Contacts of the strand formed by residues 18 - 25 (chain D) in PDB entry 4NQC
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 VAL 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D MET* 3.9 28.9 - - + -
11D THR 5.4 0.9 - - - +
12D ALA* 3.9 17.5 - - + -
17D ILE* 1.3 74.6 - - - +
19D GLN* 1.3 63.9 + - - +
20D ILE* 4.6 3.6 - - + -
73D LEU 3.7 0.9 - - - +
74D LEU* 3.5 6.3 - - - +
75D LEU* 3.0 43.8 + - + +
78D LEU* 3.8 13.6 - - + +
105D LEU* 3.8 43.1 - - + -
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Residues in contact with GLN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D MET* 3.5 20.8 - - - +
18D VAL* 1.3 75.3 - - - +
20D ILE* 1.3 60.7 + - - +
21D ASN* 2.9 33.3 + - - +
70D TYR* 3.2 11.5 + - - -
72D TYR* 3.6 44.3 - - + -
73D LEU 3.5 2.5 - - - -
74D LEU* 3.8 14.0 - - + +
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Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PRO* 4.6 2.2 - - + -
10D MET* 4.2 12.1 - - - -
18D VAL* 4.6 7.4 - - + -
19D GLN* 1.3 71.0 - - - +
21D ASN* 1.3 65.5 + - - +
34D TRP* 3.5 24.1 - - + -
72D TYR* 3.1 3.9 - - - -
73D LEU* 2.8 46.4 + - + +
75D LEU* 4.4 14.4 - - + -
86D TYR* 3.7 39.7 - - + -
103D THR* 3.4 39.5 - - + +
105D LEU* 4.6 11.0 - - + -
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASP 4.5 0.4 - - - -
6D GLN* 3.4 9.0 - - - +
7D PRO* 3.3 29.6 - - + +
10D MET* 6.0 1.2 - - - +
19D GLN* 2.9 26.2 + - - +
20D ILE* 1.3 76.5 - - - +
22D CYS* 1.3 60.1 + - - +
23D THR* 4.4 3.6 - - + -
34D TRP* 4.4 0.2 - - - -
70D TYR* 2.7 36.9 + - + -
71D SER 3.6 3.4 - - - -
72D TYR* 3.6 2.4 - - - +
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Residues in contact with CYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.6 20.4 - - - -
5D ASP 3.3 6.5 - - - +
6D GLN* 4.4 1.3 - - + -
21D ASN* 1.3 76.9 - - - +
23D THR* 1.3 62.9 + - - +
24D TYR* 4.4 2.2 + - - -
32D LEU* 4.4 5.8 - - - -
34D TRP* 3.5 16.4 - - + -
70D TYR* 3.4 1.7 - - - -
71D SER* 2.8 39.0 + - - +
88D CYS* 2.0 50.5 - - + -
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Residues in contact with THR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ASN* 4.1 0.5 + - - +
4D ILE* 3.6 3.3 - - - +
5D ASP* 2.9 52.1 + - - +
21D ASN* 5.6 2.7 - - + -
22D CYS* 1.3 77.5 - - - +
24D TYR* 1.3 60.2 + - - +
68D LYS 5.5 1.1 - - - +
69D GLY 3.3 10.3 - - - +
70D TYR* 3.9 22.2 - - + -
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ASN* 3.4 4.3 - - - +
4D ILE* 3.8 25.4 - - + -
22D CYS* 4.7 1.3 - - - -
23D THR* 1.3 77.7 - - - +
25D GLN* 1.3 60.5 + - - +
26D THR* 3.9 22.0 - - + -
29D PHE* 3.5 37.9 - + + -
32D LEU* 3.6 31.0 - - + -
64D LEU* 3.6 15.5 - - + +
66D ARG* 3.8 16.5 + - - +
68D LYS 5.3 0.2 - - - +
69D GLY* 3.0 49.7 + - - +
70D TYR* 3.6 5.8 - - - -
90D VAL* 4.0 4.9 - - + -
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Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLN* 3.7 7.9 + - + +
3D ASN* 2.8 50.6 + - + +
24D TYR* 1.3 73.1 - - - +
26D THR* 1.3 60.5 + - - +
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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