Contacts of the strand formed by residues 16 - 25 (chain B) 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 SER 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B SER* 3.9 2.6 + - - -
13B ILE* 2.8 36.1 + - - +
14B ASP* 4.0 4.8 + - - -
15B ASN* 1.3 79.8 + - - +
17B ASN* 1.3 68.5 + - - +
18B ALA* 3.3 1.0 + - - +
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Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 4.9 9.9 - - - +
11B ILE 3.3 21.4 + - - +
12B SER* 4.1 5.5 - - - +
15B ASN 4.2 1.4 + - - -
16B SER* 1.3 73.0 - - - +
18B ALA* 1.3 59.8 + - - +
19B GLY* 3.6 20.5 + - - +
166B THR* 4.9 4.4 + - - -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 2.7 20.4 + - + +
13B ILE* 3.8 34.5 - - + -
16B SER 3.3 1.9 + - - +
17B ASN* 1.3 74.6 - - - +
19B GLY* 1.3 59.1 + - - +
144B ASN* 5.3 2.6 + - - -
145B VAL* 3.8 20.3 - - + +
148B GLU* 5.0 11.7 - - + +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 3.7 3.1 - - - -
11B ILE* 2.9 29.9 + - - +
17B ASN* 3.6 16.9 + - - -
18B ALA* 1.3 81.7 - - - +
20B ARG* 1.3 61.3 + - - -
145B VAL* 3.8 10.8 - - - -
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.3 28.5 - - + -
9B PHE 3.3 8.7 - - - +
10B ASP* 3.1 33.1 + - - +
19B GLY* 1.3 74.5 - - - -
21B ILE* 1.3 73.5 + - - +
22B ILE* 4.2 9.8 + - + +
141B GLU* 4.0 5.7 + - - +
142B GLY* 3.4 19.9 + - - -
145B VAL* 3.7 4.8 - - - +
171B TRP* 3.5 34.0 - - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.0 6.1 - - - +
9B PHE* 2.9 36.0 + - + +
11B ILE* 4.0 24.7 - - + -
20B ARG* 1.3 77.4 - - - +
22B ILE* 1.3 64.8 + - - +
23B PHE* 3.4 41.9 - - + -
60B PHE* 6.0 0.2 - - + -
121B ILE* 4.8 4.7 - - + -
139B VAL* 4.0 14.1 - - + -
141B GLU 3.4 9.9 - - - +
142B GLY 4.0 4.0 - - - +
145B VAL* 3.9 21.1 - - + -
146B VAL* 3.9 19.1 - - + -
149B MET* 4.2 9.6 - - - -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LYS* 4.3 4.3 - - + -
7B VAL 3.4 9.6 - - - +
8B PHE* 4.3 6.5 - - + -
20B ARG* 4.3 14.4 - - + +
21B ILE* 1.3 75.3 - - - +
23B PHE* 1.3 64.9 + - - +
139B VAL* 3.7 3.1 - - - +
140B ILE* 2.9 45.6 + - + +
141B GLU* 2.9 51.0 + - + +
171B TRP* 3.5 50.9 - - + +
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LYS* 3.0 10.4 - - - +
7B VAL* 2.8 56.3 + - + -
8B PHE* 4.7 0.7 - - - -
9B PHE* 3.5 42.6 - + - -
21B ILE* 3.4 26.5 - - + -
22B ILE* 1.3 73.0 - - - +
24B GLU* 1.3 63.4 + - - +
25B LEU* 4.0 1.0 + - + -
37B PHE* 4.7 1.8 - + - -
103B GLY 5.5 0.2 - - - -
105B LEU* 3.6 40.4 - - + -
121B ILE* 4.0 17.0 - - + -
138B LYS 3.4 6.5 - - - +
139B VAL* 3.4 37.9 - - + -
140B ILE* 4.4 2.9 - - - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 4.5 5.0 + - - -
4B ARG* 3.3 52.6 + - + +
5B SER 3.5 5.6 - - - +
6B LYS* 4.4 14.1 - - + -
23B PHE* 1.3 73.6 - - - +
25B LEU* 1.3 65.2 + - - +
26B PHE* 3.7 10.4 - - - -
137B GLY* 3.2 4.0 - - - -
138B LYS* 2.9 43.4 + - + +
140B ILE* 3.8 25.6 - - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.0 23.6 - - - +
5B SER* 2.8 26.9 + - - +
7B VAL* 3.9 33.7 - - + -
23B PHE* 4.7 0.9 - - + -
24B GLU* 1.3 76.2 - - - +
26B PHE* 1.3 60.2 + - - +
27B SER* 2.8 16.2 + - - +
34B CYS* 3.8 31.9 - - + +
37B PHE* 3.8 20.4 - - + -
38B ARG* 4.2 12.1 - - + +
105B LEU* 4.0 17.7 - - + -
136B PHE* 3.6 13.9 - - + +
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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