Contacts of the helix formed by residues 6 - 19 (chain B) in PDB entry 5BNG
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 PRO 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PHE* 1.3 93.5 - - + +
7B LYS* 1.3 65.3 + - - +
8B VAL* 4.1 11.4 - - + -
9B ALA* 3.0 35.1 + - + +
10B THR* 3.1 14.9 + - - -
38B THR 5.5 3.4 - - - +
40B LEU* 4.5 16.4 - - + -
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Residues in contact with LYS 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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5B PHE 4.2 5.6 - - - +
6B PRO* 1.3 72.5 - - + +
8B VAL* 1.3 62.0 + - + +
10B THR* 3.6 10.9 + - - -
11B ASN* 2.9 25.1 - - - +
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Residues in contact with VAL 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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6B PRO* 4.1 13.7 - - + -
7B LYS* 1.3 78.6 - - + +
9B ALA* 1.3 68.5 + - + +
10B THR 3.1 0.2 - - - -
11B ASN* 3.1 20.4 + - - +
12B ILE* 3.3 21.2 + - + +
38B THR* 5.8 3.8 - - - +
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Residues in contact with ALA 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 PHE 5.1 2.0 - - - +
6B PRO* 3.0 32.4 + - + +
8B VAL* 1.3 83.3 - - + +
10B THR* 1.3 59.8 + - - +
12B ILE 3.8 0.2 + - - -
13B MET* 3.0 32.3 + - - +
38B THR* 4.0 21.4 - - - +
40B LEU* 4.1 23.8 - - + -
48B TRP* 6.0 0.2 - - - -
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Residues in contact with THR 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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5B PHE 4.7 4.2 + - - -
6B PRO 3.1 14.8 + - - -
7B LYS* 3.7 9.8 + - - -
8B VAL 3.1 0.4 - - - -
9B ALA* 1.3 76.2 - - - +
11B ASN* 1.3 59.7 + - - +
13B MET* 3.2 6.3 + - - +
14B ARG* 2.8 62.0 + - + +
48B TRP* 4.7 17.3 - - + +
5M G 4.8 9.9 + - - +
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Residues in contact with ASN 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 LYS 2.9 18.2 + - - +
8B VAL* 3.1 12.0 + - - +
10B THR* 1.3 75.9 - - - +
12B ILE* 1.3 67.9 + - + +
14B ARG* 2.9 37.3 + - - +
15B ALA* 3.1 23.9 + - - +
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Residues in contact with ILE 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 VAL* 3.3 18.3 + - + +
10B THR 3.3 0.2 - - - -
11B ASN* 1.3 81.8 - - + +
13B MET* 1.3 60.7 + - - +
15B ALA* 3.8 10.7 + - - +
16B TRP* 3.8 8.7 + - - +
34B LEU* 4.0 23.8 - - + +
37B ASP* 4.1 29.2 - - + +
38B THR* 3.9 19.3 - - + -
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Residues in contact with MET 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 ALA 3.0 22.9 - - - +
10B THR 3.2 1.7 + - - +
12B ILE* 1.3 77.0 - - - +
14B ARG* 1.3 65.2 + - - +
16B TRP* 3.9 1.4 + - - +
17B LEU* 3.5 14.6 + - - +
34B LEU* 4.2 24.7 - - - -
38B THR* 4.3 12.1 - - + -
40B LEU* 5.2 8.7 - - + -
45B VAL* 4.0 19.3 - - + +
48B TRP* 3.4 64.7 - - + +
49B PHE* 3.3 39.1 - - + -
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Residues in contact with ARG 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 THR* 2.8 48.4 + - + +
11B ASN* 2.9 46.0 + - - +
13B MET* 1.3 76.9 - - - +
15B ALA* 1.3 65.2 + - - +
17B LEU* 3.4 4.9 + - - +
18B PHE* 3.2 37.8 + - + +
48B TRP* 4.1 13.0 - - + -
56B ILE* 5.4 9.2 - - + -
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Residues in contact with ALA 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 ASN 3.1 14.8 + - - +
12B ILE* 4.0 7.2 - - - +
13B MET 3.3 0.4 - - - -
14B ARG* 1.3 74.0 - - - +
16B TRP* 1.3 55.8 + - - +
17B LEU 3.1 0.3 + - - -
18B PHE* 3.2 5.0 + - - +
19B GLN* 2.8 56.4 + - - +
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Residues in contact with TRP 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 ILE 3.8 11.8 + - - +
13B MET 4.4 3.4 - - - +
14B ARG 3.5 0.2 - - - -
15B ALA* 1.3 77.9 - - - +
17B LEU* 1.3 63.9 + - - +
19B GLN* 4.0 11.4 + - - -
20B HIS* 2.7 59.0 + + + -
23B HIS* 3.5 17.3 - + - -
24B PRO* 3.7 25.8 - - + -
25B TYR 3.8 0.7 - - - -
26B PRO* 3.3 33.4 - - + -
30B GLN* 3.1 45.5 - - + +
34B LEU* 4.5 22.7 - - + -
49B PHE* 3.6 20.0 - + + -
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Residues in contact with LEU 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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13B MET 3.5 13.1 + - - +
14B ARG* 3.4 9.6 + - - +
15B ALA 3.1 0.6 - - - -
16B TRP* 1.3 84.7 - - - +
18B PHE* 1.3 64.9 + - + +
20B HIS 2.8 30.7 + - - +
21B LEU* 3.1 6.3 + - + +
24B PRO* 4.2 12.8 - - + -
48B TRP* 4.4 5.4 - - + -
49B PHE* 4.1 21.1 - - + -
52B ALA* 4.2 13.2 - - + -
53B ARG* 4.9 2.9 - - + -
56B ILE* 3.7 47.1 - - + -
57B VAL* 3.7 25.1 - - + -
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Residues in contact with PHE 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 ARG* 3.2 30.1 + - + +
15B ALA* 4.1 2.9 - - - +
17B LEU* 1.3 86.4 - - + +
19B GLN* 1.3 59.9 + - - +
20B HIS 3.1 1.7 + - - -
21B LEU* 3.6 37.8 + - + +
56B ILE* 3.5 35.2 - - + -
60B MET* 3.9 29.4 - - + -
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Residues in contact with GLN 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 ALA* 2.8 38.3 + - - +
16B TRP* 3.6 9.6 - - - +
17B LEU 3.1 0.4 - - - -
18B PHE* 1.3 77.8 - - + +
20B HIS* 1.3 86.1 + - + +
21B LEU 3.9 0.4 - - - -
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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
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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