Contacts of the strand formed by residues 211 - 215 (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 LEU 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C TYR* 4.2 14.8 - - + +
210C HIS* 1.4 79.5 - - - +
212C ILE* 1.4 61.9 + - - +
213C GLN* 3.6 35.1 + - + +
228C THR* 3.8 15.9 - - + +
230C PHE 3.5 3.6 - - - -
231C ARG* 3.6 34.1 - - + -
260C GLN 3.3 2.4 - - - +
261C LEU* 3.3 4.7 - - - -
262C ALA* 2.8 38.8 + - + +
264C PRO* 3.8 24.9 - - + -
27I LEU* 5.3 4.7 - - + +
28I LEU* 4.2 4.5 - - + -
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ILE* 3.6 24.9 - - + -
196C TYR* 3.9 9.6 - - - +
197C GLY* 3.7 30.5 - - - +
210C HIS* 4.3 14.3 - - + +
211C LEU* 1.4 70.2 - - - +
213C GLN* 1.3 55.2 + - - +
228C THR 3.7 0.7 - - - -
229C LEU* 2.7 44.9 + - + +
230C PHE* 2.8 38.9 + - + +
247C SER* 3.8 14.4 - - - +
259C LEU* 5.0 1.8 - - + -
260C GLN 3.5 3.4 - - - -
261C LEU* 4.6 3.8 - - + -
279C PHE* 4.1 20.9 - - + -
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Residues in contact with GLN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TYR* 5.2 7.6 + - - -
211C LEU* 3.6 34.8 - - + +
212C ILE* 1.3 76.2 - - - +
214C ARG* 1.3 60.3 + - - +
215C LYS 4.2 0.4 - - - -
226C LEU* 3.5 27.9 - - + +
227C VAL 3.2 7.1 - - - +
228C THR* 3.4 22.2 + - - +
229C LEU* 4.7 0.4 - - - -
258C GLU 3.8 0.5 - - - +
259C LEU* 3.3 11.5 - - - +
260C GLN* 2.7 73.5 + - + +
262C ALA* 3.6 10.5 - - - +
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Residues in contact with ARG 214 (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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213C GLN* 1.3 72.9 - - - +
215C LYS* 1.3 60.3 + - - +
216C LYS* 3.4 34.2 + - - +
225C SER 3.3 6.1 - - - +
226C LEU* 3.4 3.0 - - - -
227C VAL* 2.8 46.5 + - + +
229C LEU* 3.8 22.8 - - + +
252C LYS 3.9 20.4 + - - -
253C LEU* 3.7 20.3 - - + +
254C GLU* 4.1 13.3 - - - +
257C ASP* 2.7 35.9 + - + +
258C GLU 3.4 6.3 - - - +
259C LEU* 4.2 2.0 - - + -
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Residues in contact with LYS 215 (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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184C LYS* 6.4 0.4 - - + -
213C GLN 4.2 0.4 - - - -
214C ARG* 1.3 69.9 - - - +
216C LYS* 1.3 70.8 + - - +
225C SER* 3.5 12.6 - - - +
226C LEU* 3.8 19.7 - - + +
256C GLY 4.6 0.7 - - - +
257C ASP* 3.4 4.2 - - - -
258C GLU* 2.7 52.8 + - + +
260C GLN* 5.8 4.0 - - + +
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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