Contacts of the helix formed by residues 663 - 668 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633C THR 3.2 7.5 + - - -
634C SER* 3.0 33.0 + - - +
636C LEU 3.2 21.0 + - - -
638C TYR* 3.2 44.7 - - - +
641C GLU* 3.0 30.2 + - - +
661C ALA* 3.5 8.7 - - - +
662C ALA* 1.3 77.6 - - - +
664C LEU* 1.3 65.4 + - - +
665C SER* 4.0 14.6 - - - +
666C THR* 3.1 29.2 - - - +
634D SER 5.9 0.6 + - - -
638D TYR* 3.1 21.5 - - + +
662D ALA* 4.2 6.3 - - - +
663D ARG* 4.5 21.3 - - + +
705D GLN* 5.3 0.6 - - - +
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Residues in contact with LEU 664 (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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501C VAL* 3.4 30.5 - - + -
662C ALA 4.0 6.3 - - - +
663C ARG* 1.3 71.0 - - - +
665C SER* 1.3 64.0 + - - +
667C VAL* 3.0 26.4 + - + +
668C LYS* 3.6 5.0 + - - -
698C TYR* 3.7 40.6 + - + +
701C LEU* 3.9 16.6 - - + -
702C TYR* 3.7 41.1 - - + +
638D TYR* 2.9 32.0 + - + +
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Residues in contact with SER 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C ARG* 4.0 16.5 - - - +
664C LEU* 1.3 75.0 - - - +
666C THR* 1.3 64.0 + - - +
667C VAL 3.0 1.2 + - - -
668C LYS* 3.1 27.2 + - - +
702C TYR* 5.4 11.3 - - - -
638D TYR* 4.4 2.2 + - - -
705D GLN* 3.4 40.5 + - - +
707D ASP* 4.0 13.5 - - - -
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Residues in contact with THR 666 (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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633C THR* 3.9 9.0 - - - +
641C GLU* 2.6 44.0 + - + +
645C MET* 3.2 32.4 - - - +
659C ILE* 4.5 10.1 - - + -
661C ALA* 4.1 15.3 - - + -
663C ARG* 3.1 30.7 + - - +
664C LEU 3.1 0.2 - - - -
665C SER* 1.3 79.0 + - - +
667C VAL* 1.3 58.8 + - + +
668C LYS 3.5 0.4 + - - -
669C ASN 5.4 0.2 + - - -
705D GLN* 5.7 0.4 - - - -
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Residues in contact with VAL 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C GLY* 4.0 22.0 - - - -
500C ILE 5.1 0.7 - - - +
501C VAL* 5.3 6.1 - - + -
645C MET* 5.1 2.9 - - - -
659C ILE* 3.7 33.7 - - + +
661C ALA* 3.9 16.4 - - + -
664C LEU* 3.0 23.5 + - + +
666C THR* 1.3 80.5 - - - +
668C LYS* 1.3 64.4 + - - +
669C ASN 3.2 3.1 - - - -
670C ALA* 3.1 18.2 + - + +
673C ILE* 3.3 37.8 - - + +
698C TYR* 5.4 0.7 - - - +
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Residues in contact with LYS 668 (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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664C LEU 3.6 4.1 + - - -
665C SER* 3.1 23.7 + - - +
666C THR 3.5 0.6 - - - -
667C VAL* 1.3 76.9 - - - +
669C ASN* 1.3 72.0 + - - +
670C ALA 3.4 3.4 + - - +
673C ILE* 4.6 1.1 - - - +
687C HIS* 3.3 68.0 - - + +
698C TYR* 5.1 0.2 - - - -
702C TYR* 4.3 10.7 + - + -
707D ASP* 2.8 32.8 + - - +
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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