Contacts of the strand formed by residues 113 - 116 (chain C) in PDB entry 2W4V
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 TYR 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C LEU* 5.6 3.1 - - + -
106C ARG* 2.6 31.9 + - - -
111C LEU* 3.6 3.4 - - + +
112C ILE* 1.3 87.7 - - + +
114C THR* 1.3 57.5 + - - +
115C TYR* 1.9 77.1 + + - -
120C CYS* 2.9 30.9 - - + +
121C ILE 3.3 8.7 - - - -
122C ALA* 4.9 3.4 - - + +
150C PRO* 2.6 42.8 - - + +
151C HIS* 2.9 22.7 - - + -
152C LEU* 3.9 13.9 - - + +
155C VAL* 2.9 9.5 - - - +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU 3.8 14.6 - - - +
86C GLU 3.4 12.1 - - - +
88C MET* 3.8 14.8 - - + -
103C LEU* 3.7 13.0 - - + +
106C ARG* 2.3 39.8 + - - +
112C ILE 4.9 0.5 - - - -
113C TYR* 1.3 79.6 + - - +
115C TYR* 1.3 76.9 + - - +
121C ILE* 2.8 56.7 + - + +
150C PRO* 4.3 0.2 - - - -
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C GLU 2.9 12.4 + - - +
87C ASP* 3.3 20.0 - - + +
88C MET* 3.0 34.6 + - - +
113C TYR* 1.9 48.7 + + - -
114C THR* 1.3 73.2 - - - +
116C SER* 1.4 65.0 - - - +
117C GLY 3.3 8.7 - - - +
118C LEU 5.5 0.4 - - - -
119C PHE* 3.7 14.1 - - - -
120C CYS* 4.3 0.7 - - + -
145C LYS* 4.8 34.5 - - + -
149C PRO 4.7 0.7 - - - -
150C PRO* 2.9 25.8 - - + -
151C HIS 2.7 23.7 + - - -
154C SER* 3.1 16.0 - - - -
155C VAL* 3.9 8.5 - - + +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C MET* 4.6 7.2 - - - -
114C THR 3.7 0.2 + - - -
115C TYR* 1.4 57.8 - - - +
117C GLY* 1.3 64.8 + - - +
118C LEU 3.2 2.9 + - - -
119C PHE* 2.9 29.2 + - - +
120C CYS 4.9 0.2 - - - -
121C ILE* 3.8 20.5 - - - +
669C ARG* 5.2 3.0 + - - -
696C VAL* 5.5 7.8 - - - +
699C GLY 4.3 4.0 - - - +
700C ILE* 2.7 33.4 - - - +
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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