Contacts of the helix formed by residues 377 - 382 (chain C) in PDB entry 2R6C
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 MET 377 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376C MET* 1.3 74.6 - - - +
378C SER* 1.3 59.6 + - - +
379C ASP 2.9 11.2 + - - -
380C ILE* 3.2 19.8 + - - +
381C ARG* 3.3 9.2 + - - +
387C GLU* 3.3 47.9 - - + +
393C VAL* 4.3 27.4 - - + -
395C PHE* 4.5 8.3 - - - -
417C ALA* 4.5 14.8 - - + +
418C LYS* 4.2 26.9 - - + -
241F GLU 5.1 3.8 + - - +
243F SER* 4.6 25.1 - - - +
246F GLN* 4.8 1.2 + - - +
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Residues in contact with SER 378 (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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376C MET* 4.6 2.3 - - - +
377C MET* 1.3 75.8 - - - +
379C ASP* 1.3 64.4 + - - +
380C ILE 3.3 0.8 + - - -
381C ARG* 3.8 14.8 - - - -
382C GLU* 3.4 40.4 + - - +
240F LEU 3.9 11.4 - - - -
241F GLU* 2.6 47.9 + - - +
294F PRO* 5.1 5.6 - - - -
324F LEU* 5.4 0.2 - - - -
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Residues in contact with ASP 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C LEU* 3.5 35.9 - - + +
374C ARG* 2.9 40.2 + - - -
375C PRO* 3.5 5.5 - - + +
376C MET* 2.8 37.1 + - - +
377C MET 2.9 1.2 + - - -
378C SER* 1.3 81.5 + - - +
380C ILE* 1.3 59.7 + - - +
382C GLU* 5.1 2.3 + - - +
383C SER* 4.6 4.5 + - - -
241F GLU* 4.8 1.6 - - - +
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Residues in contact with ILE 380 (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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207C ILE* 4.1 23.6 - - + -
209C ALA* 4.3 9.2 - - + -
323C GLN* 5.8 0.9 - - - -
361C SER* 3.4 23.1 - - - +
362C GLN 3.8 13.0 - - - +
363C LEU* 3.5 25.6 - - + -
377C MET* 3.2 11.4 + - - +
379C ASP* 1.3 74.3 - - - +
381C ARG* 1.3 69.3 + - - +
382C GLU 3.3 2.0 - - - -
383C SER* 2.9 32.0 + - - +
384C GLY 4.2 2.1 - - - +
385C SER 4.8 1.1 - - - +
386C ILE* 4.5 15.5 - - + +
387C GLU* 6.0 0.9 - - - +
393C VAL* 4.1 22.2 - - + -
395C PHE* 4.5 5.6 - - + -
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Residues in contact with ARG 381 (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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377C MET 3.3 4.4 + - - +
378C SER* 3.7 20.6 + - - -
380C ILE* 1.3 78.9 - - - +
382C GLU* 1.3 58.8 + - + +
383C SER 2.9 6.4 + - - -
384C GLY 3.3 12.0 + - - -
385C SER* 3.2 38.3 + - - +
387C GLU* 3.3 42.0 + - - +
388C GLN* 3.1 42.5 + - - +
294F PRO* 4.3 33.7 - - + +
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Residues in contact with GLU 382 (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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378C SER* 3.4 28.3 + - - +
379C ASP 5.3 1.8 - - - +
380C ILE 3.3 0.8 - - - -
381C ARG* 1.3 75.7 - - + +
383C SER* 1.3 58.1 + - - +
384C GLY 3.6 2.8 + - - -
241F GLU* 5.7 1.2 - - - +
294F PRO* 5.5 3.6 - - + +
295F SER* 4.9 14.4 - - - +
321F TYR* 5.3 0.2 + - - -
324F LEU* 3.2 45.5 - - + +
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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