Contacts of the helix formed by residues 385 - 389 (chain C) in PDB entry 2C11
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 VAL 385 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C GLU* 3.3 30.3 - - + +
368C ALA 3.5 4.0 - - - +
369C LEU* 4.0 4.0 - - + -
383C ARG 3.9 5.4 - - - +
384C TYR* 1.3 74.3 - - - +
386C ASP* 1.3 49.2 + - - +
387C GLY 2.5 20.0 + - - -
388C GLY* 2.6 17.4 + - - +
624C GLY 4.8 2.5 - - - +
625C PHE* 3.4 38.4 - - + -
645C SER* 3.9 10.1 - - - +
646C SER 4.8 0.9 - - - +
649C ASN* 4.6 6.1 - - + -
650C GLN* 3.1 42.7 - - + +
653C PRO* 5.8 2.7 - - + -
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Residues in contact with ASP 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ALA* 3.1 23.5 + - + +
369C LEU 4.6 1.6 + - - -
384C TYR* 3.2 13.4 - - - +
385C VAL* 1.3 71.3 - - - +
387C GLY* 1.3 55.3 + - - +
388C GLY 3.0 2.9 - - - -
389C PHE* 3.0 13.1 + - - +
390C GLY 3.0 22.3 + - - -
391C MET* 3.5 7.2 - - - +
468C LEU* 3.3 19.8 - - + +
471C PAQ 2.4 44.6 + - - -
473C TYR* 2.8 27.0 + - - -
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Residues in contact with GLY 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C PHE* 3.0 47.0 - - - +
366C GLN 5.7 0.2 - - - -
367C GLU* 2.5 29.2 + - - -
385C VAL 2.5 7.7 + - - -
386C ASP* 1.3 71.4 - - - +
388C GLY* 1.3 58.0 + - - -
389C PHE 3.1 3.2 + - - -
390C GLY 3.7 0.8 + - - -
391C MET* 3.7 2.2 - - - +
647C VAL* 3.5 11.7 - - - -
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Residues in contact with GLY 388 (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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97C PHE* 5.7 0.7 - - - -
170C PRO* 3.9 26.7 - - - +
344C PHE* 5.0 0.5 - - - -
385C VAL 2.6 13.4 + - - -
387C GLY* 1.3 78.1 - - - +
389C PHE* 1.3 62.1 + - - +
646C SER 4.7 1.6 + - - -
647C VAL* 3.2 26.5 - - - +
650C GLN* 3.9 15.0 - - - +
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Residues in contact with PHE 389 (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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97C PHE* 5.9 0.3 - - - -
171C VAL* 5.9 0.2 - - + -
176C TYR* 4.0 17.0 - + - -
212C THR* 4.4 10.8 - - + -
213C THR 4.8 1.1 - - - -
216C ARG* 3.8 20.2 - - - -
344C PHE* 4.0 5.6 - - - -
384C TYR* 4.4 8.7 - + - -
386C ASP* 3.0 12.7 + - - +
387C GLY 4.2 0.4 - - - -
388C GLY* 1.3 82.9 - - - +
390C GLY* 1.3 59.3 + - - +
393C LYS* 3.3 26.5 + - - +
394C TYR* 3.7 29.1 - + + -
468C LEU* 3.4 15.3 - - + -
469C LEU* 5.1 2.7 - - + -
471C PAQ 3.7 37.2 - + - -
650C GLN* 2.7 37.5 - - + -
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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