Contacts of the helix formed by residues 4 - 19 (chain A) in PDB entry 3BQP
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 PHE 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ASP* 6.0 0.4 - - - -
2A GLY 3.2 0.8 - - - -
3A GLY* 1.3 75.5 - - - +
5A CYS* 1.3 64.9 + - - +
6A GLU 3.4 2.2 - - - -
7A VAL* 3.4 13.4 - - + +
8A CYS* 2.9 23.7 + - - +
46A GLN* 4.0 8.3 - - + -
49A GLN* 3.9 25.4 - - + -
50A PHE* 3.7 47.8 - + + -
53A GLU* 3.5 31.6 - - - -
54A TYR* 3.9 18.4 - + - -
77A ALA* 4.1 10.2 + - + +
82A MG 4.6 8.3 - - - -
4B PHE* 4.8 0.9 - + - -
49B GLN* 3.3 32.8 - - - -
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Residues in contact with CYS 5 (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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2A GLY* 3.0 19.4 + - - +
3A GLY 3.4 0.4 - - - -
4A PHE* 1.3 77.2 - - - +
6A GLU* 1.3 71.6 + - + +
8A CYS* 3.5 2.9 - - - +
9A LYS* 3.1 38.0 + - - +
77A ALA 3.4 12.8 + - - +
78A CYS* 2.1 53.4 - - - -
79A PRO* 5.2 0.7 - - + -
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Residues in contact with GLU 6 (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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2A GLY 4.8 0.4 + - - -
3A GLY 5.2 1.0 + - - -
4A PHE 3.4 0.2 - - - -
5A CYS* 1.3 85.1 - - + +
7A VAL* 1.3 63.3 + - - +
9A LYS* 2.9 37.6 + - - +
10A LYS* 3.1 28.9 + - - +
43A TYR* 4.9 15.3 - - + +
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Residues in contact with VAL 7 (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 PHE* 3.4 27.5 - - + +
6A GLU* 1.3 77.1 - - - +
8A CYS* 1.3 59.9 + - - +
10A LYS* 3.2 3.0 + - - +
11A LEU* 2.9 28.2 + - - +
39A LEU* 3.9 8.1 - - + -
43A TYR* 3.9 24.0 - - + +
46A GLN* 3.4 31.7 + - + +
47A CYS* 3.7 33.4 - - + +
50A PHE* 4.1 11.7 - - + -
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Residues in contact with CYS 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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4A PHE 2.9 18.8 + - - +
5A CYS 3.5 4.0 - - - +
7A VAL* 1.3 77.6 - - - +
9A LYS* 1.3 62.3 + - - +
11A LEU 3.3 0.2 + - - -
12A VAL* 2.9 34.3 + - - +
50A PHE* 3.4 38.1 - - + -
72A CYS* 2.0 50.0 - - - -
75A ILE* 3.9 9.9 - - - -
77A ALA* 3.9 7.9 - - + -
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Residues in contact with LYS 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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5A CYS* 3.1 27.2 + - - +
6A GLU* 2.9 39.0 + - - +
7A VAL 3.3 0.2 - - - -
8A CYS* 1.3 75.5 - - - +
10A LYS* 1.3 57.8 + - + +
13A GLY* 2.9 26.0 + - - -
68A PRO* 3.6 19.5 - - + +
69A SER* 4.2 20.4 - - - +
72A CYS* 3.8 20.4 - - + -
78A CYS* 4.0 7.6 - - - -
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Residues in contact with LYS 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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6A GLU* 3.1 18.2 + - - +
7A VAL* 3.8 6.5 - - - +
8A CYS 3.2 0.2 - - - -
9A LYS* 1.3 78.2 - - + +
11A LEU* 1.3 62.8 + - - +
13A GLY* 3.4 1.5 + - - -
14A TYR* 3.0 22.0 + - - +
39A LEU* 3.9 16.5 - - + +
40A PRO* 4.6 15.4 - - + +
43A TYR* 3.3 53.4 - - + -
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Residues in contact with LEU 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 VAL 2.9 17.1 + - - +
8A CYS 4.3 0.7 - - - +
10A LYS* 1.3 75.9 - - - +
12A VAL* 1.4 68.2 + - + +
