Contacts of the strand formed by residues 191 - 196 (chain C) in PDB entry 4WRL
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 ILE 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C VAL* 3.7 24.0 - - + -
112C ALA 3.6 20.6 - - - +
113C GLN 3.7 7.6 - - - -
115C VAL* 4.2 20.0 - - + -
125C LEU* 4.2 26.2 - - + -
126C PRO* 4.4 2.0 - - + -
127C CYS* 4.2 24.9 - - + +
174C ASP* 4.4 1.3 - - - -
175C TYR* 2.8 45.8 + - + +
176C GLN* 5.8 0.2 - - - -
177C CYS* 4.5 6.5 - - - -
188C SER* 5.2 0.2 - - - +
189C ILE 3.8 7.6 - - - +
190C SER* 1.3 79.4 - - - +
192C ARG* 1.3 63.4 + - - +
193C LEU 3.6 2.3 + - - -
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Residues in contact with ARG 192 (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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113C GLN 2.8 16.3 + - - +
114C GLU* 3.4 19.7 - - + +
115C VAL* 2.9 27.5 + - - +
173C GLN 4.5 1.1 - - - +
174C ASP* 2.8 41.8 + - - +
190C SER* 4.2 1.0 + - - -
191C ILE* 1.3 71.9 - - - +
193C LEU* 1.3 66.7 + - - +
194C LYS* 3.7 31.8 - - + +
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Residues in contact with LEU 193 (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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115C VAL* 3.5 34.8 - - + +
117C VAL* 4.2 3.8 - - + -
123C ALA* 3.9 25.4 - - + -
125C LEU* 4.3 10.5 - - + -
164C ILE* 4.1 15.5 - - + -
167C ALA* 5.0 2.2 - - + -
171C GLN* 3.9 17.7 - - + +
172C SER* 3.3 22.7 - - - -
173C GLN 2.9 10.8 + - - +
175C TYR* 3.7 23.3 - - + -
191C ILE 3.6 0.8 + - - -
192C ARG* 1.3 76.6 - - - +
194C LYS* 1.3 73.0 + - - +
195C VAL* 3.9 16.6 - - + -
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Residues in contact with LYS 194 (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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114C GLU* 5.2 6.7 + - - +
115C VAL 2.7 16.4 + - - +
116C VAL* 3.4 18.1 - - + +
117C VAL* 2.9 30.0 + - - +
172C SER* 4.3 5.6 - - - +
192C ARG* 3.7 32.8 + - + +
193C LEU* 1.3 76.2 - - - +
195C VAL* 1.3 64.1 + - - +
196C GLN* 5.3 8.3 - - + +
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Residues in contact with VAL 195 (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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117C VAL* 3.5 4.9 - - + +
118C PHE 4.0 4.5 - - - +
119C GLU* 3.8 26.2 - - + +
167C ALA* 3.9 18.8 - - + +
168C LYS 3.4 39.9 - - - +
169C PHE* 3.3 27.4 - - - +
171C GLN* 4.5 0.7 - - + -
172C SER* 3.1 17.9 + - - +
193C LEU* 3.9 21.1 - - + -
194C LYS* 1.3 78.0 - - - +
196C GLN* 1.3 62.4 - - - +
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Residues in contact with GLN 196 (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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116C VAL* 3.6 27.5 - - + +
117C VAL 2.9 12.8 + - - +
118C PHE* 3.3 36.4 - - + +
119C GLU* 2.9 26.6 + - - -
169C PHE* 5.0 1.3 - - - -
194C LYS* 5.0 8.5 - - + +
195C VAL* 1.3 77.4 - - - +
197C LYS* 1.3 65.2 + - - +
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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