Contacts of the helix formed by residues 663 - 668 (chain B) in PDB entry 2FGJ
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 663 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A SER 4.3 4.6 + - - -
638A TYR* 3.3 22.9 - - - +
662A ALA* 4.1 6.7 + - - +
663A ARG* 3.9 31.4 - - + +
705A GLN* 5.7 0.2 - - - -
634B SER* 2.5 45.2 + - - +
636B LEU 3.5 15.8 + - - -
638B TYR* 3.1 45.7 - - - +
641B GLU* 4.1 15.1 + - - +
661B ALA* 3.7 7.4 - - + +
662B ALA* 1.3 76.2 - - - +
664B LEU* 1.3 65.2 + - - +
665B SER* 3.2 15.7 - - - +
666B THR* 3.1 34.4 + - - +
667B VAL 4.2 0.3 + - - -
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Residues in contact with LEU 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A TYR* 3.7 19.5 + - + -
501B VAL* 3.8 31.4 - - + -
502B GLY 5.5 0.2 - - - +
662B ALA 3.5 13.5 + - - +
663B ARG* 1.3 71.6 - - - +
665B SER* 1.3 61.7 + - - +
666B THR 3.3 0.5 + - - -
667B VAL* 3.3 23.1 + - + +
668B LYS* 3.7 5.9 + - - +
698B TYR* 3.6 54.7 + - + +
701B LEU* 4.3 21.1 - - + +
702B TYR* 4.1 27.6 - - + +
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Residues in contact with SER 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 4.9 2.0 + - - -
705A GLN* 3.0 46.3 + - - +
706A SER 5.9 0.2 - - - -
707A ASP 4.8 8.1 - - - -
663B ARG* 4.0 13.9 - - - +
664B LEU* 1.3 74.9 - - - +
666B THR* 1.3 65.1 + - - +
667B VAL 3.3 0.2 - - - -
668B LYS* 3.2 27.8 - - - +
702B TYR* 5.8 9.1 - - - -
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Residues in contact with THR 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLN* 5.3 1.8 - - - -
633B THR* 4.0 8.7 - - - +
641B GLU* 2.9 45.3 + - + +
645B MET* 3.5 35.1 - - + +
659B ILE* 4.5 7.6 - - + -
661B ALA* 3.7 19.0 - - + +
663B ARG* 3.2 26.5 + - - +
665B SER* 1.3 81.0 + - - +
667B VAL* 1.3 57.1 + - - +
668B LYS 3.5 2.1 + - - -
669B ASN 4.9 1.2 + - - -
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Residues in contact with VAL 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B GLY* 3.7 25.8 - - - -
500B ILE 4.5 0.9 - - - +
501B VAL* 3.9 23.8 - - + -
645B MET* 5.4 2.0 - - - -
659B ILE* 3.7 33.9 - - + +
661B ALA* 4.1 10.3 - - + +
663B ARG 4.9 0.2 - - - +
664B LEU* 3.3 15.9 - - + +
666B THR* 1.3 75.2 - - - +
668B LYS* 1.3 63.8 + - - +
669B ASN 3.2 2.9 - - - -
670B ALA* 3.1 22.7 + - + +
673B ILE* 3.5 24.9 - - + +
698B TYR* 5.2 1.3 - - - +
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Residues in contact with LYS 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ASP* 3.2 38.7 + - - +
664B LEU 3.7 5.4 + - - +
665B SER* 3.2 25.7 + - - +
666B THR 3.3 2.4 + - - -
667B VAL* 1.3 78.3 - - - +
669B ASN* 1.3 85.7 + - - +
670B ALA 3.4 2.1 + - - +
673B ILE* 4.4 5.9 - - - +
687B HIS* 3.4 57.0 + - + +
702B TYR* 5.5 6.1 - - + +
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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