Contacts of the strand formed by residues 314 - 317 (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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASN 5.6 3.4 - - - +
35A ASP 3.6 5.4 - - - +
37A VAL* 3.6 30.5 - - + -
121A MET* 4.7 7.0 - - + -
195A LEU* 4.5 4.9 - - + -
249A ILE* 3.8 39.9 - - + -
272A PRO* 5.4 3.6 - - + -
273A VAL 3.1 3.8 + - - +
274A ALA* 3.3 8.5 - - + -
275A ILE* 2.8 31.5 + - - +
312A ALA* 4.2 0.9 - - - +
313A ASP* 1.3 88.7 - - + +
315A ILE* 1.3 66.1 + - - +
316A PHE* 3.6 17.0 - - + -
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Residues in contact with ILE 315 (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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31A LEU* 4.0 15.7 - - + -
35A ASP* 2.7 17.8 + - + +
36A LEU* 3.7 2.5 - - + -
37A VAL 3.0 22.6 + - - -
275A ILE* 3.5 15.0 - - + -
277A HIS* 4.3 2.5 - - + -
304A LEU* 3.5 54.1 - - + +
307A MET* 3.7 24.9 - - + -
308A LYS* 4.3 10.3 - - + -
312A ALA* 4.7 4.0 - - + -
314A ILE* 1.3 79.5 - - - +
316A PHE* 1.3 63.8 + - - +
317A THR* 3.2 20.2 + - + +
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Residues in contact with PHE 316 (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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37A VAL* 3.4 24.7 - - + -
39A PRO* 4.5 6.7 - - + -
82A ASP* 3.3 44.6 - - + -
121A MET* 3.6 24.9 - - - -
168A SER* 4.6 4.7 - - - -
195A LEU* 3.7 15.7 - - + -
197A TYR* 4.1 6.1 - + - -
251A MET* 3.4 22.9 - - + -
275A ILE 2.9 13.7 + - - +
276A TYR* 3.6 32.2 - + + -
277A HIS* 2.8 28.4 + - - +
314A ILE* 3.6 23.6 - - + -
315A ILE* 1.3 68.5 - - - +
317A THR* 1.3 58.3 + - - +
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Residues in contact with THR 317 (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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36A LEU* 3.9 16.4 - - + -
37A VAL 3.0 4.8 + - - -
38A PHE* 4.1 0.5 - - - -
39A PRO* 3.2 17.9 - - - +
277A HIS* 3.0 37.3 - - - -
304A LEU* 3.9 10.8 - - + +
315A ILE* 3.7 15.5 - - + +
316A PHE* 1.3 73.4 - - - +
318A TYR* 1.3 59.6 + - - +
319A TYR* 3.1 13.5 + - - +
320A ALA* 3.2 40.7 - - + +
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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