Contacts of the strand formed by residues 2179 - 2183 (chain C) in PDB entry 1W21
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 ARG2179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136C ARG* 3.6 44.6 - - - +
2165C ILE* 3.1 5.7 - - - -
2166C SER* 2.7 42.3 + - - +
2177C ASN 4.2 0.2 + - - -
2178C THR* 1.3 73.7 - - - +
2180C VAL* 1.3 71.4 + - - +
2181C GLU* 3.4 22.8 + - - +
2196C ARG* 5.8 3.6 - - - +
3168D GLU* 3.6 25.6 + - - +
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Residues in contact with VAL2180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2163C ALA* 4.2 6.7 - - + -
2164C LEU 3.6 5.8 - - - +
2165C ILE* 4.4 12.3 - - + -
2178C THR 4.0 1.5 + - - +
2179C ARG* 1.3 80.5 - - - +
2181C GLU* 1.3 60.4 + - - +
2182C CYS* 3.8 13.0 - - - +
2183C ILE* 3.8 28.9 - - + -
2213C TRP* 6.0 1.0 - - - -
3106D LEU 6.0 0.4 - - - +
3107D SER* 5.2 1.1 - - - +
3108D LYS 5.4 1.1 - - - +
3168D GLU* 4.6 2.2 + - - -
3169D MET 4.0 15.3 + - - +
3170D GLY* 3.4 35.9 - - - +
3171D GLN* 4.0 6.7 - - + +
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Residues in contact with GLU2181 (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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2136C ARG* 5.0 0.3 + - - -
2138C PHE* 3.9 23.9 - - + -
2164C LEU* 2.9 32.7 + - + +
2166C SER* 2.9 30.1 + - - +
2179C ARG* 3.4 23.8 + - - +
2180C VAL* 1.3 73.7 - - - +
2182C CYS* 1.3 66.1 + - - +
2196C ARG* 3.9 13.6 - - - +
2198C SER* 2.9 23.7 + - - +
2213C TRP* 3.7 25.6 - - - +
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Residues in contact with CYS2182 (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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2163C ALA* 3.3 6.8 - - - +
2164C LEU* 2.8 35.6 + - - +
2180C VAL* 3.4 4.4 - - - +
2181C GLU* 1.3 84.4 - - - +
2183C ILE* 1.3 66.6 + - - +
2198C SER 4.2 3.4 - - - -
2199C ILE* 3.5 14.8 - - - -
2200C CYS* 2.1 53.8 - - + -
2211C VAL* 5.8 0.7 - - + -
2213C TRP* 3.3 28.7 - - + +
3106D LEU 5.4 0.2 - - - -
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Residues in contact with ILE2183 (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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2160C PRO 4.9 0.9 - - - +
2162C ARG 3.7 10.3 - - - +
2163C ALA* 3.9 8.3 - - + -
2180C VAL* 3.8 25.4 - - + -
2182C CYS* 1.3 76.2 - - - +
2184C GLY* 1.3 61.2 + - - +
2200C CYS* 3.3 16.0 - - - +
2202C SER* 3.8 9.6 - - - -
2211C VAL* 5.9 1.2 - - - +
2213C TRP* 5.1 1.4 - - - +
3105D ILE* 3.6 26.6 + - + +
3106D LEU 3.7 8.7 + - - +
3107D SER* 3.6 22.9 - - - -
3108D LYS* 3.6 32.3 - - + +
3110D ASN* 6.2 0.2 - - - +
3466D TRP* 3.6 30.7 - - + -
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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
------------------------------------------------------------
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