Contacts of the strand formed by residues 161 - 169 (chain B) in PDB entry 2WJZ
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 GLU 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B VAL* 5.7 0.5 - - - +
112B LYS 4.8 1.0 - - - +
113B LEU* 3.3 22.2 - - + +
114B ARG* 2.8 46.6 + - + +
115B SER* 4.3 2.6 + - - -
144B ARG* 3.0 37.3 + - - +
156B THR 3.5 2.3 - - - +
157B GLU* 3.3 2.1 + - - -
158B TYR* 2.9 37.8 + - - +
159B ASP 3.1 3.5 - - - +
160B GLY* 1.3 77.8 - - - +
162B ILE* 1.3 63.8 + - - +
163B PHE* 3.8 4.0 - - + -
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Residues in contact with ILE 162 (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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144B ARG* 3.6 14.4 + - - -
155B THR* 3.6 34.8 - - + +
156B THR 3.4 4.7 - - - +
157B GLU* 4.2 15.0 - - + +
160B GLY 4.0 6.2 + - - +
161B GLU* 1.3 74.1 - - - +
163B PHE* 1.3 66.4 + - - +
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Residues in contact with PHE 163 (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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113B LEU* 4.2 12.6 - - + -
120B HIS* 4.2 4.7 - + - -
139B PHE* 4.4 2.5 - + - -
141B HIS* 3.5 35.9 - + - -
144B ARG* 3.6 36.8 - - + +
155B THR* 3.5 7.9 + - - -
156B THR* 3.0 65.3 + - + -
158B TYR* 4.3 17.5 - - + -
161B GLU* 3.8 9.6 - - + -
162B ILE* 1.3 76.0 - - - +
164B PRO* 1.3 85.5 - - + +
165B SER* 3.1 14.6 + - - -
176B GLN* 4.4 4.9 - - + -
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Residues in contact with PRO 164 (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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87B MET* 3.4 16.6 - - + +
144B ARG* 3.7 7.2 - - - +
145B ALA* 3.5 26.9 + - + +
147B CYS* 4.2 12.8 - - - +
152B VAL* 4.1 23.1 - - + -
154B GLY 3.4 9.6 - - - +
163B PHE* 1.3 96.7 - - + +
165B SER* 1.3 57.9 - - - +
166B ALA 3.1 15.5 - - - +
167B VAL* 4.0 14.8 - - + -
176B GLN* 4.4 2.4 - - - +
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Residues in contact with SER 165 (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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87B MET* 4.6 0.4 - - - -
126B VAL* 3.4 13.9 - - - +
139B PHE* 3.7 19.5 - - - -
154B GLY 3.1 2.4 + - - -
155B THR 3.2 15.2 + - - -
156B THR* 2.7 34.7 + - - -
163B PHE* 3.1 7.1 + - - -
164B PRO* 1.3 73.4 - - - +
166B ALA* 1.3 59.6 + - - +
176B GLN* 2.9 36.2 + - - -
177B PHE* 3.6 6.5 - - - -
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Residues in contact with ALA 166 (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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87B MET* 4.6 0.7 - - - -
126B VAL* 4.8 0.4 - - + -
128B PHE* 3.5 23.3 - - + -
152B VAL 3.9 0.3 - - - -
153B LEU* 2.9 21.6 + - + -
154B GLY* 3.1 31.5 + - - +
164B PRO* 3.1 3.7 - - - +
165B SER* 1.3 81.3 - - - +
167B VAL* 1.3 68.4 + - - +
174B GLY 3.2 11.7 - - - +
175B PHE* 4.0 8.1 - - + -
177B PHE* 4.7 0.7 - - + -
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Residues in contact with VAL 167 (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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87B MET* 3.9 21.5 - - + -
90B LEU* 4.6 2.2 - - + -
91B PHE* 4.0 17.0 - - + -
106B ILE* 3.3 28.0 - - + -
145B ALA* 5.1 0.2 - - + -
147B CYS* 3.7 23.8 - - - -
151B HIS 3.2 16.6 - - - +
152B VAL* 4.5 0.2 - - - -
153B LEU* 3.7 7.6 - - - +
164B PRO* 4.0 6.7 - - + -
166B ALA* 1.3 77.6 - - - +
168B ARG* 1.3 66.8 + - - +
173B LEU* 3.5 2.4 - - - -
174B GLY* 2.8 38.4 + - - +
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Residues in contact with ARG 168 (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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106B ILE* 4.4 0.7 - - - -
129B LYS* 5.3 4.9 - - - +
130B ASP* 2.5 42.2 + - - -
131B THR* 4.2 4.8 + - - -
132B PHE* 5.1 2.4 - - - -
150B GLU 4.1 7.4 + - - +
151B HIS* 2.8 34.5 + - - +
152B VAL 4.9 7.9 + - - -
153B LEU* 3.9 34.3 - - + +
167B VAL* 1.3 79.0 - - - +
169B LYS* 1.3 60.9 + - - +
170B GLY* 3.7 20.9 + - - +
172B ILE 3.3 4.9 - - - -
173B LEU* 3.5 23.4 - - + +
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Residues in contact with LYS 169 (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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104B SER 5.4 0.6 + - - -
105B LEU 3.0 27.4 + - - +
106B ILE* 3.6 23.7 - - + +
107B GLU* 2.7 33.5 + - - +
151B HIS* 3.4 25.8 - - + +
168B ARG* 1.3 72.1 - - - +
170B GLY* 1.3 61.9 + - - +
171B ARG 3.2 1.0 + - - -
172B ILE* 3.1 31.4 + - + +
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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