Contacts of the helix formed by residues 7 - 17 (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 SER 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY 3.5 4.6 + - - -
6A PRO* 1.3 76.6 - - - +
8A LEU* 1.3 59.4 + - - +
9A PRO* 3.4 12.0 - - - +
10A SER* 3.1 26.3 + - - -
11A ALA* 2.9 30.0 + - - +
92A VAL* 6.2 0.2 - - - -
96A VAL* 4.1 12.3 - - - -
100A TYR* 3.4 9.1 + - - -
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Residues in contact with LEU 8 (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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7A SER* 1.3 73.4 - - - +
9A PRO* 1.4 74.4 - - + +
11A ALA* 3.1 4.2 + - - +
12A PHE* 3.1 32.3 + - + -
42A LEU* 5.6 1.6 - - + -
46A MSE 3.8 34.8 - - + -
69A VAL* 4.8 5.8 - - + -
72A LEU* 4.4 14.1 - - + -
73A VAL* 4.1 17.9 - - + -
77A TRP* 3.7 30.7 - - + -
92A VAL* 4.6 15.3 - - + +
96A VAL* 3.9 18.5 - - + +
99A LEU* 4.0 12.6 - - + -
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Residues in contact with PRO 9 (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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7A SER* 3.4 13.7 - - - +
8A LEU* 1.4 96.9 - - + +
10A SER* 1.3 56.2 + - - +
12A PHE* 3.3 10.0 + - + +
13A ASP* 3.0 34.0 + - - +
77A TRP* 4.2 22.9 - - + +
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Residues in contact with SER 10 (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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4A THR* 5.4 1.7 - - - -
5A GLY 3.4 15.3 + - - -
7A SER* 3.1 20.3 + - - -
9A PRO* 1.3 75.2 - - - +
11A ALA* 1.3 59.7 + - - +
13A ASP* 3.1 12.5 + - - +
14A ILE* 3.0 32.1 + - - +
100A TYR* 3.2 19.3 - - - -
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Residues in contact with ALA 11 (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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7A SER 2.9 18.1 + - - +
8A LEU* 3.1 6.5 + - - +
10A SER* 1.3 75.4 - - - +
12A PHE* 1.3 62.7 + - - +
14A ILE* 3.3 4.7 + - - +
15A LEU* 3.2 25.5 + - - +
43A LEU* 6.0 0.2 - - + -
46A MSE 3.9 18.6 - - + -
96A VAL* 6.4 0.2 - - + -
99A LEU* 4.9 7.6 - - + -
100A TYR* 3.4 19.6 + - + -
103A LEU* 3.9 19.7 - - + +
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Residues in contact with PHE 12 (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* 3.1 31.7 + - + -
9A PRO* 3.5 9.2 - - + +
11A ALA* 1.3 76.6 - - - +
13A ASP* 1.3 58.1 + - - +
15A LEU* 3.4 9.6 + - + +
16A GLY 2.8 23.9 + - - -
46A MSE 3.5 58.3 - - + +
49A LEU* 4.1 13.9 - - + -
50A LYS* 3.6 26.9 - - + +
73A VAL* 4.5 3.4 - - + -
77A TRP* 3.3 59.7 - + + +
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Residues in contact with ASP 13 (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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9A PRO* 3.0 23.2 + - - +
10A SER* 3.1 14.5 + - - +
12A PHE* 1.3 78.5 - - - +
14A ILE* 1.3 59.0 + - + +
16A GLY* 3.2 3.0 + - - +
17A ALA* 2.8 30.2 + - - +
50A LYS* 5.0 7.7 + - - +
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Residues in contact with ILE 14 (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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10A SER* 3.0 19.8 + - - +
11A ALA* 3.5 6.7 - - - +
13A ASP* 1.3 76.9 - - + +
15A LEU* 1.3 62.4 + - - +
17A ALA* 3.3 15.3 + - - +
18A ALA* 3.3 13.5 + - - +
100A TYR* 3.7 33.7 - - + +
103A LEU* 4.1 18.6 - - + -
108A LEU* 3.4 39.8 - - + +
109A CYS* 4.0 13.9 - - + -
113A MSE 6.1 0.7 - - + -
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Residues in contact with LEU 15 (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 3.2 12.7 + - - +
12A PHE* 3.4 11.4 - - - +
14A ILE* 1.3 74.7 - - - +
16A GLY* 1.3 67.2 + - - +
18A ALA* 3.0 13.0 + - - +
19A GLY 4.3 0.2 + - - -
23A LEU* 3.5 32.1 - - + +
26A LEU* 4.2 12.1 - - + -
43A LEU* 3.9 20.6 - - + -
46A MSE 4.1 17.7 - - + +
47A VAL* 3.9 37.5 - - + +
50A LYS* 4.2 8.5 - - + -
103A LEU* 3.7 24.9 - - + -
108A LEU* 4.3 3.1 - - + -
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Residues in contact with GLY 16 (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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12A PHE 2.8 14.9 + - - -
13A ASP* 3.2 4.5 + - - -
15A LEU* 1.3 74.7 - - - +
17A ALA* 1.3 60.5 + - - +
18A ALA 3.2 0.7 + - - -
19A GLY* 3.9 7.8 + - - -
20A GLN* 5.2 6.2 + - - -
23A LEU* 5.2 0.9 - - - -
50A LYS* 3.4 29.7 - - - +
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Residues in contact with ALA 17 (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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13A ASP 2.8 16.5 + - - +
14A ILE* 3.8 8.7 - - - +
15A LEU 3.1 0.6 - - - -
16A GLY* 1.3 74.3 - - - +
18A ALA* 1.3 60.7 + - - +
19A GLY 3.3 1.6 + - - -
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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