Contacts of the strand formed by residues 211 - 214 (chain A) in PDB entry 2V5I
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 THR 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LYS* 6.5 1.6 - - - -
187A ASP* 2.9 19.3 + - - -
188A GLY* 3.4 6.1 - - - -
189A LEU 3.0 23.5 + - - +
209A ILE 4.3 0.4 + - - -
210A LEU* 1.3 72.5 + - - +
212A ILE* 1.3 61.6 + - - +
213A ASN* 3.8 26.8 + - - +
234A VAL* 3.5 15.9 + - + +
236A ASN* 3.9 9.2 - - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.3 26.7 - - + +
191A ILE* 4.0 13.9 - - + -
205A PHE* 3.7 32.3 - - + -
210A LEU* 4.4 12.6 - - + +
211A THR* 1.3 72.4 - - - +
213A ASN* 1.3 58.5 + - - +
214A CYS* 4.0 20.0 - - - -
218A PHE* 5.6 3.1 - - + -
226A PHE* 4.2 9.4 - - + -
229A MET* 4.1 7.2 - - + -
234A VAL 2.8 14.5 + - - +
235A ILE* 4.0 24.2 - - + +
236A ASN* 2.8 33.6 + - - +
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Residues in contact with ASN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A SER* 5.8 0.3 + - - -
188A GLY* 5.4 2.1 - - - -
189A LEU 2.8 13.3 + - - +
190A LEU* 3.4 19.5 - - + +
191A ILE 2.9 23.8 + - - -
211A THR* 3.9 20.5 - - - +
212A ILE* 1.3 72.2 - - - +
214A CYS* 1.3 63.8 + - - +
215A LYS* 5.0 6.5 - - + -
236A ASN* 3.0 32.1 + - - +
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Residues in contact with CYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 4.0 22.4 - - + -
212A ILE* 4.0 13.2 - - - -
213A ASN* 1.3 75.0 - - - +
215A LYS* 1.3 65.2 + - - +
216A ALA 3.6 10.1 - - - +
218A PHE* 4.4 10.5 - - - -
235A ILE* 4.3 6.1 - - - -
236A ASN 2.9 20.9 + - - +
237A GLN* 3.3 37.4 - - - +
238A PRO* 3.7 21.8 - - + -
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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