Contacts of the strand formed by residues 168 - 174 (chain B) in PDB entry 2J3W
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 THR 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TRP* 6.4 0.2 - - + -
117B ILE 3.8 0.9 - - - +
118B ILE* 3.5 3.3 - - - +
119B GLU* 2.7 44.1 + - + +
120B LYS 4.9 0.2 - - - -
121B GLU 5.1 0.6 - - - -
122B PRO* 4.5 14.9 - - - +
123B LEU* 4.3 22.9 - - + +
136B THR 5.6 0.5 + - - -
137B LEU* 4.2 8.5 - - + +
140B ALA* 3.7 29.6 - - + -
163B HIS 3.7 2.9 - - - +
164B TRP* 4.0 15.9 - - - -
165B HIS 4.0 0.2 - - - -
166B LYS 3.8 0.2 + - - -
167B GLY* 1.3 72.9 - - - -
169B THR* 1.3 67.2 + - - +
170B LEU* 4.5 7.6 - - + -
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Residues in contact with THR 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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116B TYR* 3.9 30.5 - - + -
117B ILE 3.5 3.4 - - - +
118B ILE* 3.4 14.9 - - - +
162B VAL* 3.3 3.1 - - - -
163B HIS* 2.8 49.2 + - + -
165B HIS* 2.7 45.3 + - + +
168B THR* 1.3 74.0 - - - +
170B LEU* 1.3 76.1 + - - +
171B MET 4.2 1.3 - - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 4.1 26.5 - - + -
116B TYR* 3.5 5.4 - - - -
117B ILE* 3.0 38.7 + - + +
123B LEU* 5.2 0.7 - - + -
140B ALA* 4.0 16.4 - - + +
143B THR* 4.2 2.0 - - + -
144B GLY* 3.8 26.0 - - - +
147B VAL* 4.0 23.3 - - + -
160B VAL* 4.2 9.9 - - + -
161B THR 3.3 4.9 - - - +
162B VAL* 3.4 26.0 - - + -
168B THR* 4.5 6.3 - - + -
169B THR* 1.3 75.8 - - - +
171B MET* 1.3 62.5 + - - +
172B ILE* 3.6 6.4 + - + +
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Residues in contact with MET 171 (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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114B THR* 3.8 18.4 - - + -
115B TYR 3.6 2.5 - - - -
116B TYR* 3.7 31.9 - - + -
159B LYS 3.4 2.4 - - - +
160B VAL* 3.2 6.9 - - - -
161B THR* 2.6 56.6 + - + +
163B HIS* 3.5 23.1 - - + +
169B THR 3.8 2.6 + - - -
170B LEU* 1.3 71.9 - - - +
172B ILE* 1.3 63.4 + - - +
173B LYS* 5.0 8.1 - - + +
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Residues in contact with ILE 172 (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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86B LEU* 4.3 15.0 - - + -
89B ILE* 5.2 2.2 - - + -
113B LYS 3.3 3.1 - - - +
114B THR* 3.3 2.8 - - - -
115B TYR* 2.7 49.5 + - + +
117B ILE* 3.7 31.0 - - + +
147B VAL* 4.5 15.7 - - + -
151B LEU* 3.6 25.1 - - + -
158B ALA* 4.5 3.4 - - + -
159B LYS 3.9 1.6 - - - -
160B VAL* 4.2 16.6 - - + -
170B LEU* 3.9 9.6 - - + +
171B MET* 1.3 78.2 - - - +
173B LYS* 1.3 59.8 + - - +
174B PHE* 4.0 20.9 - - + -
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Residues in contact with LYS 173 (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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111B ASP* 3.4 16.8 + - - +
113B LYS* 3.5 36.3 - - + +
114B THR* 2.8 24.7 + - + +
158B ALA* 3.5 2.7 - - - -
159B LYS* 2.9 46.3 + - + +
171B MET* 3.9 9.1 + - + -
172B ILE* 1.3 72.4 - - - +
174B PHE* 1.3 64.7 + - - +
175B ASP* 4.6 1.2 - - - +
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Residues in contact with PHE 174 (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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82B VAL* 3.8 21.5 - - + -
85B ILE* 4.5 3.4 - - + -
86B LEU* 3.7 34.3 - - + -
113B LYS* 2.9 38.3 + - - +
115B TYR* 3.9 16.6 - + - -
151B LEU* 4.0 18.8 - - + -
156B PHE* 3.6 36.3 - + + -
157B PRO 3.7 4.0 - - - +
158B ALA* 3.7 11.2 - - + -
172B ILE* 4.0 10.5 - - + -
173B LYS* 1.3 81.0 - - - +
175B ASP* 1.3 70.8 + - - +
176B GLU 3.7 0.3 + - - -
178B VAL* 4.1 13.2 - - + -
179B ILE* 4.3 8.7 - - + -
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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