Contacts of the helix formed by residues 367 - 373 (chain C) in PDB entry 6AH0
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 ARG 367 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346C ASP* 5.8 2.9 - - - +
347C ILE 3.3 14.8 - - - +
348C TYR* 4.8 1.6 - - - +
365C SER 3.4 3.6 + - - -
366C GLN* 1.3 78.4 - - - +
368C SER* 1.3 61.4 + - - +
369C PHE 3.1 3.4 - - - -
370C VAL* 2.9 21.3 + - - +
371C GLU 3.0 3.3 + - - -
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C ARG 5.9 0.7 - - - -
343C LEU* 3.5 10.1 + - - +
347C ILE 2.5 20.6 + - - -
348C TYR* 4.4 1.0 - - - +
349C PHE* 4.8 9.0 - - - +
366C GLN 3.3 2.9 + - - -
367C ARG* 1.3 71.0 - - - +
369C PHE* 1.3 57.7 + - - +
370C VAL 3.2 0.2 - - - -
371C GLU* 3.6 4.5 - - - +
372C PHE* 2.8 28.1 + - - +
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Residues in contact with PHE 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C LEU 3.1 17.3 + - - -
344C TRP* 4.7 7.3 - - - +
345C GLY 5.3 2.2 - - - +
367C ARG 3.0 1.4 + - - -
368C SER* 1.3 77.3 - - - +
370C VAL* 1.3 57.5 + - - +
373C ILE* 2.9 24.2 + - - +
374C LEU 3.3 7.1 + - - -
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Residues in contact with VAL 370 (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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271C PRO 5.6 8.7 - - - -
366C GLN* 5.3 2.2 - - - +
367C ARG 2.9 8.3 + - - -
369C PHE* 1.3 78.4 - - - +
371C GLU* 1.3 60.8 + - - +
372C PHE 3.4 0.3 + - - -
374C LEU* 3.4 7.1 + - - +
375C GLU* 2.8 31.0 + - - +
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Residues in contact with GLU 371 (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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386A PRO* 5.1 8.3 - - - +
366C GLN* 4.1 8.1 + - - +
367C ARG 3.0 12.1 + - - -
368C SER* 3.8 3.8 - - - +
370C VAL* 1.3 78.1 - - - +
372C PHE* 1.3 57.2 + - - +
375C GLU* 5.1 4.6 + - - +
376C PRO 5.1 2.1 - - - -
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Residues in contact with PHE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PRO* 5.4 9.7 - - - +
368C SER 2.8 15.2 + - - -
371C GLU* 1.3 79.5 - - - +
373C ILE* 1.3 55.7 + - - +
376C PRO* 5.3 3.5 - - - +
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Residues in contact with ILE 373 (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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368C SER 4.2 0.2 + - - -
369C PHE* 2.9 13.8 + - - +
370C VAL 3.6 0.6 + - - -
372C PHE* 1.3 80.8 - - - +
374C LEU* 1.3 64.3 + - - +
375C GLU 3.2 1.3 - - - -
376C PRO* 3.5 2.6 - - - +
377C LEU* 3.0 20.8 + - - -
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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