Contacts of the helix formed by residues 92 - 106 (chain B) in PDB entry 4BSX
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 VAL 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.7 13.2 - - + +
69B VAL* 4.2 21.5 - - + -
72B LEU* 4.0 24.7 - - + -
90B PRO* 3.2 21.9 + - + +
91B ASP* 1.3 73.6 + - - +
93B SER* 1.3 61.5 + - - +
94B TRP 3.3 2.4 + - - -
95B ALA* 3.3 4.0 + - - +
96B VAL* 2.8 48.0 + - + +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 3.2 25.7 + - - -
92B VAL* 1.3 80.4 - - - +
94B TRP* 1.3 58.5 + - - +
96B VAL* 3.4 7.1 + - - +
97B ALA* 2.9 26.7 + - - +
117B ALA* 4.3 2.8 - - - +
120B GLU* 4.4 4.9 - - - -
121B ALA* 3.4 33.3 + - - +
124B THR* 3.6 13.8 - - - +
125B LEU* 4.3 2.3 - - - +
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Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 5.2 1.9 + - - +
92B VAL 3.3 0.4 - - - -
93B SER* 1.3 79.1 + - - +
95B ALA* 1.3 67.0 + - - +
97B ALA* 3.2 2.2 + - - +
98B ARG* 3.0 55.5 + - + +
118B TYR* 4.5 2.7 - + - -
121B ALA* 4.1 9.0 - - + -
125B LEU* 3.9 33.0 - - + -
128B ARG* 6.3 0.2 - - - -
132B ARG* 3.4 47.1 - - + -
135B GLU* 3.8 17.9 - - + -
136B LEU* 3.4 37.4 - - + +
139B GLU* 3.0 30.3 + - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.6 9.6 - - + -
69B VAL* 3.9 37.5 - - + -
92B VAL 3.6 8.5 - - - +
94B TRP* 1.3 78.3 - - - +
96B VAL* 1.3 59.0 + - + +
98B ARG* 3.2 12.6 + - - +
99B LEU* 2.9 34.3 + - + +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO 4.1 6.3 - - - +
7B SER* 3.9 21.3 - - - +
8B LEU* 3.9 28.3 - - + +
11B ALA* 6.0 0.2 - - + -
69B VAL* 6.3 0.2 - - + -
92B VAL* 2.8 42.1 + - + +
93B SER* 3.7 6.7 - - - +
95B ALA* 1.3 79.1 - - + +
97B ALA* 1.3 56.4 + - - +
99B LEU* 3.2 7.8 + - + +
100B TYR* 2.8 47.4 + - + -
117B ALA* 4.6 7.2 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER 2.9 14.8 + - - +
94B TRP* 3.2 11.2 + - - +
96B VAL* 1.3 75.5 - - - +
98B ARG* 1.3 56.3 + - - +
100B TYR* 3.3 1.9 + - - +
101B HIS* 2.8 28.9 + - - +
114B ARG* 4.5 0.7 - - - +
117B ALA* 3.6 24.6 - - - +
118B TYR* 3.6 43.2 - - + -
121B ALA* 4.5 1.6 - - + -
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 3.5 57.4 + - - +
39B GLY* 4.7 5.2 - - - +
94B TRP* 3.0 40.5 + - - +
95B ALA* 3.4 12.6 - - - +
97B ALA* 1.3 73.7 - - - +
99B LEU* 1.3 66.5 + - - +
101B HIS* 3.2 6.0 + - - +
102B LEU* 3.2 28.2 + - - +
118B TYR* 3.7 5.2 - - - +
132B ARG* 4.6 10.5 - - - +
135B GLU* 4.7 4.4 + - - -
139B GLU* 2.9 43.9 + - - +
143B ARG* 4.2 5.2 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 14.6 - - + -
11B ALA* 4.9 7.0 - - + -
39B GLY* 3.8 17.0 - - - +
42B LEU* 4.1 15.9 - - + -
43B LEU* 3.7 41.4 - - + +
46B MSE 3.5 31.9 - - + -
95B ALA* 2.9 20.6 + - + +
96B VAL* 3.5 10.5 - - + +
98B ARG* 1.3 76.0 - - - +
100B TYR* 1.3 63.5 + - + +
102B LEU* 3.2 7.4 + - + +
103B LEU* 2.9 32.0 + - + +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.6 13.1 - - + +
7B SER 3.4 26.4 + - - -
10B SER* 3.2 32.1 - - - -
11B ALA* 3.4 15.9 + - + -
14B ILE* 3.7 23.9 - - + +