14A TYR* 3.0 14.2 + - + +
15A LEU* 3.2 21.6 + - + +
32A LEU* 4.3 14.4 - - + +
35A GLY* 3.4 40.6 - - - +
36A CYS* 3.6 5.8 - - - +
39A LEU* 4.0 7.9 - - + -
47A CYS* 3.8 15.9 - - - -
50A PHE* 3.8 20.9 - - + -
51A VAL* 3.3 30.3 - - + -
58A LEU* 5.0 1.3 - - + -
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Residues in contact with VAL 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 CYS* 2.9 24.1 + - - +
11A LEU* 1.4 77.8 - - + +
13A GLY* 1.3 56.6 + - - +
15A LEU* 3.2 8.1 + - + +
16A ASP* 2.7 27.5 + - - +
32A LEU* 6.4 0.4 - - + -
50A PHE* 5.2 3.4 - - + -
58A LEU* 4.3 13.0 - - + -
62A LEU* 4.0 21.3 - - + -
66A MET 3.3 24.2 - - - +
68A PRO* 3.7 18.2 - - + -
71A VAL* 3.9 24.0 - - + -
72A CYS* 4.0 6.5 - - - -
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Residues in contact with GLY 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 LYS 2.9 20.3 + - - -
10A LYS* 3.7 1.8 - - - -
11A LEU 3.2 0.4 - - - -
12A VAL* 1.3 75.9 - - - +
14A TYR* 1.3 62.7 + - - +
16A ASP* 3.3 2.0 + - - +
17A ARG* 3.0 34.8 + - - +
68A PRO* 3.6 17.2 - - - +
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Residues in contact with TYR 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 LYS 3.0 13.2 + - - +
11A LEU 3.0 7.4 + - - +
13A GLY* 1.3 75.6 - - - +
15A LEU* 1.3 87.0 + - + +
17A ARG* 4.8 3.6 - - - +
18A ASN* 2.9 67.1 + - + +
31A ALA* 4.3 9.7 + - + +
34A LYS* 5.0 3.6 - - - +
35A GLY* 3.5 26.2 - - - -
38A PHE* 3.4 51.1 - + + -
39A LEU* 4.4 11.7 - - + -
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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 LEU* 3.2 24.6 + - + +
12A VAL* 3.2 10.3 + - - +
14A TYR* 1.3 107.1 - - + +
16A ASP* 1.3 58.6 + - - +
18A ASN* 3.1 1.1 + - - +
19A LEU* 2.8 59.9 + - + +
28A ILE* 4.3 2.0 - - + -
31A ALA* 4.1 19.1 - - + +
32A LEU* 3.8 18.6 - - + -
62A LEU* 3.7 31.6 - - + -
66A MET* 4.0 10.5 - - - -
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Residues in contact with ASP 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 VAL 2.7 16.3 + - - +
13A GLY* 3.6 8.9 - - - +
15A LEU* 1.3 73.5 - - - +
17A ARG* 1.3 64.4 + - + +
19A LEU 3.8 10.0 - - - +
66A MET* 3.4 47.3 - - - +
67A ASP* 4.3 3.4 + - - +
68A PRO* 3.6 14.8 - - + +
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Residues in contact with ARG 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 GLY* 3.0 23.6 + - - +
14A TYR* 5.1 2.0 - - - +
16A ASP* 1.3 81.6 - - + +
18A ASN* 1.3 76.4 + - - +
19A LEU 4.7 1.2 - - - +
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Residues in contact with ASN 18 (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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14A TYR* 2.9 57.1 + - + +
15A LEU* 5.0 0.4 - - - -
17A ARG* 1.3 91.2 + - - +
19A LEU* 1.3 60.5 + - - +
20A GLU* 4.3 3.6 + - - +
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Residues in contact with LEU 19 (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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15A LEU* 2.8 35.1 + - + +
16A ASP 3.8 7.4 - - - +
17A ARG 4.7 1.2 - - - +
18A ASN* 1.3 76.1 + - + +
20A GLU* 1.3 70.0 + - - +
21A LYS 3.5 1.2 + - - -
23A SER* 3.8 15.5 - - - +
27A GLU* 4.3 12.6 - - + +
28A ILE* 3.7 29.2 - - + -
31A ALA* 3.9 31.0 - - + -
66A MET* 3.5 22.2 - - + +
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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