Contacts of the strand formed by residues 2196 - 2202 (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 ARG2196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2129C SER* 3.1 32.3 + - - -
2130C CYS 3.0 33.3 + - - -
2131C ASP* 4.3 7.3 + - - +
2136C ARG* 5.6 6.2 - - - +
2138C PHE* 3.7 17.8 - - - -
2179C ARG* 5.8 3.8 - - - +
2181C GLU* 3.9 19.5 - - - +
2189C SER* 2.9 31.1 + - - +
2190C CYS* 3.3 16.7 - - - +
2191C HIS* 3.6 21.2 - - + +
2195C SER* 1.3 77.0 - - - +
2197C MET* 1.3 62.9 + - - +
2198C SER* 3.9 5.0 + - - +
2213C TRP 3.8 0.3 - - - +
2214C TYR* 3.4 4.0 - - - -
2215C GLY* 3.0 25.6 + - - +
2216C GLY 4.6 1.2 + - - -
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Residues in contact with MET2197 (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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2189C SER* 3.0 5.9 + - - -
2190C CYS* 2.7 39.1 + - - +
2195C SER 3.9 1.4 + - - -
2196C ARG* 1.3 72.5 - - - +
2198C SER* 1.3 62.3 + - - +
2199C ILE* 4.1 8.5 - - + -
2212C VAL* 3.9 18.4 - - + -
2213C TRP 3.0 16.2 - - - +
2214C TYR* 4.1 12.3 - - + -
2237C CYS* 3.8 27.1 - - - -
2244C CYS* 3.8 25.6 - - + -
2246C VAL* 3.8 17.3 - - + -
2264C PHE* 3.6 32.8 - - + -
2267C GLY* 4.4 6.7 - - - -
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Residues in contact with SER2198 (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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2164C LEU* 4.2 3.1 - - - -
2181C GLU* 2.9 45.5 + - - +
2182C CYS* 4.2 7.4 - - - -
2188C THR 3.6 4.9 - - - -
2189C SER* 2.7 22.7 + - - -
2196C ARG* 3.9 2.7 + - - +
2197C MET* 1.3 70.9 + - - +
2199C ILE* 1.3 62.3 + - - +
2213C TRP* 2.7 42.5 + - - +
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Residues in contact with ILE2199 (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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2182C CYS* 3.5 3.3 - - - -
2187C SER* 3.1 29.9 - - - -
2188C THR* 3.0 32.1 + - + -
2197C MET* 4.1 12.6 - - + -
2198C SER* 1.3 80.7 - - - +
2200C CYS* 1.3 64.1 + - - +
2201C MET* 4.2 10.3 - - + -
2210C ALA* 4.0 22.0 - - + -
2211C VAL 3.4 9.9 - - - +
2212C VAL* 3.9 18.6 - - + -
2232C THR* 5.1 0.7 - - + -
2246C VAL* 4.0 7.4 - - + -
2248C MET* 4.2 9.6 - - + -
2264C PHE* 3.6 35.9 - - + -
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Residues in contact with CYS2200 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2140C LEU* 5.1 0.2 - - - -
2164C LEU* 3.5 21.1 - - - -
2182C CYS* 2.1 56.3 - - + -
2183C ILE 3.3 23.8 - - - +
2184C GLY* 4.2 4.0 - - - +
2186C SER 3.1 7.4 - - - +
2187C SER* 4.1 4.5 - - - -
2199C ILE* 1.3 76.2 - - - +
2201C MET* 1.3 65.8 + - - +
2202C SER 4.2 0.3 + - - -
2209C SER 3.8 0.9 - - - +
2210C ALA* 3.4 0.3 - - - -
2211C VAL* 3.0 31.8 + - + +
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Residues in contact with MET2201 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2184C GLY* 3.0 1.6 - - - -
2185C TRP* 2.7 43.4 + - + -
2186C SER* 2.9 10.9 + - - +
2199C ILE* 4.2 4.0 - - - -
2200C CYS* 1.3 79.5 - - - +
2202C SER* 1.3 61.5 + - - +
2208C ALA* 5.0 0.4 - - + -
2209C SER 3.3 4.9 - - - +
2210C ALA* 3.8 14.4 - - + -
2230C LEU* 3.4 44.2 - - + +
2231C ARG* 3.7 12.3 - - - +
2232C THR* 3.5 42.6 - - + -
2248C MET* 3.7 30.7 - - + -
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Residues in contact with SER2202 (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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2183C ILE 3.8 4.9 - - - -
2184C GLY* 3.7 13.9 - - - -
2185C TRP* 3.5 13.9 - - - +
2200C CYS 4.2 0.6 + - - -
2201C MET* 1.3 75.3 - - - +
2203C GLY* 1.3 63.6 + - - +
2208C ALA* 3.1 5.5 - - - +
2209C SER* 3.1 36.3 + - - -
2211C VAL* 5.9 0.2 - - - +
3105D ILE* 3.6 11.3 - - - +
3464D TRP* 4.7 1.3 - - - -
3466D TRP* 3.5 32.6 - - - -
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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