Contacts of the helix formed by residues 92 - 106 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER* 6.2 0.4 - - - -
8A LEU* 4.6 12.8 - - + +
69A VAL* 4.2 21.3 - - + -
72A LEU* 4.0 24.7 - - + -
90A PRO* 3.4 21.7 + - + +
91A ASP* 1.3 74.8 + - - +
93A SER* 1.3 60.4 + - - +
94A TRP 3.2 2.9 + - - -
95A ALA* 3.4 4.1 + - - +
96A VAL* 2.8 48.1 + - + +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.3 24.3 + - - -
92A VAL* 1.3 80.0 - - - +
94A TRP* 1.3 59.0 + - - +
96A VAL* 3.5 7.0 + - - +
97A ALA* 2.9 27.5 + - - +
117A ALA 4.2 3.5 - - - +
120A GLU* 4.4 4.9 - - - -
121A ALA* 3.3 34.0 + - - +
124A THR* 3.7 13.5 - - - -
125A LEU* 4.4 1.9 - - - +
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Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 5.3 1.7 + - - +
92A VAL 3.3 0.4 - - - -
93A SER* 1.3 77.8 + - - +
95A ALA* 1.3 66.9 + - - +
97A ALA* 3.2 2.7 + - - +
98A ARG* 3.0 53.4 + - + +
118A TYR* 4.6 2.5 - + - -
121A ALA* 4.1 8.3 - - + -
125A LEU* 3.9 34.1 - - + -
132A ARG* 3.4 45.8 - - + -
135A GLU* 3.8 18.2 - - + -
136A LEU* 3.5 36.8 - - + +
139A GLU* 3.1 31.5 + - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.6 9.9 - - + -
69A VAL* 3.9 37.7 - - + -
92A VAL* 3.4 8.7 + - + +
94A TRP* 1.3 79.3 - - - +
96A VAL* 1.3 63.6 + - + +
98A ARG* 3.2 11.3 + - - +
99A LEU* 2.9 29.4 + - + +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 4.1 6.7 - - + +
7A SER* 3.9 19.1 - - - +
8A LEU* 3.9 29.6 - - + +
92A VAL* 2.8 44.5 + - + +
93A SER* 3.7 6.7 - - - +
95A ALA* 1.3 74.7 - - + +
97A ALA* 1.3 56.3 + - - +
99A LEU* 3.3 7.8 + - + +
100A TYR* 2.8 48.1 + - + -
117A ALA* 4.5 8.1 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER 2.9 18.4 + - - +
94A TRP* 3.4 11.4 - - - +
96A VAL* 1.3 73.1 - - - +
98A ARG* 1.3 57.0 + - - +
100A TYR* 3.3 2.1 + - - +
101A HIS* 2.9 28.9 + - - +
114A ARG* 4.5 0.5 - - - +
117A ALA* 3.6 25.1 - - - +
118A TYR* 3.6 42.5 - - + -
121A ALA* 4.5 1.6 - - + -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.4 58.8 + - - +
39A GLY* 4.7 5.4 - - - +
94A TRP* 3.0 40.1 + - - +
95A ALA* 3.2 11.9 + - - +
97A ALA* 1.3 72.5 - - - +
99A LEU* 1.3 66.9 + - - +
101A HIS* 3.1 14.8 + - - +
102A LEU* 3.1 20.4 + - - +
118A TYR* 3.7 4.5 - - - +
132A ARG* 4.6 9.3 - - - +
135A GLU* 4.6 4.8 + - - -
139A GLU* 2.9 43.6 + - - +
143A ARG* 4.2 4.5 - - - +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.0 13.7 - - + -
11A ALA* 4.9 7.4 - - + -
39A GLY* 3.7 27.6 - - - +
42A LEU* 4.2 14.4 - - + -
43A LEU* 3.7 31.5 - - + +
46A MSE 3.5 31.4 - - + -
69A VAL* 6.2 0.2 - - + -
95A ALA* 2.9 21.7 + - + +
96A VAL* 3.4 12.1 - - + +
98A ARG* 1.3 75.5 - - - +
100A TYR* 1.3 62.5 + - + +
102A LEU* 3.2 7.6 + - + +
