Contacts of the helix formed by residues 10 - 20 (chain B) in PDB entry 1QQW
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 ASP 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B SER* 4.4 6.6 + - - -
5B ARG* 3.0 56.0 + - - +
6B ASP 3.2 17.8 - - - +
7B PRO* 3.2 7.3 + - - +
9B SER* 1.3 77.1 - - - +
11B GLN* 1.3 63.3 + - - +
12B MET 3.4 1.8 - - - -
13B GLN* 3.8 17.0 - - + +
14B HIS* 2.8 55.1 + - + +
471C GLN* 5.3 0.7 - - - +
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO 3.6 6.4 + - - +
8B ALA 4.2 12.3 - - - +
9B SER 3.2 4.7 - - - +
10B ASP* 1.3 76.4 - - - +
12B MET* 1.3 75.3 + - - +
14B HIS* 3.2 5.3 + - - +
15B TRP* 2.9 29.7 + - - +
266B PHE* 5.5 0.9 - - + -
171C ASN* 3.2 38.5 + - - +
172C PRO* 4.5 3.1 - - - +
173C GLN* 3.4 42.7 + - + +
174C THR* 4.2 5.2 - - + -
178C ASP* 5.2 1.3 - - - +
400D GLY* 2.9 30.5 + - - +
401D ALA 5.5 0.9 - - - -
402D PRO* 6.0 0.2 - - - +
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Residues in contact with MET 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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9B SER 4.9 1.2 + - - -
10B ASP 3.4 0.2 - - - -
11B GLN* 1.3 91.0 + - - +
13B GLN* 1.3 58.0 + - - +
15B TRP* 3.1 8.0 + - - +
16B LYS* 2.9 30.8 + - - +
171C ASN* 4.2 9.2 - - - +
178C ASP* 3.7 3.8 + - - +
180C ASP* 3.6 19.1 - - + +
181C MET* 3.4 37.9 - - + +
402D PRO* 4.5 17.9 - - + -
404D TYR* 3.5 36.8 - - - +
409D PHE* 3.7 33.8 - - + +
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Residues in contact with GLN 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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5B ARG* 5.1 0.2 - - - +
10B ASP* 3.2 25.2 + - + +
12B MET* 1.3 77.8 - - - +
14B HIS* 1.3 61.9 + - + +
16B LYS* 3.5 16.4 + - - +
17B GLU* 3.1 46.9 + - - +
180C ASP* 5.3 1.0 + - - +
471C GLN* 3.2 40.8 + - - +
473C PHE* 4.8 2.6 - - - -
409D PHE* 3.7 15.5 - - - -
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Residues in contact with HIS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 4.3 22.5 + - + +
10B ASP* 2.8 47.7 + - + +
11B GLN* 3.7 4.8 + - - +
13B GLN* 1.3 74.8 - - + +
15B TRP* 1.3 64.8 + - - +
17B GLU* 3.1 21.3 + - - +
18B GLN* 3.0 30.0 + - + +
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Residues in contact with TRP 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 GLN* 2.9 18.4 + - - +
12B MET* 3.4 11.2 - - - +
14B HIS* 1.3 77.0 - - - +
16B LYS* 1.3 62.1 + - - +
18B GLN* 3.4 27.1 + - - +
19B ARG* 3.5 53.0 + - + +
400D GLY* 3.0 30.1 + - - +
401D ALA* 3.4 24.2 - - + +
402D PRO* 3.5 24.5 - - + -
409D PHE 3.0 28.5 - - - -
410D GLY 3.7 20.0 - - - -
411D ALA* 4.3 4.3 - - - -
412D PRO* 5.3 3.6 - - + -
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Residues in contact with LYS 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 MET 2.9 14.7 + - - +
13B GLN* 3.7 18.4 - - - +
15B TRP* 1.3 82.5 - - - +
17B GLU* 1.3 64.6 + - - +
18B GLN 3.1 0.7 - - - -
19B ARG* 3.1 26.8 + - - +
408D SER 3.9 24.3 + - - +
409D PHE* 3.7 29.0 - - + +
410D GLY* 4.9 4.8 - - - +
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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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13B GLN* 3.1 33.9 + - - +
14B HIS* 3.4 26.9 - - - +
16B LYS* 1.3 77.7 - - - +
18B GLN* 1.3 62.8 + - - +
19B ARG 4.3 0.4 - - - -
20B ALA* 4.2 9.4 + - - +
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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 HIS* 3.0 17.6 + - + +
15B TRP* 3.6 27.6 - - - +
16B LYS 3.1 0.4 - - - -
17B GLU* 1.3 79.2 - - - +
19B ARG* 1.3 80.6 + - - +
20B ALA* 3.0 5.7 + - - +
22B GLN* 2.7 22.6 + - - -
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Residues in contact with ARG 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 TRP* 3.5 59.5 + - + +
16B LYS* 3.1 17.6 + - - +
17B GLU 4.3 0.7 - - - -
18B GLN* 1.3 110.5 + - - +
20B ALA* 1.3 65.7 + - - +
22B GLN* 3.0 36.9 - - + +
409D PHE 5.5 0.7 - - - +
410D GLY* 5.1 6.7 - - - +
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Residues in contact with ALA 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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17B GLU 4.5 7.2 - - - +
18B GLN 3.0 11.3 + - - +
19B ARG* 1.3 77.0 - - - +
21B ALA* 1.3 62.1 + - + +
22B GLN* 3.2 10.4 - - - +
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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