Contacts of the helix formed by residues 13 - 22 (chain B) in PDB entry 3BQT
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 GLY 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A TRP* 6.4 2.0 - - - -
68A HIS* 6.1 2.0 - - - -
7B SER* 5.2 1.8 - - - -
11B ASN 3.7 4.4 + - - -
12B ILE* 1.3 77.8 - - - +
14B LYS* 1.3 66.0 + - - -
15B VAL* 3.3 2.9 - - - -
16B LEU* 3.3 8.3 + - - +
17B GLU* 3.0 19.7 + - - +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 4.1 43.8 + - + +
7B SER* 5.7 2.2 - - - -
13B GLY* 1.3 70.8 - - - -
15B VAL* 1.3 56.5 + - + +
17B GLU* 3.2 13.6 - - - +
18B GLN* 2.8 55.9 + - + +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 3.6 39.3 - - + -
68A HIS* 4.9 11.7 - - + -
75A LYS* 5.4 4.3 - - - +
13B GLY* 3.3 0.8 - - - -
14B LYS* 1.3 74.4 - - + +
16B LEU* 1.3 67.0 + - - +
18B GLN* 3.3 12.9 + - - +
19B ASP* 3.0 42.7 + - - +
54B GLU* 6.0 2.2 - - - +
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Residues in contact with LEU 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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11B ASN 3.9 7.9 - - - +
12B ILE* 3.4 37.9 - - + -
13B GLY 3.3 13.3 + - - +
15B VAL* 1.3 76.6 - - - +
17B GLU* 1.3 71.4 + - - +
19B ASP* 3.4 3.8 + - - +
20B LEU* 3.1 31.4 + - + +
43B ILE* 5.0 10.3 - - + +
50B VAL* 5.9 2.2 - - + -
54B GLU* 4.1 38.3 + - + +
57B ALA* 4.6 7.6 - - + -
58B LEU* 3.7 25.6 - - + -
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Residues in contact with GLU 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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6B LEU* 3.3 31.5 + - + +
7B SER* 3.3 26.6 + - - -
12B ILE* 3.7 13.6 - - + +
13B GLY 3.0 10.3 + - - +
14B LYS* 3.2 14.2 - - - +
16B LEU* 1.3 80.6 - - - +
18B GLN* 1.3 59.5 + - + +
20B LEU* 2.8 30.6 + - - +
21B ILE* 2.9 28.1 + - + +
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Residues in contact with GLN 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 LYS* 2.8 47.2 + - - +
15B VAL* 3.6 13.7 - - - +
16B LEU 3.3 0.2 - - - -
17B GLU* 1.3 77.6 - - + +
19B ASP* 1.3 58.5 + - - +
21B ILE* 3.0 31.2 - - + +
22B LYS* 3.0 29.2 + - - +
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Residues in contact with ASP 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 VAL* 3.0 39.5 + - - +
16B LEU* 3.8 4.5 - - + +
18B GLN* 1.3 74.3 - - - +
20B LEU* 1.3 63.2 + - - +
22B LYS* 2.6 37.3 + - + +
23B ALA* 3.2 7.8 + - - +
43B ILE* 2.9 34.4 - - + +
46B ASN* 5.3 1.2 + - - -
47B ASP* 6.6 0.4 - - - -
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Residues in contact with LEU 20 (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 LEU* 4.3 13.2 - - + -
12B ILE* 5.0 3.8 - - + -
16B LEU* 3.1 24.4 + - + +
17B GLU* 2.8 11.3 + - - +
19B ASP* 1.3 77.1 - - - +
21B ILE* 1.3 69.1 + - - +
23B ALA* 2.8 17.4 + - - +
24B GLY 3.1 3.5 + - - -
25B ILE* 3.1 50.9 + - + +
31B LEU* 4.9 8.3 - - + -
39B ALA* 4.3 15.5 - - + -
43B ILE* 4.4 19.3 - - + -
58B LEU* 3.7 28.0 - - + -
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Residues in contact with ILE 21 (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 LEU* 4.3 8.5 - - + -
17B GLU* 2.9 33.1 + - + +
18B GLN* 3.0 19.7 - - + +
20B LEU* 1.3 75.7 - - - +
22B LYS* 1.3 56.9 + - + +
23B ALA 2.9 5.7 + - - -
24B GLY* 2.9 14.9 + - - -
25B ILE 3.5 12.7 + - - +
26B LYS* 4.3 30.7 + - + +
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Residues in contact with LYS 22 (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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18B GLN* 3.0 30.2 + - - +
19B ASP* 2.6 43.5 + - + +
20B LEU 3.4 0.2 - - - -
21B ILE* 1.3 76.1 - - + +
23B ALA* 1.3 58.3 + - - +
24B GLY 3.4 0.6 + - - -
46B ASN* 3.8 17.8 + - - +
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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