96B VAL* 2.8 33.3 + - + +
97B ALA 3.8 3.8 - - - +
99B LEU* 1.3 75.8 - - + +
101B HIS* 1.3 66.5 + - - +
103B LEU* 3.8 5.3 - - + +
104B ALA* 2.9 26.7 + - - +
109B CYS* 4.0 11.3 - - - -
113B MSE 3.8 36.6 - - + -
114B ARG* 4.0 17.2 - - - +
117B ALA* 4.3 5.6 - - + -
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY 4.9 4.8 + - - -
37B CYS* 6.0 1.4 - - - -
97B ALA 2.8 14.6 + - - +
98B ARG 3.4 8.1 - - - +
99B LEU 3.2 0.4 - - - -
100B TYR* 1.3 79.6 - - - +
102B LEU* 1.3 78.1 + - + +
104B ALA* 3.9 1.6 - - - +
105B GLU* 3.1 58.2 + - + +
114B ARG* 3.5 30.4 + - + +
118B TYR* 4.4 2.5 - - + -
143B ARG* 3.3 61.7 + - + +
142D ASN* 5.9 2.0 - - - -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 5.2 4.5 - - + -
37B CYS* 4.3 28.7 - - + -
38B GLN 3.9 5.4 - - - +
39B GLY* 3.8 7.2 - - - +
40B GLN* 3.6 40.8 - - + +
43B LEU* 3.7 24.2 - - + -
98B ARG 3.2 15.1 + - - +
99B LEU* 3.2 6.0 + - - +
101B HIS* 1.3 90.5 - - + +
103B LEU* 1.3 64.8 + - - +
105B GLU* 3.3 8.1 + - + +
106B GLU* 3.0 30.6 + - + +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 4.0 33.9 - - + +
14B ILE* 4.1 21.1 - - + -
15B LEU* 3.7 28.7 - - + -
26B LEU* 5.4 1.6 - - + -
43B LEU* 4.3 16.8 - - + -
99B LEU* 2.9 25.3 + - + +
100B TYR* 3.8 10.8 - - + +
101B HIS 3.3 0.2 - - - -
102B LEU* 1.3 76.3 - - - +
104B ALA* 1.3 60.4 + - - +
106B GLU* 3.2 5.9 + - + -
107B LYS 3.2 3.5 + - - -
108B LEU* 2.9 42.4 + - + +
109B CYS* 4.0 11.9 - - - -
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Residues in contact with ALA 104 (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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100B TYR 2.9 18.4 + - - +
101B HIS 3.9 2.9 - - - +
103B LEU* 1.3 76.8 - - - +
105B GLU* 1.3 57.8 + - - +
107B LYS* 2.9 22.7 + - - +
109B CYS* 3.4 26.2 - - - +
110B PRO 4.2 0.7 - - - +
111B ALA* 4.0 24.5 - - + +
114B ARG* 4.4 14.6 - - + +
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Residues in contact with GLU 105 (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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101B HIS* 3.1 53.2 + - + +
102B LEU* 3.6 9.0 - - + +
104B ALA* 1.3 74.5 - - - +
106B GLU* 1.3 64.3 + - + +
107B LYS* 3.1 19.3 + - - +
114B ARG* 4.5 8.9 + - - +
141D ARG* 3.1 35.4 + - - -
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Residues in contact with GLU 106 (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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22B LYS* 4.6 7.7 + - + +
25B TYR* 3.4 19.6 + - - -
26B LEU* 3.8 26.0 - - + +
29B LYS* 2.8 32.8 + - - +
30B LEU* 5.5 3.9 - - + +
43B LEU* 6.2 2.2 - - + -
102B LEU* 3.0 21.6 + - + +
103B LEU* 3.2 5.8 + - + +
104B ALA 3.2 0.4 - - - -
105B GLU* 1.3 80.1 - - + +
107B LYS* 1.3 72.5 + - - +
108B LEU* 3.3 25.4 + - + +
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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
------------------------------------------------------------
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