Contacts of the helix formed by residues 4 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 4.8 1.6 - + - -
49A GLN* 3.4 33.7 - - - -
1B ASP* 5.9 0.7 - - - -
2B GLY 3.2 0.8 - - - -
3B GLY* 1.3 75.5 - - - +
5B CYS* 1.3 65.7 + - - +
6B GLU 3.4 2.2 - - - -
7B VAL* 3.4 13.2 - - + +
8B CYS* 2.9 23.3 + - - +
46B GLN* 4.0 8.1 - - + -
49B GLN* 4.0 24.7 - - + -
50B PHE* 3.7 48.2 - + + -
53B GLU* 3.5 31.9 - - - -
54B TYR* 3.9 18.2 - + - -
77B ALA* 4.0 9.1 + - + +
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Residues in contact with CYS 5 (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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2B GLY 3.0 15.7 + - - +
3B GLY 3.4 0.8 - - - -
4B PHE* 1.3 77.3 - - - +
6B GLU* 1.3 69.9 + - + +
8B CYS* 3.5 1.5 - - - +
9B LYS* 3.1 37.6 + - - +
77B ALA 3.3 17.0 + - - +
78B CYS* 2.1 53.8 - - - -
79B PRO* 4.3 7.6 - - + -
80B SER 6.1 0.2 - - - -
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Residues in contact with GLU 6 (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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3B GLY 5.2 0.8 + - - -
4B PHE 3.4 0.6 - - - -
5B CYS* 1.3 83.3 - - + +
7B VAL* 1.3 62.3 + - - +
9B LYS* 2.9 36.2 + - - +
10B LYS* 3.1 38.0 + - - +
43B TYR* 4.9 13.0 - - + +
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Residues in contact with VAL 7 (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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4B PHE* 3.4 25.0 - - + +
6B GLU* 1.3 75.3 - - - +
8B CYS* 1.3 64.0 + - - +
10B LYS* 3.3 3.2 + - - +
11B LEU* 2.8 29.4 + - + +
39B LEU* 3.9 7.9 - - + -
43B TYR* 3.8 24.5 - - + -
46B GLN* 3.5 34.6 + - + +
47B CYS* 3.7 33.9 - - + +
50B PHE* 4.0 11.7 - - + -
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Residues in contact with CYS 8 (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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4B PHE 2.9 19.0 + - - +
5B CYS 3.5 3.6 - - - +
7B VAL* 1.3 78.7 - - - +
9B LYS* 1.3 55.7 + - - +
12B VAL* 2.8 41.1 + - - +
50B PHE* 3.4 37.7 - - + -
72B CYS* 2.0 51.6 - - + -
75B ILE* 3.9 9.0 - - - -
77B ALA* 4.0 5.8 - - + -
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Residues in contact with LYS 9 (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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5B CYS* 3.1 29.4 + - - +
6B GLU* 2.9 40.5 + - - +
7B VAL 3.3 0.2 - - - -
8B CYS* 1.3 75.2 - - - +
10B LYS* 1.3 59.3 + - + +
13B GLY* 2.9 26.0 + - - -
68B PRO* 3.6 22.1 - - + +
69B SER* 4.3 18.8 - - - +
72B CYS* 3.8 17.7 - - + -
78B CYS* 4.1 5.8 - - - -
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Residues in contact with LYS 10 (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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6B GLU* 3.1 23.6 + - - +
7B VAL 3.7 6.5 - - - +
9B LYS* 1.3 75.1 - - + +
11B LEU* 1.3 64.6 + - - +
13B GLY* 3.4 2.0 + - - -
14B TYR* 3.0 22.5 + - - +
17B ARG* 4.7 3.3 + - - +
39B LEU* 3.9 19.0 - - + +
40B PRO* 4.8 12.8 - - + -
43B TYR* 3.0 52.7 + - + -
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Residues in contact with LEU 11 (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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7B VAL 2.8 21.7 + - - +
8B CYS 4.0 2.2 - - - +
10B LYS* 1.3 73.4 - - - +
12B VAL* 1.3 63.9 + - + +
14B TYR* 3.1 14.2 + - + +
15B LEU* 3.1 23.6 + - + +
32B LEU* 4.0 18.8 - - + +
35B GLY* 3.7 37.2 - - - +
36B CYS* 3.9 5.2 - - - +
39B LEU* 4.1 6.9 - - + +
47B CYS* 3.9 15.7 - - - -
50B PHE* 3.9 18.4 - - + -
51B VAL* 3.3 31.2 - - + -