103A LEU* 2.9 31.9 + - + +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 3.6 14.2 - - + +
7A SER 3.4 25.8 + - - -
10A SER* 3.2 32.2 - - - -
11A ALA* 3.4 15.2 + - + -
14A ILE* 3.7 23.3 - - + +
96A VAL* 2.8 32.8 + - + +
97A ALA 3.9 3.6 - - - +
99A LEU* 1.3 72.2 - - + +
101A HIS* 1.3 67.0 + - - +
103A LEU* 3.7 7.5 - - + +
104A ALA* 2.9 25.8 + - - +
109A CYS* 4.0 12.2 - - - -
113A MSE 3.8 36.1 - - + -
114A ARG* 4.0 17.0 - - - +
117A ALA* 4.3 5.8 - - + -
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Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 4.9 5.0 + - - -
37A CYS* 6.0 1.2 - - - -
97A ALA 2.9 14.7 + - - +
98A ARG 3.1 8.5 + - - +
100A TYR* 1.3 79.2 - - - +
102A LEU* 1.3 78.0 + - + +
104A ALA* 3.3 1.6 + - - +
105A GLU* 3.0 60.4 + - + +
114A ARG* 3.6 31.1 + - + +
118A TYR* 4.4 2.9 - - + -
143A ARG* 3.4 56.0 + - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.2 4.0 - - + -
37A CYS* 4.3 27.1 - - + -
38A GLN 4.0 7.2 - - - +
39A GLY 3.7 6.5 - - - +
40A GLN* 3.5 41.5 - - + +
43A LEU* 3.7 26.2 - - + -
98A ARG 3.1 13.1 + - - +
99A LEU* 3.2 3.6 + - - +
101A HIS* 1.3 91.6 - - + +
103A LEU* 1.3 63.9 + - - +
105A GLU* 3.2 8.3 + - + +
106A GLU* 3.0 30.7 + - + +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.9 29.6 - - + +
14A ILE* 4.1 25.4 - - + -
15A LEU* 3.7 29.2 - - + -
26A LEU* 5.4 0.9 - - + -
43A LEU* 4.3 16.8 - - + -
99A LEU* 2.9 21.9 + - + +
100A TYR* 3.8 13.5 - - + +
101A HIS 3.3 0.2 - - - -
102A LEU* 1.3 76.6 - - - +
104A ALA* 1.3 60.4 + - - +
106A GLU* 3.3 4.3 + - + -
107A LYS 3.2 3.3 + - - -
108A LEU* 2.8 45.4 + - + +
109A CYS* 3.9 11.2 - - - -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR 2.9 17.4 + - - +
101A HIS 3.8 3.6 - - - +
103A LEU* 1.3 75.9 - - - +
105A GLU* 1.3 57.7 + - - +
107A LYS* 3.0 21.7 + - - +
109A CYS* 3.4 27.0 - - - +
110A PRO 4.2 0.7 - - - +
111A ALA* 4.1 22.0 - - + -
114A ARG* 4.4 15.7 - - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A HIS* 3.0 52.7 + - + +
102A LEU* 3.6 9.2 - - + +
104A ALA* 1.3 73.0 - - - +
106A GLU* 1.3 64.6 + - + +
107A LYS* 3.0 22.9 + - - +
114A ARG* 4.5 9.2 + - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 4.7 8.1 + - + +
25A TYR* 3.4 19.2 + - - -
26A LEU* 3.8 26.1 - - + +
29A LYS* 2.8 33.4 + - - +
30A LEU* 5.5 4.5 - - + +
43A LEU* 6.2 2.0 - - + -
102A LEU* 3.0 22.0 + - + +
103A LEU* 3.3 5.8 + - + +
104A ALA 3.2 0.2 - - - -
105A GLU* 1.3 79.5 - - + +
107A LYS* 1.3 71.5 + - - +
108A LEU* 3.3 25.1 + - + +
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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
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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