Contacts of the strand formed by residues 2209 - 2214 (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 SER2209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2200C CYS 3.8 0.7 - - - +
2201C MET* 3.3 2.4 - - - -
2202C SER* 3.1 36.5 + - - -
2203C GLY* 5.8 0.3 - - - -
2207C ASN 5.2 0.2 + - - -
2208C ALA* 1.3 76.4 - - - +
2210C ALA* 1.3 63.9 + - - +
2211C VAL* 4.1 5.9 + - - +
2222C ILE 3.2 12.1 - - - -
2223C PRO* 4.3 1.8 - - - -
2230C LEU* 4.0 5.6 - - - -
3104D HIS* 5.8 0.7 - - - +
3105D ILE* 6.1 0.2 - - - +
3461D LEU* 4.0 33.7 - - - +
3462D GLY 4.4 10.7 + - - -
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Residues in contact with ALA2210 (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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2199C ILE* 4.0 12.6 - - + -
2200C CYS 3.4 4.3 - - - -
2201C MET* 3.8 31.4 - - + -
2209C SER* 1.3 74.9 - - - +
2211C VAL* 1.3 63.2 + - - +
2212C VAL* 4.2 1.1 - - + -
2221C GLU* 3.2 6.6 - - - +
2222C ILE* 2.7 53.5 + - + +
2230C LEU* 3.7 5.0 - - + +
2248C MET* 4.8 1.1 - - + -
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Residues in contact with VAL2211 (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* 5.8 0.7 - - + -
2183C ILE 5.9 0.9 - - - +
2199C ILE* 3.4 4.8 - - - -
2200C CYS* 3.0 32.3 + - + +
2202C SER* 5.9 0.2 - - - +
2209C SER* 5.2 7.0 - - - +
2210C ALA* 1.3 77.0 - - - +
2212C VAL* 1.3 63.8 + - - +
2213C TRP* 3.4 30.9 - - + +
2218C PRO* 4.2 7.9 - - + -
2220C THR 3.5 8.3 - - - +
2221C GLU* 4.6 4.0 - - + +
3104D HIS* 3.8 47.8 - - + +
3105D ILE* 4.0 19.1 - - + +
3461D LEU* 5.6 0.2 - - + -
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Residues in contact with VAL2212 (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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2197C MET* 3.9 24.2 - - + -
2198C SER 3.7 2.9 - - - -
2199C ILE* 3.9 13.5 - - + -
2210C ALA* 5.2 0.7 - - + -
2211C VAL* 1.3 75.2 - - - +
2213C TRP* 1.3 62.3 + - - +
2218C PRO* 3.8 1.2 - - - +
2219C ILE* 2.8 26.0 + - - -
2220C THR* 2.7 24.4 + - - +
2222C ILE* 4.3 11.9 - - + -
2264C PHE* 3.6 28.0 - - + -
2267C GLY* 3.5 36.1 - - - +
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Residues in contact with TRP2213 (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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2180C VAL 6.0 0.7 - - - -
2181C GLU 3.7 18.6 - - - +
2182C CYS* 3.3 29.7 - - + +
2183C ILE 5.1 1.3 - - - +
2196C ARG 4.4 0.7 - - - -
2197C MET* 3.0 11.1 - - - +
2198C SER* 2.7 43.1 + - - +
2211C VAL* 3.4 34.3 - - + +
2212C VAL* 1.3 76.1 - - - +
2214C TYR* 1.3 60.7 + - - +
2216C GLY* 3.5 26.9 - - - +
2217C ARG 3.1 21.3 - - - +
2218C PRO* 3.8 14.8 - - + -
2219C ILE* 4.4 0.4 - - - -
3105D ILE 4.5 3.8 + - - -
3106D LEU* 3.3 52.5 - - + -
3169D MET* 4.0 17.5 - - + -
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Residues in contact with TYR2214 (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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2090C PHE* 4.3 1.4 - - - -
2192C ASP* 2.7 35.0 + - - -
2194C MET* 3.9 7.8 - - - +
2195C SER* 3.5 33.9 + - - -
2196C ARG 3.4 11.0 - - - -
2197C MET* 4.1 13.0 - - + -
2213C TRP* 1.3 74.8 - - - +
2215C GLY* 1.3 67.1 + - - +
2216C GLY 3.0 2.7 + - - -
2217C ARG* 2.7 24.5 + - - +
2219C ILE* 3.6 22.1 - - + +
2266C GLU* 3.6 54.9 + - + +
2267C GLY* 4.0 3.6 - - - +
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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