Contacts of the strand formed by residues 203 - 208 (chain C) in PDB entry 2VKM
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 203 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C VAL* 5.0 0.2 - - + -
202C ILE* 1.3 72.1 - - - +
204C VAL* 1.3 63.2 + - - +
205C ARG 3.6 17.3 - - - +
206C VAL* 3.9 17.3 - - + -
217C CYS 3.9 5.2 - - - +
220C TYR* 4.0 14.8 - - + +
221C ASN* 2.8 32.1 + - - +
225C SER* 3.8 21.8 - - - +
236C LEU* 5.9 1.3 - - + -
285C LEU* 4.1 23.3 - - + -
286C TYR 3.2 14.4 - - - +
287C LEU* 3.8 18.6 - - + -
331C THR* 3.9 22.4 - - + +
333C MET* 4.4 6.1 - - - -
382C CYS* 4.0 0.9 - - - +
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Residues in contact with VAL 204 (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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202C ILE* 3.9 15.9 - - + +
203C ILE* 1.3 76.6 - - - +
205C ARG* 1.3 62.9 + - + +
217C CYS* 3.7 13.7 - - - +
220C TYR* 4.2 6.6 - - - -
286C TYR* 2.8 29.3 + - + +
287C LEU 4.6 0.2 - - - -
288C MET* 4.5 4.7 - - + +
295C SER* 4.2 18.4 - - - +
376C THR* 4.2 19.7 - - + +
379C MET* 3.8 23.1 - - + -
382C CYS* 3.5 27.2 - - - -
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Residues in contact with ARG 205 (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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278B ASN* 4.5 13.1 - - - +
365B PHE* 3.7 38.5 - - - +
203C ILE* 3.6 3.7 - - - +
204C VAL* 1.3 83.0 - - + +
206C VAL* 1.3 73.3 + - - +
207C GLU* 2.8 32.3 + - - +
210C GLY 4.6 0.4 + - - -
212C ASP* 3.3 46.0 + - - +
220C TYR* 3.8 8.0 - - - -
286C TYR* 2.9 60.8 + - + +
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Residues in contact with VAL 206 (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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203C ILE* 3.9 9.0 - - + -
205C ARG* 1.3 81.5 - - - +
207C GLU* 1.3 73.6 + - - +
208C ILE* 4.6 7.0 - - + -
212C ASP* 3.5 5.4 - - - +
213C LEU* 2.9 46.1 + - + +
220C TYR* 3.7 39.1 + - + -
236C LEU* 6.3 1.8 - - + -
240C VAL* 5.1 4.0 - - + -
244C ALA* 6.1 1.1 - - + -
283C ILE* 4.9 2.9 - - + -
284C SER 3.4 8.7 - - - +
285C LEU* 3.9 22.7 - - + -
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Residues in contact with GLU 207 (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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365B PHE* 4.1 6.8 - - - +
205C ARG* 2.8 36.1 + - - +
206C VAL* 1.3 79.6 - - - +
208C ILE* 1.3 72.7 + - - +
209C ASN 4.0 0.4 - - - -
210C GLY* 3.4 32.8 + - - +
211C GLN 3.3 5.2 - - - +
212C ASP* 4.1 4.3 - - - -
283C ILE* 3.5 2.3 - - - +
284C SER* 3.0 43.5 + - - +
286C TYR* 2.5 36.1 + - + -
297C ARG* 4.4 5.9 + - - -
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Residues in contact with ILE 208 (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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206C VAL* 4.6 8.3 - - + -
207C GLU* 1.3 83.2 - - - +
209C ASN* 1.3 69.9 + - + +
211C GLN* 2.9 24.4 + - - +
213C LEU* 4.1 15.3 - - + -
244C ALA* 4.7 9.2 - - + +
247C SER* 3.3 38.1 + - - +
248C ILE* 4.1 17.0 - - + -
251C ALA* 4.8 1.6 - - + -
281C PRO* 3.4 33.0 - - + -
282C VAL 3.6 2.9 - - - +
283C ILE* 4.0 24.9 - - + -
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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