Contacts of the strand formed by residues 169 - 178 (chain A) in PDB entry 3ZWG
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 HIS 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.9 18.7 - - + +
28A ASN* 4.4 12.5 + - - -
29A VAL 3.0 24.9 + - - -
30A LYS 3.8 8.5 + - - -
32A LYS* 3.5 34.6 + - + -
165A ASN* 2.9 21.1 + - - -
167A SER* 3.3 4.6 - - - -
168A GLY* 1.3 82.8 - - - +
170A ALA* 1.3 60.5 + - - +
58B ASP* 3.4 16.9 + - - +
79B ARG* 4.5 18.5 + - - -
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Residues in contact with ALA 170 (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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23A LEU* 3.7 4.1 - - - +
32A LYS 2.8 11.2 + - - +
33A ILE* 3.4 20.8 - - + -
34A ALA 2.9 26.2 + - - -
106A VAL* 3.8 21.5 - - + -
115A ASN* 4.2 8.1 - - - +
164A MET* 4.1 9.2 - - + -
165A ASN* 3.2 10.1 - - - +
167A SER 4.3 1.3 - - - +
169A HIS* 1.3 73.3 - - - +
171A ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 171 (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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16A PHE* 4.7 4.0 - - + +
19A LEU* 3.6 32.3 - - + +
20A LYS* 4.1 34.8 - - + +
23A LEU* 4.2 15.3 - - + -
34A ALA* 3.7 4.0 - - + -
163A PHE* 3.5 2.3 - - - +
164A MET* 3.3 24.9 - - - +
165A ASN* 2.8 13.8 + - + +
169A HIS 5.1 0.7 - - - +
170A ALA* 1.3 80.9 - - - +
172A LEU* 1.3 63.3 + - - +
58B ASP* 3.3 28.3 - - + +
60B VAL* 3.8 22.9 - - + -
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Residues in contact with LEU 172 (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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19A LEU* 3.9 3.7 - - - +
33A ILE* 4.3 11.9 - - + -
34A ALA 3.1 11.6 + - - +
35A VAL* 3.5 17.4 - - + -
36A GLY 3.0 25.1 + - - +
102A VAL* 4.4 6.5 - - + -
104A PHE* 4.2 20.0 - - + -
117A TRP* 3.7 44.9 - - + -
163A PHE 3.3 15.3 - - - +
164A MET* 4.0 8.1 - - + -
170A ALA 4.2 0.4 - - - -
171A ILE* 1.3 71.5 - - - +
173A GLU* 1.3 59.8 + - - +
174A ILE* 3.7 29.4 - - + -
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Residues in contact with GLU 173 (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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14A LEU* 4.1 19.7 - - + +
15A GLY* 4.2 12.4 - - - -
16A PHE 4.1 9.4 + - - -
19A LEU* 3.7 11.4 - - + +
36A GLY 3.7 3.1 - - - -
149A TRP* 3.8 17.9 - - + -
161A ARG* 3.9 0.3 + - - +
162A GLY* 3.0 3.8 - - - -
163A PHE 2.8 38.6 + - - +
171A ILE 4.1 0.8 - - - -
172A LEU* 1.3 72.8 - - - +
174A ILE* 1.3 61.9 + - - +
175A HIS* 2.9 31.3 + - + +
60B VAL* 3.3 34.0 - - + +
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Residues in contact with ILE 174 (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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14A LEU* 4.2 1.2 - - - +
36A GLY 3.0 10.3 + - - +
37A ILE* 3.4 17.0 - - + -
38A ASP* 2.9 23.2 + - - +
102A VAL* 3.5 33.9 - - + -
117A TRP* 4.2 11.2 - - + -
119A VAL* 3.9 24.7 - - + -
160A SER* 4.7 2.7 - - - -
161A ARG 3.2 10.3 - - - +
162A GLY* 4.3 0.7 - - - -
172A LEU* 3.7 29.2 - - + -
173A GLU* 1.3 80.3 - - - +
175A HIS* 1.3 77.8 + - - +
176A VAL* 4.4 13.2 - - + -
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Residues in contact with HIS 175 (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 GLY 5.0 1.6 - - - -
14A LEU* 4.4 15.0 - - + +
38A ASP* 3.1 37.4 + - + +
40A GLU* 5.7 0.2 - - - +
149A TRP* 4.4 2.7 - + - -
159A LYS 3.8 0.5 - - - +
160A SER* 3.6 1.7 - - - -
161A ARG* 2.6 78.2 + - + +
173A GLU* 2.9 35.5 + - + +
174A ILE* 1.3 77.2 + - - +
176A VAL* 1.3 63.7 + - - +
177A THR* 3.8 13.6 + - + +
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Residues in contact with VAL 176 (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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37A ILE* 4.6 2.5 - - + -
38A ASP 3.1 7.4 + - - +
40A GLU* 2.8 33.6 + - - +
41A SER* 3.9 14.1 - - - -
45A TRP* 3.7 38.8 - - + -
100A LEU* 4.1 17.3 - - + -
102A VAL* 6.3 0.2 - - + -
119A VAL* 4.7 2.2 - - + -
154A LEU* 4.3 13.2 - - + -
158A LEU* 4.3 10.5 - - + -
159A LYS 3.6 8.5 - - - +
160A SER* 4.6 9.2 - - - -
174A ILE* 4.1 15.0 - - + -
175A HIS* 1.3 73.7 - - - +
177A THR* 1.3 61.2 + - - +
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Residues in contact with THR 177 (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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40A GLU* 3.6 24.2 - - + -
41A SER* 4.4 4.9 - - - -
158A LEU* 3.5 5.0 - - - +
159A LYS* 2.9 49.9 + - - +
161A ARG* 5.9 3.7 - - + +
175A HIS* 4.2 18.3 + - + +
176A VAL* 1.3 80.5 - - - +
178A LYS* 1.3 71.4 + - - +
179A ALA 3.3 0.2 + - - -
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Residues in contact with LYS 178 (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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40A GLU 3.3 24.2 + - - -
41A SER* 3.6 15.7 - - - +
42A GLY* 4.3 10.9 - - - -
67A HIS* 3.6 25.0 + - - -
157A GLY 3.7 7.9 - - - +
158A LEU* 4.5 3.1 - - + -
159A LYS* 3.9 5.4 + - - -
177A THR* 1.3 81.2 + - - +
179A ALA* 1.3 65.5 + - - +
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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