Contacts of the strand formed by residues 158 - 164 (chain F) 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 LEU 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F SER* 3.5 44.2 - - - +
43F LYS* 4.6 9.9 - - + -
94F MET* 3.7 37.2 - - + -
100F LEU* 5.4 0.2 - - + -
121F VAL* 4.4 11.2 - - + -
153F GLY* 3.8 1.2 - - - -
154F LEU* 2.9 31.5 + - + -
155F GLY 2.8 13.2 + - - +
156F TYR* 3.7 13.5 - - + +
157F GLY* 1.3 86.3 - - - +
159F LYS* 1.3 62.7 + - - +
176F VAL* 4.3 8.7 - - + -
177F THR 3.5 7.6 - - - +
178F LYS* 4.5 2.0 - - + -
179F ALA* 3.6 6.4 - - - +
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Residues in contact with LYS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F SER* 5.3 11.2 - - - -
152F ARG 3.7 6.7 - - - +
153F GLY* 3.8 15.7 - - - +
154F LEU* 3.9 6.5 - - - +
158F LEU* 1.3 75.6 - - - +
160F SER* 1.3 64.6 + - - +
161F ARG* 6.1 4.5 - - - +
175F HIS 3.8 1.0 - - - +
176F VAL* 3.6 3.3 - - - +
177F THR* 3.0 49.7 + - - +
178F LYS 3.8 9.7 + - - -
179F ALA* 3.7 29.2 + - + +
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Residues in contact with SER 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F TRP* 4.9 4.2 - - - -
119F VAL* 3.6 41.4 + - - +
143F PHE* 5.1 3.6 - - - -
150F HIS 3.6 1.4 - - - +
151F SER* 3.1 6.3 - - - -
152F ARG* 2.9 47.1 + - - +
154F LEU* 3.8 11.5 - - - +
159F LYS* 1.3 77.3 - - - +
161F ARG* 1.3 59.5 - - - +
174F ILE* 4.7 2.0 - - - -
175F HIS 3.7 5.2 - - - -
176F VAL* 4.6 5.4 - - - +
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Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F TRP* 4.5 0.7 - - - -
149F TRP* 3.4 43.8 - - + -
150F HIS 3.5 4.0 - - - +
151F SER* 3.7 17.9 - - - +
159F LYS* 6.1 4.7 - - + +
160F SER* 1.3 75.3 - - - +
162F GLY* 1.3 59.3 + - - +
173F GLU 3.8 0.5 - - - +
174F ILE* 3.2 3.9 - - - +
175F HIS* 2.6 86.0 + - - +
177F THR* 5.8 3.7 - - + +
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F TRP* 3.4 25.9 - - - -
148F GLY 3.9 0.2 - - - +
149F TRP* 3.3 8.2 - - - -
150F HIS 2.9 34.1 + - - -
161F ARG* 1.3 78.5 - - - +
163F PHE* 1.3 59.5 + - - -
173F GLU 3.0 10.5 - - - -
174F ILE* 4.0 4.0 - - - -
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Residues in contact with PHE 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F TRP* 4.1 2.4 - - - -
147F ASN* 3.3 47.8 - - - -
148F GLY* 3.4 20.6 - - - -
149F TRP* 3.6 45.1 - + + -
162F GLY* 1.3 73.9 - - - +
164F MET* 1.3 75.8 + - - +
165F ASN* 4.3 4.5 - - + -
171F ILE* 3.5 7.5 - - + +
172F LEU* 3.3 8.6 - - - +
173F GLU* 2.8 35.9 + - + +
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Residues in contact with MET 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 3.8 29.4 - - + -
104F PHE* 4.8 2.0 - - + -
105F SER 4.1 4.9 - - - +
106F VAL* 3.9 17.5 - - + -
115F ASN* 4.1 10.1 - - - -
116F TRP 3.6 39.5 - - - +
117F TRP* 3.4 27.7 - - + +
145F GLY* 3.3 10.7 - - - -
146F ASP* 3.5 0.7 + - - +
147F ASN* 3.1 23.9 + - - -
148F GLY 4.3 2.9 + - - -
163F PHE* 1.3 82.4 - - - +
165F ASN* 1.3 70.4 + - - +
170F ALA* 4.1 7.4 - - + -
171F ILE 3.4 12.1 - - - +
172F LEU* 4.0 6.5 - - + -
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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