Contacts of the helix formed by residues 10 - 19 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F LYS* 5.8 1.6 - - - +
174F ASP* 4.5 9.4 + - - -
232F PHE* 3.3 43.9 + - - +
10I ASN* 5.8 1.4 + - - -
11J LYS* 1.3 70.4 + - - +
12J GLY* 3.4 20.5 + - - +
13J ILE* 3.4 30.4 + - + +
14J LYS 3.5 1.4 + - - -
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Residues in contact with LYS 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F ASP* 2.7 39.9 + - - +
10I ASN* 5.8 1.8 - - - +
12I GLY 5.9 0.9 - - - -
13I ILE* 3.6 35.7 - - + +
16I VAL* 6.0 0.3 - - - +
10J ASN* 1.3 79.8 - - - +
12J GLY* 1.3 60.3 + - - +
13J ILE 3.3 0.2 - - - -
14J LYS* 3.6 13.4 - - + +
15J GLN* 3.1 27.2 + - - +
230J GLU 4.8 2.1 + - - -
231J ASP* 3.3 50.3 + - + +
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Residues in contact with GLY 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LYS* 5.9 1.8 - - - -
10J ASN* 3.4 10.7 + - - -
11J LYS* 1.3 75.0 - - - +
13J ILE* 1.3 65.7 + - - +
15J GLN* 3.4 14.5 + - - +
16J VAL* 3.4 18.6 + - - +
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Residues in contact with ILE 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LYS* 3.7 34.7 - - + +
231F ASP* 3.1 55.6 - - + +
232F PHE* 3.9 24.2 - - + -
10J ASN* 3.5 31.4 + - + +
11J LYS 3.3 0.2 - - - -
12J GLY* 1.3 75.4 - - - +
14J LYS* 1.3 63.6 - - - +
16J VAL* 3.2 18.3 + - - +
17J TYR* 3.3 24.3 - - + -
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Residues in contact with LYS 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ARG* 5.8 0.4 - - - +
174F ASP* 3.5 35.4 + - + +
177F GLU* 3.8 27.0 + - + +
178F ALA* 4.9 2.5 - - + -
232F PHE* 3.8 16.9 - - + -
10J ASN 3.5 5.2 + - - +
11J LYS* 3.6 19.5 - - + +
13J ILE* 1.3 80.1 - - - +
15J GLN* 1.3 66.6 + - - +
17J TYR* 3.1 9.8 + - - +
18J MET* 2.9 46.5 + - + +
89J PHE* 5.3 5.4 + - - +
227J ARG* 3.8 22.8 - - - +
231J ASP* 4.4 11.7 + - - -
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Residues in contact with GLN 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I VAL* 3.6 44.4 - - + +
11J LYS 3.1 18.6 + - - +
12J GLY* 3.8 8.5 - - - +
13J ILE 3.3 0.8 - - - -
14J LYS* 1.3 78.8 - - - +
16J VAL* 1.3 59.3 + - + +
18J MET* 3.2 20.6 + - - +
19J SER* 2.8 35.6 + - - +
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Residues in contact with VAL 16 (chain J).
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 6.0 0.4 - - - +
15F GLN* 3.7 47.3 - - + +
12J GLY 3.4 14.3 + - - +
13J ILE* 3.2 9.8 + - - +
14J LYS 3.2 0.6 - - - -
15J GLN* 1.3 76.0 - - + +
17J TYR* 1.3 66.4 + - + +
19J SER* 3.1 21.9 + - - -
20J LEU* 3.7 9.3 + - + +
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Residues in contact with TYR 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F PRO 4.7 5.6 - - - -
89F PHE* 3.4 29.3 - + - -
178F ALA* 3.5 44.4 - - + +
181F ARG* 3.2 21.7 - - - +
182F ALA* 4.2 9.6 - - + -
228F VAL* 3.8 24.6 - - + -
231F ASP* 2.3 34.3 + - - -
232F PHE* 4.3 4.9 - + - -
13J ILE* 3.3 35.7 - - + -
14J LYS* 3.1 6.8 + - - +
16J VAL* 1.3 82.8 - - + +
18J MET* 1.3 59.8 + - - +
20J LEU* 3.4 25.6 - - + +
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Residues in contact with MET 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F GLU* 4.5 22.2 - - - +
178F ALA* 5.3 0.4 - - - -
181F ARG* 3.1 53.5 + - - +
14J LYS* 2.9 49.8 + - + +
15J GLN* 3.6 25.0 + - - +
16J VAL 3.2 0.4 - - - -
17J TYR* 1.3 76.3 - - + +
19J SER* 1.3 58.1 + - - +
20J LEU 3.3 0.9 - - - -
89J PHE 3.6 24.0 - - - +
90J ARG* 4.0 13.0 - - + -
91J LYS* 6.2 0.7 - - - +
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Residues in contact with SER 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LYS* 5.7 2.6 + - - -
15J GLN* 2.8 26.3 + - - +
16J VAL* 3.1 12.9 + - - -
18J MET* 1.3 75.7 - - - +
20J LEU* 1.3 64.5 + - - +
21J PRO* 3.3 8.7 - - - +
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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