Contacts of the helix formed by residues 637 - 647 (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 ASP 637 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635C ALA 4.2 1.0 + - - -
636C LEU* 1.3 77.4 - - - +
638C TYR* 1.3 63.5 + - - +
639C GLU* 3.1 17.2 + - - +
640C SER* 2.9 41.8 + - - -
641C GLU* 3.1 18.7 + - - +
502D GLY 4.1 9.0 - - - +
503D ARG* 3.9 19.6 - - + +
504D SER* 2.8 31.8 + - - +
662D ALA* 4.0 13.9 - - + +
701D LEU* 5.6 6.3 - - + -
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Residues in contact with TYR 638 (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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637C ASP* 1.3 74.5 - - - +
639C GLU* 1.3 56.4 + - - +
641C GLU* 4.0 3.0 - - - +
642C HIS* 3.0 31.7 + - - +
663C ARG* 3.2 43.9 - - - -
662D ALA 3.7 19.2 + - - -
663D ARG* 3.2 27.1 - - - +
664D LEU* 3.3 20.9 + - + +
665D SER* 4.6 2.6 + - - -
701D LEU* 3.2 29.3 - - + +
702D TYR* 5.4 1.3 - - - -
704D LEU* 3.3 36.3 - - + -
705D GLN* 3.3 26.2 + - + +
706D SER* 5.2 0.7 - - - -
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Residues in contact with GLU 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C ASP* 3.1 10.8 + - - +
638C TYR* 1.3 78.8 - - - +
640C SER* 1.3 64.7 + - - +
642C HIS* 3.4 5.0 + - - +
643C VAL* 3.2 32.3 + - + +
503D ARG* 2.9 46.9 + - - +
700D TYR* 3.4 21.2 + - - +
701D LEU* 5.0 6.7 - - + +
704D LEU* 4.0 12.5 - - + +
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Residues in contact with SER 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582C ALA 4.9 1.2 - - - +
583C GLY* 5.6 1.5 - - - -
613C ARG* 3.7 26.2 + - - -
636C LEU* 3.7 22.7 - - - -
637C ASP* 2.9 28.4 + - - -
639C GLU* 1.3 76.2 - - - +
641C GLU* 1.3 64.0 + - - +
643C VAL* 3.5 9.2 + - - +
644C ILE* 3.4 26.2 + - - +
504D SER* 4.4 0.5 - - - -
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Residues in contact with GLU 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C THR* 2.6 40.9 + - + +
634C SER* 5.0 0.2 - - - -
636C LEU* 4.1 7.9 - - + +
637C ASP 3.1 16.3 + - - +
638C TYR* 4.1 3.6 - - - +
640C SER* 1.3 73.6 - - - +
642C HIS* 1.3 55.0 + - - +
644C ILE* 3.1 6.6 + - - +
645C MET* 2.8 44.9 + - + +
663C ARG* 3.0 28.9 + - - +
666C THR* 2.6 38.7 + - - -
705D GLN* 4.6 10.7 - - - +
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Residues in contact with HIS 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C TYR 3.0 20.5 + - - +
639C GLU* 3.5 8.1 - - - +
641C GLU* 1.3 78.2 - - - +
643C VAL* 1.3 55.9 + - + +
645C MET* 4.7 5.7 - - - +
646C ARG* 2.9 82.1 + - + +
704D LEU* 4.2 19.7 - - + +
705D GLN* 3.5 27.3 + - - +
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Residues in contact with VAL 643 (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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580C LYS 4.6 2.9 - - - +
583C GLY* 3.9 27.8 - - - +
639C GLU* 3.2 21.5 + - + +
640C SER* 3.7 10.5 - - - +
641C GLU 3.2 0.4 - - - -
642C HIS* 1.3 77.0 - - + +
644C ILE* 1.3 62.0 + - - +
646C ARG* 3.8 4.5 + - - +
647C ASN* 2.9 42.6 + - - +
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Residues in contact with ILE 644 (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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581C LEU 4.0 7.2 - - - +
582C ALA* 3.4 34.1 - - - +
613C ARG* 4.4 4.5 - - + -
616C ILE* 4.6 15.0 - - + -
629C PHE* 4.1 27.1 - - + -
633C THR* 4.2 14.1 - - + -
636C LEU* 3.9 22.0 - - + -
640C SER 3.4 13.8 + - - +
641C GLU* 3.1 7.7 + - - +
643C VAL* 1.3 77.7 - - - +
645C MET* 1.3 62.7 + - - +
647C ASN* 3.2 17.0 + - - +
648C MET* 3.3 13.2 + - + +
651C ILE* 3.5 14.6 - - + +
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Residues in contact with MET 645 (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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497C VAL* 5.3 3.1 - - + -
629C PHE* 5.5 2.9 - - - -
633C THR* 5.5 3.1 - - - -
641C GLU* 2.8 38.7 + - + +
642C HIS* 4.2 7.2 - - - +
644C ILE* 1.3 77.1 - - + +
646C ARG* 1.3 61.2 + - - +
648C MET* 3.1 49.4 - - + +
649C HIS 4.9 0.2 + - - -
659C ILE* 3.7 25.8 - - + -
666C THR* 3.2 34.5 - - - +
667C VAL* 5.1 3.1 - - - -
669C ASN 6.5 0.7 - - - -
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Residues in contact with ARG 646 (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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642C HIS* 2.9 60.1 + - + +
643C VAL* 4.2 4.0 - - - +
645C MET* 1.3 74.6 - - - +
647C ASN* 1.3 61.9 + - - +
648C MET 3.2 2.8 + - - -
649C HIS* 4.4 8.0 + - - +
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Residues in contact with ASN 647 (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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580C LYS 3.6 7.5 + - - -
581C LEU* 2.9 47.2 + - + +
643C VAL* 2.9 28.2 + - - +
644C ILE 3.2 11.5 + - - +
646C ARG* 1.3 76.6 - - - +
648C MET* 1.3 58.3 + - - +
649C HIS 3.2 2.9 - - - -
650C LYS* 2.8 35.8 + - + +
651C ILE* 2.9 16.4 + - + +
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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