -
90B ILE* 2.9 13.2 + - + +
91B PHE 3.6 7.0 - - - +
93B LEU* 1.3 75.3 - - - +
95B LEU* 1.3 57.6 + - - +
97B ASP* 3.2 1.8 + - - +
98B THR* 2.8 35.9 + - - -
319B TYR* 5.4 2.7 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
73B MET* 3.8 28.8 - - + -
91B PHE* 2.9 27.8 + - + +
92B ASN* 3.6 9.6 - - - +
94B ALA* 1.3 77.1 - - - +
96B ALA* 1.3 62.6 + - - +
98B THR* 3.2 8.5 + - + -
99B LEU* 3.2 40.8 + - + +
175B TRP* 4.1 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASN 3.1 9.7 + - - +
93B LEU* 3.1 11.3 + - - +
95B LEU* 1.3 81.2 - - - +
97B ASP* 1.3 62.5 + - - +
99B LEU* 3.1 16.8 + - - +
100B VAL* 3.1 14.4 + - - +
133B ASN* 4.3 16.7 - - - +
136B THR* 3.5 28.0 - - - +
137B SER* 4.7 4.5 - - - +
175B TRP* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASN* 3.4 27.3 - - - +
93B LEU* 2.8 22.8 + - - +
94B ALA* 3.6 6.9 - - - +
96B ALA* 1.3 72.6 - - - +
98B THR* 1.3 64.4 + - - +
100B VAL* 3.1 7.5 - - - +
101B LEU* 2.9 31.6 + - - +
133B ASN* 4.1 10.6 - - - +
137B SER* 4.8 4.3 + - - -
311B ASN* 5.0 3.5 - - - +
312B SER* 3.5 28.1 + - - +
315B ASN* 3.3 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.8 20.5 - - + +
69B ASN* 3.9 10.3 - - - +
70B CYS* 4.6 13.0 - - - -
73B MET* 3.7 17.2 - - + -
94B ALA 2.8 20.0 + - - -
95B LEU* 3.2 13.5 - - + -
97B ASP* 1.3 78.3 - - - +
99B LEU* 1.3 69.3 + - + +
101B LEU* 3.3 5.2 + - - +
102B LEU* 3.2 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.2 29.6 + - + +
96B ALA* 3.1 8.8 + - - +
98B THR* 1.3 86.0 - - + +
100B VAL* 1.3 63.5 + - - +
102B LEU* 3.2 28.5 + - + +
103B THR* 3.5 10.0 - - - +
129B ILE* 3.8 33.0 - - + +
132B TYR* 6.0 1.8 - - + -
175B TRP* 4.1 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA 3.1 9.9 + - - +
97B ASP* 3.1 15.0 - - - +
99B LEU* 1.3 76.1 - - - +
101B LEU* 1.3 70.9 + - - +
103B THR* 2.6 29.7 + - - +
104B LEU* 3.7 5.7 + - + +
107B GLN* 5.2 0.4 - - - +
129B ILE* 3.5 18.8 - - + +
130B ASP* 4.7 6.1 - - + +
133B ASN* 3.9 24.9 - - + +
309B TYR* 3.7 32.1 - - + +
312B SER* 3.5 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.6 39.0 - - + +
62B CYS* 3.5 12.0 - - - +
65B GLY* 3.2 35.4 - - - -
66B LEU* 3.3 17.7 - - + +
69B ASN* 3.6 14.4 - - - +
97B ASP 2.9 25.8 + - - +
98B THR* 3.5 5.2 - - - +
100B VAL* 1.3 79.4 - - + +
102B LEU* 1.3 61.5 + - - +
103B THR 3.1 1.2 + - - -
104B LEU* 3.2 27.3 + - + +
105B PRO* 3.4 7.8 - - - +
309B TYR 4.7 0.2 - - - +
312B SER* 3.9 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B CYS* 5.1 1.6 - - - -
66B LEU* 4.0 26.9 - - + -
98B THR* 3.2 25.1 + - + +
99B LEU* 3.4 20.2 - - + +
100B VAL 3.2 0.4 - - - -
101B LEU* 1.3 76.6 - - - +
103B THR* 1.3 58.4 + - + +
104B LEU 3.4 0.2 - - - -
105B PRO* 3.2 16.1 - - - +
106B PHE* 3.6 17.2 - - - -
129B ILE* 6.0 1.1 - - + -
----------------------------------------------------------
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