Contacts of the helix formed by residues 10 - 19 (chain F) in PDB entry 2QC8
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 ASN 10 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LYS* 1.3 77.3 + - - +
12F GLY* 3.4 12.6 + - - -
13F ILE* 3.3 30.1 + - + +
14F LYS* 3.4 9.0 + - - +
11G LYS* 6.1 0.3 - - - +
174G ASP* 4.7 4.3 + - - -
232G PHE* 3.4 37.6 + - - +
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Residues in contact with LYS 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASN* 1.3 79.6 - - - +
12F GLY* 1.3 60.4 + - - +
13F ILE 3.3 0.2 - - - -
14F LYS* 3.5 11.8 + - + +
15F GLN* 3.1 27.4 + - - +
230F GLU 4.5 2.8 + - - -
231F ASP* 3.4 43.3 + - + +
174G ASP* 2.7 40.1 + - - +
10J ASN* 5.8 1.6 - - - +
12J GLY 5.9 0.7 - - - -
13J ILE* 3.7 35.4 - - + +
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Residues in contact with GLY 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASN* 3.4 11.2 + - - -
11F LYS* 1.3 74.8 - - - +
13F ILE* 1.3 67.2 + - - +
15F GLN* 3.3 13.6 + - - +
16F VAL* 3.4 18.8 + - - +
11G LYS* 5.9 1.8 - - - -
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Residues in contact with ILE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASN* 3.5 33.0 + - + +
11F LYS 3.3 0.2 - - - -
12F GLY* 1.3 76.3 - - - +
14F LYS* 1.3 65.0 + - - +
16F VAL* 3.1 19.0 + - - +
17F TYR* 3.4 24.3 - - + -
11G LYS* 3.7 33.2 - - + +
231G ASP* 3.2 50.9 - - + +
232G PHE* 4.0 21.1 - - + -
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Residues in contact with LYS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASN 3.4 7.0 + - - +
11F LYS* 3.8 15.7 - - + +
12F GLY 3.3 0.2 - - - -
13F ILE* 1.3 79.5 - - - +
15F GLN* 1.3 68.7 + - - +
17F TYR* 3.0 9.8 + - - +
18F MET* 2.9 44.5 + - + +
89F PHE 5.1 5.6 + - - -
227F ARG* 3.7 24.5 - - - +
231F ASP* 4.2 11.3 + - - -
173G ARG* 5.7 0.4 - - - +
174G ASP* 3.3 36.6 + - + +
177G GLU* 3.8 26.2 - - + +
178G ALA* 5.0 2.9 - - - +
232G PHE* 3.8 15.8 - - + -
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Residues in contact with GLN 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LYS 3.1 17.8 + - - +
12F GLY* 3.7 8.1 - - - +
13F ILE 3.2 0.4 - - - -
14F LYS* 1.3 79.7 - - - +
16F VAL* 1.3 57.8 + - + +
18F MET* 3.2 21.1 + - - +
19F SER* 2.8 39.6 + - - +
91F LYS* 6.3 1.2 - - - +
16J VAL* 3.7 46.5 - - + +
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Residues in contact with VAL 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F GLY 3.4 16.2 - - - +
13F ILE* 3.5 9.0 - - - +
14F LYS 3.1 0.6 - - - -
15F GLN* 1.3 78.0 - - + +
17F TYR* 1.3 67.1 + - + +
19F SER* 3.3 20.5 + - - -
20F LEU* 3.7 11.1 + - + +
15G GLN* 3.7 44.2 - - + +
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Residues in contact with TYR 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ILE* 3.4 29.4 - - + -
14F LYS* 3.0 6.7 + - - +
16F VAL* 1.3 82.0 - - + +
18F MET* 1.3 62.5 - - + +
20F LEU* 3.1 29.6 + - + +
88G PRO 4.7 5.8 - - - -
89G PHE* 3.3 30.5 - + - -
178G ALA* 3.7 45.1 - - + +
181G ARG* 3.3 17.6 - - + +
182G ALA* 4.2 9.0 - - + -
228G VAL* 3.7 24.0 - - + -
231G ASP* 2.3 33.8 + - - -
232G PHE* 4.7 4.3 - + - -
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Residues in contact with MET 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 2.9 45.7 + - + +
15F GLN* 3.2 26.4 + - - +
17F TYR* 1.3 77.2 - - + +
19F SER* 1.3 57.9 + - - +
89F PHE 3.8 22.9 - - - +
90F ARG* 4.0 13.7 - - + +
91F LYS* 6.2 0.2 - - - +
177G GLU* 4.3 26.9 - - - +
178G ALA 4.9 0.4 - - - -
181G ARG* 2.9 62.5 + - - +
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Residues in contact with SER 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLN* 2.8 24.5 + - - +
16F VAL* 3.4 12.2 + - - -
17F TYR 3.2 0.4 - - - -
18F MET* 1.3 74.6 - - - +
20F LEU* 1.3 64.0 + - - +
21F PRO* 3.4 7.4 - - - +
91G LYS* 5.4 4.5 + - - -
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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