Contacts of the helix formed by residues 10 - 20 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 4.6 6.0 - - - -
5A ARG* 2.5 59.3 + - - +
6A ASP 3.1 20.2 + - - +
7A PRO* 3.5 4.4 + - - +
8A ALA 3.3 0.2 - - - -
9A SER* 1.3 74.9 - - - +
11A GLN* 1.3 65.4 + - - +
12A MET 3.7 0.4 - - - -
13A GLN* 4.0 20.3 - - + +
14A HIS* 3.1 41.3 + - + +
180D ASP* 5.5 0.2 - - - -
471D GLN* 5.1 1.7 - - - +
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Residues in contact with GLN 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 PRO 3.9 4.2 + - - +
8A ALA 3.8 14.6 + - - +
9A SER 3.2 4.6 + - - -
10A ASP* 1.3 71.7 - - - +
12A MET* 1.3 86.5 + - - +
14A HIS* 2.9 17.3 + - - +
15A TRP* 3.0 18.2 + - - +
266A PHE* 5.5 1.3 - - + -
400C GLY 2.9 30.3 + - - +
401C ALA 5.5 1.6 - - - -
402C PRO* 5.8 0.2 - - - +
171D ASN* 3.4 38.1 + - - +
172D PRO* 4.8 3.1 - - - +
173D GLN* 3.0 35.1 + - + +
174D THR* 4.2 5.2 - - + -
178D ASP* 4.7 1.3 - - - +
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Residues in contact with MET 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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9A SER 5.0 0.6 + - - +
11A GLN* 1.3 93.5 + - - +
13A GLN* 1.3 63.3 + - - +
15A TRP* 3.3 6.3 + - - +
16A LYS* 2.9 24.4 + - - +
402C PRO* 4.6 17.9 - - + -
404C TYR* 3.1 34.5 - - - +
409C PHE* 3.5 36.6 - - + +
171D ASN* 4.5 8.1 - - - +
172D PRO* 6.5 0.4 - - + -
178D ASP* 4.2 3.5 + - - +
180D ASP* 3.2 36.1 - - + +
181D MET* 3.6 21.5 - - + +
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Residues in contact with GLN 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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5A ARG* 5.1 0.4 - - - +
10A ASP* 3.9 28.2 - - + +
11A GLN 2.9 1.6 + - - -
12A MET* 1.3 79.3 - - - +
14A HIS* 1.3 57.6 + - + +
16A LYS* 3.1 16.8 + - - +
17A GLU* 2.8 57.8 + - - +
409C PHE* 3.3 16.5 - - - -
180D ASP* 5.2 1.2 + - - +
471D GLN* 3.1 40.1 + - - +
473D PHE* 4.4 3.6 - - - -
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Residues in contact with HIS 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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7A PRO* 4.3 21.8 + - + +
10A ASP* 3.1 32.5 + - + +
11A GLN* 2.9 7.9 + - - +
13A GLN* 1.3 75.0 - - + +
15A TRP* 1.3 66.7 + - - +
17A GLU* 3.2 22.7 + - + +
18A GLN* 3.0 27.8 + - + +
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Residues in contact with TRP 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 GLN* 3.0 17.2 + - - +
12A MET* 3.5 11.0 - - - +
14A HIS* 1.3 76.0 - - - +
16A LYS* 1.3 63.7 + - - +
18A GLN* 3.0 28.7 + - - +
19A ARG* 3.5 55.4 + - + +
398C GLN 5.5 0.2 + - - -
400C GLY* 3.0 30.3 + - - +
401C ALA* 3.5 23.1 - - + +
402C PRO* 3.7 20.4 - - + -
409C PHE 3.2 26.0 - - - -
410C GLY 3.8 21.3 - - - -
411C ALA* 4.3 4.5 - - - -
412C PRO* 5.2 3.8 - - + -
173D GLN* 5.7 0.4 - - - -
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Residues in contact with LYS 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 MET 2.9 13.5 + - - +
13A GLN* 3.3 21.3 - - - +
15A TRP* 1.3 81.5 - - - +
17A GLU* 1.3 63.8 + - - +
19A ARG* 3.1 24.2 + - - +
408C SER* 3.8 14.5 + - - +
409C PHE* 3.5 48.5 - - + +
410C GLY* 4.8 2.2 - - - +
473D PHE* 6.2 1.0 - - - -
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Residues in contact with GLU 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 GLN* 2.8 38.2 + - - +
14A HIS* 3.2 31.5 + - + +
16A LYS* 1.3 79.3 - - - +
18A GLN* 1.3 60.3 + - - +
19A ARG 3.5 0.7 + - - -
20A ALA* 4.2 8.8 + - - +
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Residues in contact with GLN 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 HIS 3.0 14.6 + - - +
15A TRP* 3.0 24.3 + - - +
17A GLU* 1.3 76.9 - - - +
19A ARG* 1.3 95.5 + - - +
20A ALA* 3.2 3.2 + - - +
22A GLN* 2.8 16.6 + - - -
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Residues in contact with ARG 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 TRP* 3.5 63.3 + - + +
16A LYS* 3.1 15.5 + - - +
17A GLU 4.3 0.9 - - - -
18A GLN* 1.3 115.3 + - - +
20A ALA* 1.3 68.8 + - - +
22A GLN* 3.2 30.4 - - + +
409C PHE 5.4 0.4 - - - +
410C GLY* 5.2 6.1 - - - +
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Residues in contact with ALA 20 (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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17A GLU 4.6 6.7 - - - +
18A GLN 3.2 3.6 + - - +
19A ARG* 1.3 81.0 - - - +
21A ALA* 1.3 63.4 + - + +
22A GLN* 3.2 17.9 - - - +
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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