Contacts of the helix formed by residues 367 - 373 (chain C) in PDB entry 6G2T
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 SER 367 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLU* 3.9 22.2 - - - +
364C SER 4.3 11.4 + - - -
365C GLY* 3.2 0.7 - - - -
366C PRO* 1.3 75.5 - - - +
368C ILE* 1.3 66.7 + - - +
369C VAL* 3.2 4.4 + - - -
370C HIS* 3.7 12.9 + - - +
371C ARG* 4.0 6.9 + - - +
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Residues in contact with ILE 368 (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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356C ILE* 3.9 28.5 - - + -
360C GLU* 4.2 13.5 - - + +
361C TYR* 4.1 22.0 - - + +
364C SER* 3.2 33.0 - - - +
365C GLY 3.1 17.0 - - - +
366C PRO* 4.5 2.0 - - + +
367C SER* 1.3 78.7 - - - +
369C VAL* 1.3 64.2 + - + +
370C HIS 3.3 0.4 - - - -
371C ARG* 3.2 26.8 + - + +
372C LYS* 2.9 38.7 + - + +
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Residues in contact with VAL 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ARG* 4.0 30.1 - - + +
116C GLU* 5.1 0.4 - - - -
119C THR* 3.3 33.4 - - + +
123C PHE* 5.9 0.4 - - + -
133C VAL* 3.6 28.0 - - + -
356C ILE* 4.3 16.4 - - + -
361C TYR* 6.3 0.4 - - + -
366C PRO* 3.4 17.3 - - + +
367C SER 3.2 0.8 - - - -
368C ILE* 1.3 80.5 - - + +
370C HIS* 1.3 67.0 + - + +
373C CYS* 3.1 33.6 + - - +
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Residues in contact with HIS 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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112C LYS* 3.3 70.8 + - + +
115C ARG* 3.7 33.5 + - - +
116C GLU* 3.6 25.7 - - + +
367C SER 3.7 6.4 + - - +
369C VAL* 1.3 80.7 - - + +
371C ARG* 1.3 61.6 + - - +
373C CYS 3.1 15.1 - - - +
374C PHE 5.7 2.4 + - - -
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Residues in contact with ARG 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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364C SER* 4.2 17.6 + - - -
367C SER 4.0 3.0 + - - +
368C ILE* 3.2 31.8 + - + +
370C HIS* 1.3 82.4 - - - +
372C LYS* 1.3 62.2 + - + +
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Residues in contact with LYS 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR* 5.5 2.7 - - + -
353C GLN 5.7 1.8 + - - -
354C MET* 3.7 18.8 + - - +
355C TRP 4.7 3.4 + - - -
356C ILE* 3.6 32.3 - - + +
360C GLU* 3.0 35.6 + - - -
368C ILE* 2.9 24.4 + - + +
369C VAL 4.5 0.7 - - - +
370C HIS 4.4 0.2 - - - -
371C ARG* 1.3 78.3 - - + +
373C CYS* 1.3 64.2 + - + +
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Residues in contact with CYS 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ARG* 5.8 0.4 - - - -
132C TYR* 3.6 34.5 - - + +
133C VAL* 3.4 39.3 - - - +
356C ILE* 4.6 7.0 - - + -
369C VAL* 3.1 32.7 + - - +
370C HIS* 3.1 21.5 - - - +
372C LYS* 1.3 80.0 - - + +
374C PHE* 1.3 66.0 + - - +
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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