Contacts of the strand formed by residues 138 - 143 (chain B) in PDB entry 2WNW
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 LYS 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 3.1 32.3 + - + +
84B THR 2.9 10.1 + - - +
85B LEU* 3.5 28.6 - - + +
86B ALA 3.2 22.2 + - - +
136B HIS 3.4 3.0 + - - +
137B MET* 1.3 70.0 - - - +
139B LEU* 1.3 63.6 + - - +
140B MET* 5.3 0.8 - - + +
189B GLN* 3.5 37.2 - - + +
190B ALA* 4.5 13.0 - - + -
234B GLU* 2.8 37.3 + - - -
236B TYR* 4.0 3.0 + - - -
289B LYS* 3.8 1.2 - - - +
291B LEU* 6.3 0.6 - - - +
329B ILE* 5.9 0.2 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 4.3 8.7 - - + -
86B ALA* 3.6 27.8 - - + -
88B MET* 4.2 17.9 - - + -
127B ILE* 4.3 4.7 - - + -
131B LEU* 4.2 17.3 - - + -
137B MET* 3.5 27.5 + - + +
138B LYS* 1.3 75.8 - - - +
140B MET* 1.3 60.8 + - - +
186B ILE* 3.4 33.2 - - + -
187B ASN 3.7 18.4 + - - +
188B VAL* 3.5 3.4 - - - +
189B GLN* 2.9 29.9 + - - +
190B ALA* 3.1 6.9 + - - +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 2.9 16.0 + - - +
87B ARG* 3.1 21.9 - - + +
88B MET* 2.9 30.2 + - - +
138B LYS* 5.3 0.4 - - + +
139B LEU* 1.3 75.3 - - - +
141B ALA* 1.3 65.3 + - - +
142B SER* 3.8 7.6 - - - +
188B VAL* 4.6 0.4 - - - -
190B ALA* 3.2 25.1 - - + +
191B LEU 4.1 8.3 - - - +
192B SER* 3.6 31.9 - - - -
236B TYR* 4.1 15.3 - - + -
239B ASP* 4.9 0.2 - - - +
266B ALA* 4.4 7.9 - - + -
291B LEU* 3.7 27.4 - - + -
293B SER* 4.6 1.3 - - - -
329B ILE* 4.3 7.4 - - + -
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Residues in contact with ALA 141 (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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88B MET* 3.3 6.7 - - + -
90B ILE* 3.7 11.6 - - + +
140B MET* 1.3 74.3 - - - +
142B SER* 1.3 62.4 + - - +
177B TYR* 3.5 40.4 - - + +
188B VAL* 4.1 7.4 - - + +
190B ALA 2.9 6.9 + - - -
191B LEU* 3.2 35.1 - - + +
192B SER 3.3 4.2 + - - +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.0 40.5 + - - -
88B MET 2.9 7.4 + - - -
89B PRO* 3.2 9.2 - - - +
90B ILE* 2.9 19.3 + - - +
140B MET* 3.8 4.9 - - - +
141B ALA* 1.3 78.0 + - - +
143B PRO* 1.3 67.2 - - - +
144B TRP* 3.3 9.0 - - - -
192B SER* 2.6 29.4 + - - -
195B ASN* 5.1 0.2 - - - -
239B ASP* 3.9 0.2 - - - -
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Residues in contact with PRO 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.6 32.5 - - + +
142B SER* 1.3 85.6 - - - +
144B TRP* 1.3 61.4 + - - +
145B SER 4.4 2.7 - - - +
170B TRP* 3.5 31.4 - - + -
174B ILE* 4.4 8.1 - - + -
192B SER 3.4 19.5 - - - +
193B VAL 3.7 17.9 - - - +
194B GLN* 3.6 6.5 + - - +
195B ASN* 2.9 27.5 + - - +
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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