Contacts of the helix formed by residues 663 - 668 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A GLU* 4.9 0.2 + - - -
633A THR 3.6 2.7 + - - -
634A SER* 2.9 32.4 + - - -
636A LEU 3.0 27.7 + - - -
637A ASP 4.7 0.2 - - - -
638A TYR* 3.6 35.3 + - + +
641A GLU* 3.3 29.9 + - - +
661A ALA* 3.3 6.0 - - - +
662A ALA* 1.3 76.3 - - - +
664A LEU* 1.3 66.1 + - - +
665A SER* 3.6 12.3 - - - +
666A THR* 2.9 35.8 + - - +
634B SER* 5.6 0.2 - - - -
638B TYR* 3.3 18.2 - - - +
662B ALA* 3.6 20.4 - - - +
663B ARG* 3.9 27.7 - - + +
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A VAL* 3.7 30.5 - - + -
661A ALA 4.7 0.2 - - - +
662A ALA 3.5 11.6 + - - +
663A ARG* 1.3 71.8 - - - +
665A SER* 1.3 62.6 + - - +
667A VAL* 3.0 25.9 + - - +
668A LYS* 3.6 5.5 + - - +
687A HIS* 6.1 1.3 - - + -
698A TYR* 3.9 35.7 + - + +
701A LEU* 3.9 18.2 - - + -
702A TYR* 3.6 47.8 - - + +
638B TYR* 3.1 20.9 + - + -
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Residues in contact with SER 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 4.2 10.7 - - - -
641A GLU* 5.0 1.6 + - - +
663A ARG* 3.6 20.6 - - - +
664A LEU* 1.3 76.8 - - - +
666A THR* 1.3 63.5 + - - +
668A LYS* 3.2 27.5 + - - +
687A HIS* 6.2 0.9 - - - -
702A TYR* 6.2 0.9 - - - -
638B TYR* 4.2 3.4 + - - -
705B GLN* 4.4 16.5 + - - +
707B ASP* 3.5 25.8 - - - -
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Residues in contact with THR 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A THR* 3.8 9.3 - - - +
634A SER* 5.6 1.5 - - - +
641A GLU* 2.7 40.1 + - - +
645A MET* 4.0 28.1 - - + +
659A ILE* 4.2 11.1 - - + +
661A ALA* 3.9 18.6 - - + -
663A ARG* 2.9 31.1 + - - +
665A SER* 1.3 79.0 + - - +
667A VAL* 1.3 56.4 + - - +
668A LYS 3.8 0.3 + - - -
669A ASN 5.1 0.9 + - - -
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Residues in contact with VAL 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A GLY* 3.8 13.9 - - - -
500A ILE 4.8 0.2 - - - +
501A VAL* 3.9 24.7 - - + -
659A ILE* 3.8 45.1 - - + +
661A ALA* 3.8 10.8 - - + -
664A LEU* 3.0 14.8 + - - +
666A THR* 1.3 78.6 - - - +
668A LYS* 1.3 62.6 + - - +
669A ASN 3.2 3.8 - - - +
670A ALA* 3.2 22.5 + - + +
673A ILE* 3.4 24.3 - - + +
698A TYR* 5.2 1.3 - - - +
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Residues in contact with LYS 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LEU 3.6 3.2 + - - -
665A SER* 3.2 24.4 + - - +
666A THR 3.4 1.0 - - - -
667A VAL* 1.3 77.2 - - - +
669A ASN* 1.3 85.3 + - - +
670A ALA 3.5 2.6 + - - +
673A ILE* 4.9 1.3 - - - +
687A HIS* 3.6 52.4 + - + +
705B GLN* 6.2 2.5 - - + -
707B ASP* 3.7 37.5 + - - +
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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
------------------------------------------------------------
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