Contacts of the helix formed by residues 88 - 102 (chain B) in PDB entry 3AEV
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 LEU 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 6.5 0.4 - - + -
105A ASN* 4.1 20.4 - - + +
106A LEU* 3.7 24.2 - - + -
109A LEU* 3.8 31.4 - - + -
170A TYR* 4.3 22.0 - - + +
86B ASP* 3.0 12.1 + - - +
87B PRO* 1.3 89.1 - - + +
89B ALA* 1.3 63.9 - - - +
90B VAL 3.2 2.9 - - - -
91B TRP* 3.0 33.9 + - + +
92B LYS* 3.1 24.2 + - + +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 3.3 34.0 - - + +
65B THR* 3.9 3.3 - - + +
84B THR* 4.1 7.4 - - + -
86B ASP* 3.0 32.5 + - + +
87B PRO 3.3 0.4 - - - -
88B LEU* 1.3 78.6 - - - +
90B VAL* 1.3 62.8 + - - +
92B LYS* 3.8 11.9 - - + +
93B ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 4.0 15.9 - - + +
36B GLU* 3.8 26.7 - - + +
65B THR* 4.1 10.1 - - + -
78B ILE* 3.8 22.6 - - + +
79B THR 4.0 2.5 - - - -
80B SER* 3.6 39.7 - - - +
84B THR* 5.5 2.0 - - + -
86B ASP 4.8 0.2 + - - -
87B PRO 4.6 1.1 + - - +
88B LEU 3.1 1.4 + - - -
89B ALA* 1.3 77.0 - - + +
91B TRP* 1.3 74.7 + - + +
93B ALA* 3.3 2.8 + - - +
94B ARG* 2.9 27.0 + - - +
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Residues in contact with TRP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 3.3 44.6 - - + +
105A ASN* 6.0 2.5 - - + -
170A TYR* 3.7 41.1 + + + -
34B GLN* 3.6 35.2 - - + -
35B GLU 6.0 0.2 - - - -
36B GLU* 3.2 26.7 + - + -
87B PRO 3.1 24.0 - - - -
88B LEU* 3.0 28.3 + - + +
90B VAL* 1.3 85.1 - - + +
92B LYS* 1.3 64.4 + - - +
94B ARG* 3.2 28.9 + - - +
95B ASP* 2.9 31.1 + - - +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 4.5 18.4 - - + +
63B THR* 4.8 1.8 - - + -
86B ASP* 3.0 29.1 + - - +
88B LEU* 3.1 20.9 + - - +
89B ALA* 3.8 8.7 - - - +
91B TRP* 1.3 74.4 - - - +
93B ALA* 1.3 62.6 + - - +
95B ASP* 3.1 8.6 + - - +
96B ILE* 3.0 28.1 + - - +
112B LEU* 4.2 22.0 - - - +
113B LEU* 4.4 31.3 + - + +
114B ASN 5.1 6.3 + - - -
115B GLU* 5.4 10.0 + - - +
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 4.2 10.2 - - + +
63B THR* 3.8 26.8 - - + +
65B THR* 3.8 4.0 - - - +
67B ILE* 4.5 2.0 - - + -
78B ILE* 3.8 17.5 - - + -
89B ALA 2.9 17.1 + - - +
90B VAL 3.6 3.8 - - - +
92B LYS* 1.3 76.4 - - - +
94B ARG* 1.3 63.8 + - - +
96B ILE* 3.3 8.6 + - - +
97B VAL* 3.0 28.9 + - - +
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN 4.7 11.1 + - - -
170A TYR* 5.4 3.2 + - - -
172A GLU* 4.0 17.2 + - - +
36B GLU* 3.9 36.5 + - + -
38B VAL* 3.7 24.7 - - + +
78B ILE* 4.0 18.1 - - + +
90B VAL 2.9 14.2 + - - +
91B TRP* 3.4 32.3 - - - +
93B ALA* 1.3 78.6 - - - +
95B ASP* 1.3 85.9 + - - +
97B VAL* 3.3 4.6 + - - +
98B LEU* 3.0 41.0 + - - +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN 5.0 6.4 - - - +
170A TYR* 5.0 7.8 - - - -
91B TRP 2.9 21.8 + - - +
92B LYS* 3.1 7.1 + - - +
