Contacts of the strand formed by residues 163 - 170 (chain A) in PDB entry 1QNH
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.8 23.1 - - + -
12A SER 3.4 3.8 - - - +
13A ILE* 4.6 5.6 - - + -
59A ILE* 3.3 6.6 - - - +
60A PHE* 3.1 41.8 + - + +
63A ILE* 4.3 4.9 - - + -
149A MET* 3.9 27.6 - - + +
152A GLU* 4.0 23.6 - - + -
159A VAL* 3.8 24.8 - - + +
161A ARG 3.4 4.3 + - - +
162A SER* 1.3 72.7 + - - +
164A VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 164 (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 ILE* 3.4 5.7 - - - +
12A SER* 2.8 41.2 + - - +
57A ASN* 3.8 20.2 - - - +
58A SER 3.4 12.6 - - - +
59A ILE* 3.5 13.2 - - + -
60A PHE* 5.5 0.2 - - - -
162A SER* 3.0 28.7 - - - +
163A VAL* 1.3 75.7 - - - +
165A ILE* 1.3 75.4 + - - +
166A THR* 3.2 15.2 + - + +
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Residues in contact with ILE 165 (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 PHE* 3.7 46.0 - - + -
10A ASP 3.3 7.4 - - - +
11A ILE* 4.0 7.2 - - + -
55A TYR* 3.8 16.8 - - + +
56A LYS 3.6 0.2 - - - -
57A ASN* 2.7 34.0 + - - -
58A SER* 3.1 25.5 + - - +
59A ILE 5.9 0.4 - - - -
60A PHE* 3.7 26.2 - - + -
72A GLY 5.8 0.9 - - - +
119A PHE* 4.6 5.6 - - + -
164A VAL* 1.3 74.2 - - - +
166A THR* 1.3 55.0 + - - +
167A ASP 3.4 21.5 - - - +
168A CYS* 4.0 9.2 - - + -
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Residues in contact with THR 166 (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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10A ASP* 2.9 22.8 + - - +
11A ILE 4.9 0.2 - - - -
12A SER* 3.0 38.3 + - - +
17A ASN* 5.1 2.1 + - - -
56A LYS* 3.7 23.8 - - - +
57A ASN* 4.6 9.4 + - - +
164A VAL* 3.8 11.9 - - + +
165A ILE* 1.3 73.3 - - - +
167A ASP* 1.3 63.8 + - - +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.2 11.0 - - - -
10A ASP* 2.8 50.1 + - + +
20A ARG* 5.2 0.9 + - - -
56A LYS* 4.6 12.8 - - - +
165A ILE* 3.4 5.0 - - - +
166A THR* 1.3 82.5 + - - +
168A CYS* 1.3 82.3 + - - +
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Residues in contact with CYS 168 (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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8A PHE* 3.1 28.8 - - - +
9A PHE* 3.7 14.1 - - + -
41A CYS* 3.4 23.7 - - - +
42A THR* 5.2 0.3 - - - -
54A HIS* 3.7 11.4 + - - -
55A TYR* 4.1 11.9 - - - -
56A LYS* 3.6 31.2 - - - +
165A ILE* 4.0 2.2 - - + -
167A ASP* 1.3 88.4 + - - +
169A GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 169 (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 VAL* 3.2 5.9 - - - +
8A PHE* 2.9 35.2 + - - -
41A CYS* 3.4 24.9 + - - +
42A THR* 4.4 4.3 - - - -
168A CYS* 1.3 78.1 - - - +
170A GLU* 1.3 62.9 + - - -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A SER* 5.2 6.0 - - - -
6A LYS 3.5 11.2 - - - +
7A VAL* 4.1 1.8 - - + +
8A PHE* 3.6 12.0 - - - -
38A ARG* 3.4 44.7 + - + -
42A THR* 3.8 20.2 - - + +
169A GLY* 1.3 76.5 - - - -
171A TRP* 1.3 62.7 + - - +
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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