Contacts of the strand formed by residues 314 - 316 (chain C) in PDB entry 2C10
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 314 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C PRO 3.6 2.0 + - - +
313C PRO* 1.3 75.6 - - - +
315C GLN* 1.3 76.4 + - - +
316C PHE* 5.8 0.2 - - + -
405C PRO* 6.4 0.4 - - + -
406C TYR* 4.1 20.2 - - + +
407C LEU* 5.4 0.7 - - + -
750C PRO* 5.4 1.8 - - + -
752C LEU* 4.2 31.2 - - + -
315D GLN* 3.4 4.7 - - - -
316D PHE* 3.0 60.2 + - + +
318D PRO* 4.3 17.5 - - + -
435D ASN* 5.2 1.6 - - - +
742D LEU* 4.1 28.3 - - + -
746D ALA* 4.8 2.2 - - + -
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Residues in contact with GLN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C LEU* 1.3 86.4 - - - +
316C PHE* 1.3 67.0 + - - +
317C TYR* 5.3 2.1 - - + -
405C PRO* 5.1 16.0 - - + +
407C LEU* 3.4 17.3 + - - +
433C GLU 3.2 23.2 + - - -
434C GLN* 2.7 29.1 + - - +
435C ASN* 2.9 32.8 + - - +
313D PRO* 4.0 15.2 - - + +
314D LEU 3.3 14.8 - - - +
315D GLN* 3.6 20.9 + - + +
435D ASN* 5.6 1.6 - - + +
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Residues in contact with PHE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C CYS* 4.1 17.5 - - + -
314C LEU* 5.6 0.9 - - + -
315C GLN* 1.3 76.0 - - - +
317C TYR* 1.3 73.3 - - - +
318C PRO* 3.4 26.3 - - + +
407C LEU* 3.5 20.4 - - + -
746C ALA 4.3 4.7 - - - -
748C CYS* 4.7 3.8 - - - -
750C PRO* 3.9 22.9 - - + -
313D PRO* 3.3 4.5 - - - +
314D LEU* 2.9 67.3 + - + -
316D PHE* 3.6 31.6 - + + -
750D PRO* 3.8 22.0 - - + -
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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