58B LEU* 4.7 1.1 - - + -
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Residues in contact with VAL 12 (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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8B CYS* 2.8 29.5 + - - +
11B LEU* 1.3 75.5 - - + +
13B GLY* 1.3 58.8 + - - +
15B LEU* 3.1 11.2 + - + +
16B ASP* 2.7 27.0 + - - +
58B LEU* 4.2 13.5 - - + -
62B LEU* 4.1 17.0 - - + -
66B MET* 3.3 25.6 - - - +
68B PRO* 3.7 18.6 - - + -
71B VAL* 4.0 18.4 - - + -
72B CYS* 4.0 12.1 - - - -
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Residues in contact with GLY 13 (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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9B LYS 2.9 17.8 + - - -
10B LYS* 3.7 1.1 - - - -
11B LEU 3.2 0.2 - - - -
12B VAL* 1.3 75.9 - - - +
14B TYR* 1.3 61.1 + - - +
16B ASP* 3.2 4.0 + - - +
17B ARG* 3.0 43.9 + - - +
68B PRO* 3.4 20.7 - - - +
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Residues in contact with TYR 14 (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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10B LYS 3.0 13.7 + - - +
11B LEU* 3.1 9.6 + - + +
13B GLY* 1.3 74.4 - - - +
15B LEU* 1.3 75.6 + - + +
17B ARG* 3.3 17.6 + - - +
18B ASN* 2.8 65.5 + - + +
31B ALA* 5.9 0.7 - - + -
35B GLY* 4.4 9.6 - - - +
38B PHE* 3.3 68.8 - + + -
39B LEU* 4.4 10.5 - - + -
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Residues in contact with LEU 15 (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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11B LEU* 3.1 23.3 + - + +
12B VAL* 3.4 14.1 - - + +
14B TYR* 1.3 87.1 - - + +
16B ASP* 1.3 66.5 + - - +
17B ARG 3.0 0.2 + - - -
18B ASN* 4.5 0.7 - - - +
19B LEU* 3.0 40.1 + - + +
28B ILE* 5.6 0.4 - - + -
31B ALA* 3.9 37.2 - - + +
32B LEU* 3.5 29.8 - - + -
35B GLY* 4.9 0.2 - - - -
62B LEU* 3.7 19.3 - - + -
66B MET* 4.1 14.4 - - - +
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Residues in contact with ASP 16 (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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12B VAL 2.7 15.1 + - - +
13B GLY* 3.5 10.1 - - - +
15B LEU* 1.3 72.3 - - - +
17B ARG* 1.3 65.0 + - + +
19B LEU 4.4 6.6 - - - +
66B MET* 3.2 45.9 - - - +
67B ASP* 4.2 4.2 - - - +
68B PRO* 3.6 13.7 - - - +
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Residues in contact with ARG 17 (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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10B LYS 4.7 2.6 + - - -
13B GLY* 3.0 23.8 + - - +
14B TYR* 3.7 28.0 - - - +
15B LEU 3.0 0.6 - - - -
16B ASP* 1.3 82.8 - - + +
18B ASN* 1.3 73.8 + - - +
19B LEU 3.6 1.7 + - - +
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Residues in contact with ASN 18 (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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14B TYR* 2.8 66.0 + - + +
15B LEU* 5.1 0.9 - - - -
17B ARG* 1.3 90.2 + - - +
19B LEU* 1.3 60.9 + - - +
20B GLU 4.0 1.4 + - - -
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Residues in contact with LEU 19 (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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15B LEU* 3.0 26.9 + - + +
16B ASP 4.4 6.1 - - - +
17B ARG 4.9 1.1 - - - +
18B ASN* 1.3 78.6 - - - +
20B GLU* 1.3 68.1 + - - +
21B LYS* 3.3 1.9 + - - -
23B SER* 3.4 20.2 - - - +
27B GLU* 4.1 11.2 - - + +
28B ILE* 3.9 27.1 - - + -
31B ALA* 3.8 31.2 - - + -
66B MET* 3.6 29.7 - - + +
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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