Contacts of the strand formed by residues 249 - 253 (chain A) in PDB entry 2C1H
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 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 4.6 5.4 - - + -
166A PHE* 3.8 28.9 - - + -
194A ILE 3.4 3.2 + - - +
195A LEU* 3.8 29.6 - - + -
196A SER* 2.8 26.0 + - - -
247A ALA* 4.0 0.9 - - - +
248A ASP* 1.3 85.8 - - + +
250A VAL* 1.3 69.0 + - - +
271A VAL* 4.3 0.2 - - - -
272A PRO* 3.5 27.8 - - + +
274A ALA* 4.0 15.0 - - + -
314A ILE* 3.8 24.9 - - + -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 3.5 4.0 - - - -
198A ALA* 4.0 21.1 - - + -
239A VAL* 4.1 10.1 - - + -
242A ASP* 4.4 5.6 - - + -
243A ILE* 4.0 24.9 - - + -
247A ALA* 4.1 13.7 - - + -
249A ILE* 1.3 79.2 - - - +
251A MET* 1.3 60.8 + - - +
252A VAL* 5.8 0.2 - - - -
265A THR* 4.1 25.5 - - + +
269A PHE* 5.7 0.2 - - + -
271A VAL* 3.8 18.8 - - + +
272A PRO 3.4 4.3 + - - +
273A VAL* 3.8 8.7 - - + +
274A ALA* 3.2 19.7 + - - +
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Residues in contact with MET 251 (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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195A LEU* 3.7 10.5 - - + -
196A SER 2.7 17.8 + - - +
197A TYR* 3.7 40.6 - - + -
198A ALA* 3.1 22.3 + - - +
199A ALA 3.2 9.5 + - - -
239A VAL* 6.3 0.2 - - - -
249A ILE 4.3 0.2 - - - -
250A VAL* 1.3 75.6 - - - +
252A VAL* 1.3 78.1 + - - +
253A LYS* 4.6 0.8 - - - +
274A ALA* 3.2 17.3 - - + +
275A ILE* 3.4 17.0 - - - +
276A TYR* 3.8 11.2 - - - -
316A PHE* 3.4 47.6 - - + -
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA* 3.7 14.4 - - + +
201A TYR* 4.6 4.0 - - + -
239A VAL* 5.5 2.0 - - + -
251A MET* 1.3 79.2 - - - +
253A LYS* 1.3 64.3 + - - +
254A PRO 3.6 13.2 - - - +
258A TYR* 4.2 13.0 - - + +
261A ILE* 3.8 40.2 - - + -
262A VAL* 4.1 20.4 - - + +
265A THR* 3.9 20.0 - - + +
273A VAL* 5.2 3.8 - - + -
274A ALA 3.1 6.8 + - - +
275A ILE* 3.6 4.2 - - - +
276A TYR 3.5 21.1 + - - -
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Residues in contact with LYS 253 (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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197A TYR* 3.8 17.0 - - + -
199A ALA 3.1 10.9 + - - +
200A LYS* 3.5 31.4 - - + +
201A TYR* 2.8 30.0 + - - -
206A TYR* 3.4 26.0 - - - +
251A MET* 4.8 1.6 - - + -
252A VAL* 1.3 76.2 - - - +
254A PRO* 1.4 73.8 - - + +
276A TYR* 3.9 18.6 - - + -
278A VAL* 3.8 4.5 - - + -
1330A DSB 1.3 70.9 - - - +
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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