Contacts of the strand formed by residues 117 - 122 (chain B) in PDB entry 2WNU
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 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ALA* 3.1 3.6 - - - -
100B THR* 2.7 58.9 + - - +
102B THR* 3.8 19.5 - - + +
116B ASP* 1.3 82.5 - - - +
118B VAL* 1.3 72.1 + - - +
119B ILE* 3.6 16.6 + - + +
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Residues in contact with VAL 118 (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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98B SER 3.8 3.8 - - - +
99B ALA* 4.2 6.7 - - + +
116B ASP 4.7 2.2 - - - +
117B HIS* 1.3 82.7 + - - +
119B ILE* 1.3 64.7 + - - +
120B THR* 3.7 13.0 - - - +
121B ASN* 3.6 32.3 - - + +
126B TYR* 5.4 1.8 - - + -
128B PRO* 4.0 27.4 - - + -
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Residues in contact with ILE 119 (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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98B SER* 2.7 15.3 + - - +
100B THR* 3.8 26.7 - - + -
117B HIS* 3.6 19.0 + - + +
118B VAL* 1.3 77.1 - - - +
120B THR* 1.3 70.3 + - - +
214B ILE* 4.3 4.0 - - + -
161C VAL* 3.9 25.8 - - + +
162C VAL* 4.0 9.9 - - + -
179C VAL* 3.9 11.0 - - + -
180C LEU 3.8 11.0 - - - +
181C LEU* 3.8 18.8 - - + -
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Residues in contact with THR 120 (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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96B ALA 4.0 11.2 - - - +
97B PHE* 3.1 3.8 - - - +
98B SER* 2.8 35.3 + - - +
118B VAL* 3.7 4.1 - - - +
119B ILE* 1.3 81.7 + - - +
121B ASN* 1.3 67.3 + - - +
122B MET* 4.4 8.7 - - + +
126B TYR* 5.7 0.5 - - - -
137C LEU* 3.6 31.2 - - + -
180C LEU* 2.7 28.3 + - + +
181C LEU* 4.1 4.5 - - - +
182C ARG* 4.6 6.6 + - + +
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Residues in contact with ASN 121 (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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96B ALA 3.4 4.3 - - - -
97B PHE* 3.7 4.6 - - - +
118B VAL* 3.6 17.3 - - + +
120B THR* 1.3 76.4 - - - +
122B MET* 1.3 66.4 + - - +
123B ASN 3.4 0.3 + - - -
124B ASN* 3.1 35.9 + - - +
125B ASN 3.7 4.5 + - - -
126B TYR* 2.9 58.6 + - - +
128B PRO* 4.5 10.1 - - - +
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Residues in contact with MET 122 (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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94B LYS* 3.5 43.7 - - + +
95B ILE* 3.6 4.0 - - - +
96B ALA 2.9 28.8 + - - +
120B THR* 4.4 11.7 - - + -
121B ASN* 1.3 75.4 - - - +
123B ASN* 1.3 65.6 + - - +
124B ASN 3.2 3.0 + - - -
125B ASN* 4.5 2.1 + - - +
137C LEU* 3.6 36.8 - - + -
182C ARG* 3.7 46.4 - - - +
215C PHE* 4.8 0.7 - - + -
217C ASP* 4.5 2.7 - - - +
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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