Contacts of the strand formed by residues 258 - 263 (chain C) in PDB entry 3V56
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 GLU 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C LYS* 5.5 5.1 - - + +
184C LYS* 3.4 32.9 - - + +
185C ILE 3.2 8.5 - - - +
186C LEU* 3.8 26.8 - - + +
213C GLN 3.8 0.2 - - - +
214C ARG* 3.4 4.3 - - - +
215C LYS* 2.7 50.2 + - + +
256C GLY 3.8 5.4 + - - +
257C ASP* 1.3 79.2 - - - +
259C LEU* 1.3 63.5 + - - +
260C GLN* 5.7 0.4 - - - +
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Residues in contact with LEU 259 (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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178C LEU* 5.4 0.2 - - + -
184C LYS* 3.4 9.7 - - - +
185C ILE* 2.7 48.8 + - + +
187C VAL* 4.8 6.7 - - + -
195C ILE* 3.8 24.5 - - + -
212C ILE* 5.0 3.4 - - + -
213C GLN 3.3 12.1 - - - +
214C ARG* 4.2 3.4 - - + -
229C LEU* 3.9 24.7 - - + -
253C LEU* 3.8 34.5 - - + -
257C ASP* 6.0 0.2 - - + -
258C GLU* 1.3 79.1 - - - +
260C GLN* 1.3 61.0 + - - +
279C PHE* 3.8 15.0 - - + -
281C ALA* 4.3 13.5 - - + -
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Residues in contact with GLN 260 (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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165C PHE* 3.9 30.5 - - + -
183C ASN 5.2 2.9 - - - +
184C LYS* 4.2 24.2 - - + +
211C LEU 3.3 1.6 - - - +
212C ILE* 3.5 2.6 - - - -
213C GLN* 2.7 74.5 + - + +
215C LYS* 5.8 2.7 - - + +
226C LEU* 3.9 21.9 - - + +
258C GLU 5.7 0.9 - - - +
259C LEU* 1.3 76.2 - - - +
261C LEU* 1.3 60.3 + - - +
279C PHE* 3.8 10.5 - - - -
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Residues in contact with LEU 261 (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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165C PHE* 3.4 21.8 - - - -
166C VAL* 4.4 18.3 + - + -
168C TRP* 4.1 28.3 + - + +
183C ASN 5.9 0.2 + - - -
197C GLY* 4.3 10.1 - - - -
199C VAL* 3.6 28.7 - - + -
210C HIS* 3.7 39.0 - - + +
211C LEU 3.3 4.5 - - - +
212C ILE* 4.6 3.4 - - + +
260C GLN* 1.3 71.6 - - - +
262C ALA* 1.3 59.0 + - - +
263C ILE* 4.4 5.8 + - + -
278C PHE 4.3 2.2 - - - +
279C PHE* 3.8 28.9 - - + -
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Residues in contact with ALA 262 (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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163C TYR* 3.9 15.5 - - + -
164C THR 4.1 0.2 - - - -
165C PHE* 3.5 28.9 - - + -
210C HIS* 3.3 3.1 - - - -
211C LEU* 2.8 36.7 + - + +
213C GLN* 3.6 26.2 - - - +
260C GLN* 4.0 0.4 - - - +
261C LEU* 1.3 73.8 - - - +
263C ILE* 1.3 63.0 + - - +
264C PRO* 3.5 4.2 - - - +
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Residues in contact with ILE 263 (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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163C TYR* 3.3 3.4 - - - -
164C THR* 2.9 49.1 + - + +
166C VAL* 4.1 24.2 - - + -
199C VAL* 4.2 7.6 - - + -
201C TYR* 4.0 14.4 - - + +
208C MET* 4.1 7.6 - - + -
209C GLY 3.5 13.7 - - - +
210C HIS* 4.0 6.3 - - + -
261C LEU* 4.4 4.3 - - + -
262C ALA* 1.3 74.8 - - - +
264C PRO* 1.4 54.5 - - - +
265C ARG* 2.7 28.2 + - + -
268C ALA* 3.7 24.0 - - + -
270C ILE* 4.0 28.0 - - + -
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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