Contacts of the helix formed by residues 668 - 673 (chain W) in PDB entry 6G0L
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 ALA 668 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625W TYR* 4.1 15.0 - - + -
662W PRO* 4.2 14.6 - - + +
663W TYR* 3.5 36.2 - - + -
665W PHE* 4.9 12.3 - - + +
666W ASP 2.8 10.8 + - - +
667W ASN* 1.3 73.9 - - - +
669W GLU* 1.4 55.2 + - - +
670W GLU 3.5 2.2 - - - +
671W ARG* 3.0 30.4 + - - +
672W VAL 3.9 1.2 + - - -
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Residues in contact with GLU 669 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ALA 5.3 6.1 - - - +
17F ARG* 6.5 1.3 - - + -
663W TYR* 4.0 23.7 + - - +
665W PHE 6.1 0.4 - - - +
666W ASP 3.9 8.1 + - - +
668W ALA* 1.4 76.5 - - - +
670W GLU* 1.3 76.7 + - - +
671W ARG 3.6 0.2 + - - -
672W VAL* 4.1 4.2 - - - +
673W LEU* 3.9 23.9 + - - +
690W LEU* 3.2 32.7 - - - +
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Residues in contact with GLU 670 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666W ASP 5.3 2.6 - - - +
667W ASN 5.8 0.4 - - - -
668W ALA 3.5 0.4 - - - -
669W GLU* 1.3 86.7 + - - +
671W ARG* 1.3 58.9 + - - +
672W VAL 3.2 3.1 - - - -
673W LEU* 2.6 35.4 - - + +
675W LYS 5.7 5.4 - - - +
676W PHE 5.8 5.8 - - - -
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Residues in contact with ARG 671 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621W VAL* 3.8 22.1 - - + +
624W GLU* 3.6 35.1 + - + +
625W TYR* 3.6 31.2 + - + +
634W TYR* 6.2 1.2 - - - +
638W THR* 4.6 20.8 + - - +
667W ASN* 4.2 6.6 + - - +
668W ALA* 3.0 21.7 + - - +
670W GLU* 1.3 79.1 - - - +
672W VAL* 1.3 57.4 + - - +
673W LEU 4.3 1.4 - - - +
674W GLN* 5.6 0.7 - - - -
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Residues in contact with VAL 672 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620W ASP* 4.0 17.5 - - - +
621W VAL* 3.5 25.4 - - + -
663W TYR* 2.5 33.7 - - + +
669W GLU 4.1 4.7 - - - +
671W ARG* 1.3 79.4 - - - +
673W LEU* 1.3 78.8 + - + +
674W GLN* 2.9 16.9 - - - +
689W GLY* 4.0 9.1 - - - +
690W LEU* 5.9 0.2 - - + -
692W MET* 5.7 3.1 - - + -
693W SER* 4.3 10.1 - - - +
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Residues in contact with LEU 673 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669W GLU 3.9 15.5 - - - +
670W GLU* 2.6 31.8 + - + +
671W ARG 4.3 1.4 - - - +
672W VAL* 1.3 90.5 - - + +
674W GLN* 1.3 61.8 + - - +
675W LYS 3.4 14.6 + - - +
682W THR* 5.6 2.0 - - + -
685W ASN* 4.0 23.1 - - - +
686W VAL* 4.4 25.8 - - + +
689W GLY* 3.6 30.5 - - - -
690W LEU* 4.5 8.7 - - + +
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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
------------------------------------------------------------
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