94B ARG* 1.3 110.0 + - - +
96B ILE* 1.3 59.7 + - - +
98B LEU* 3.1 10.8 + - - +
99B ALA* 2.8 29.8 + - - +
112B LEU* 3.6 21.1 - - + +
118B TYR* 5.9 2.3 - - - -
119B LEU* 3.7 21.0 + - + +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 4.0 22.2 - - + -
63B THR* 4.8 3.6 - - + -
92B LYS 3.0 18.3 + - - +
93B ALA* 3.6 10.3 - - - +
95B ASP* 1.3 75.6 - - - +
97B VAL* 1.3 63.2 + - - +
99B ALA* 3.3 2.8 + - - +
100B ILE* 2.9 41.3 + - + +
109B ALA* 3.6 26.7 - - + +
110B PHE* 4.0 19.1 - - + -
112B LEU* 4.0 14.4 - - + -
113B LEU* 3.8 35.4 - - + -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.8 17.7 - - + -
40B ILE* 3.7 23.1 - - + +
48B LEU* 4.1 33.7 - - + -
59B ILE* 5.2 2.7 - - + -
67B ILE* 4.6 11.9 - - + -
76B VAL* 4.2 11.0 - - + -
78B ILE* 4.4 14.8 - - + -
93B ALA 3.0 21.4 + - - +
94B ARG* 3.4 9.0 - - - +
95B ASP 3.2 0.2 - - - -
96B ILE* 1.3 78.4 - - - +
98B LEU* 1.3 57.1 + - - +
100B ILE* 3.2 3.3 + - - +
101B GLY* 2.9 24.4 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.9 26.7 - - + -
39B LYS 5.3 4.7 - - - +
40B ILE* 4.9 6.5 - - + -
94B ARG* 3.0 38.6 + - - +
95B ASP* 3.1 16.1 + - - +
97B VAL* 1.3 73.1 - - - +
99B ALA* 1.3 55.1 + - - +
101B GLY* 2.9 4.7 + - - +
102B ARG* 2.7 42.0 + - + +
119B LEU* 3.8 16.2 - - + -
121B ILE* 4.4 16.2 - - + -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP 2.8 19.8 + - - +
96B ILE 3.7 4.0 - - - +
98B LEU* 1.3 71.1 - - - +
100B ILE* 1.3 64.4 + - - +
102B ARG* 2.9 14.3 + - - +
103B GLY 3.2 0.3 + - - -
104B PHE* 3.0 42.2 + - + +
109B ALA* 3.7 16.6 - - + -
112B LEU* 3.9 13.5 - - + -
119B LEU* 4.0 8.9 - - + +
172B ILE* 4.2 4.0 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 5.5 0.7 - - + -
44B ARG* 2.8 32.6 + - + +
47B VAL* 3.9 26.5 - - + -
48B LEU* 3.9 38.1 - - + +
55B THR* 4.5 2.2 - - + -
59B ILE* 4.0 7.9 - - + -
96B ILE* 2.9 35.1 + - + +
97B VAL* 3.6 4.0 - - - +
99B ALA* 1.3 75.2 - - - +
101B GLY* 1.3 59.9 + - - +
102B ARG 3.2 0.7 + - - -
103B GLY 3.2 3.6 + - - -
104B PHE 3.4 11.7 - - - +
106B PRO* 4.2 23.6 - - + -
109B ALA* 4.0 13.2 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 4.0 25.1 - - - +
41B PRO* 3.4 17.8 - - - +
44B ARG* 3.5 14.5 - - - +
97B VAL 2.9 14.1 + - - -
98B LEU* 2.9 6.0 + - - -
100B ILE* 1.3 80.1 - - - +
102B ARG* 1.3 67.7 + - - +
103B GLY 3.3 0.9 + - - -
165B TYR* 3.9 2.4 - - - -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 3.3 34.4 - - - +
98B LEU* 2.7 22.2 + - + +
99B ALA* 2.9 7.3 + - - +
101B GLY* 1.3 76.3 - - - +
103B GLY* 1.3 55.7 + - - +
104B PHE 3.6 0.4 - - - -
121B ILE* 4.1 25.8 - - + -
163B SER* 2.8 20.9 + - - +
165B TYR* 3.3 44.4 + - - +
166B GLY* 4.2 1.8 - - - -
167B LYS* 3.9 16.0 - - - +
168B THR* 2.9 37.9 + - - +
170B ALA* 4.1 17.3 - - + +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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