Contacts of the helix formed by residues 637 - 647 (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 ASP 637 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A GLY 3.8 21.5 - - - +
503A ARG* 3.7 12.4 - - - +
504A SER* 2.8 28.5 + - - +
662A ALA* 4.0 13.3 - - + +
701A LEU* 4.6 6.4 - - + +
800A ATP 5.9 0.8 + - - +
635B ALA 4.2 0.8 + - - -
636B LEU* 1.3 74.7 - - - +
638B TYR* 1.3 64.8 + - - +
639B GLU* 3.1 17.5 + - - +
640B SER* 2.7 43.0 + - - -
641B GLU* 2.9 19.6 + - - +
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Residues in contact with TYR 638 (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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662A ALA 3.7 8.1 + - - -
663A ARG* 3.3 15.5 - - - +
664A LEU* 3.1 48.3 + - + -
665A SER* 4.2 4.5 + - - -
701A LEU* 3.3 37.9 - - + +
702A TYR* 5.1 3.1 - + - -
704A LEU* 4.1 15.9 - - + -
705A GLN* 2.9 32.4 - - + +
637B ASP* 1.3 72.5 - - - +
639B GLU* 1.3 56.8 + - - +
641B GLU* 3.3 4.6 + - - +
642B HIS* 2.8 27.3 + - - +
663B ARG* 3.1 43.9 - - - +
665B SER* 5.8 0.2 - - - -
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Residues in contact with GLU 639 (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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503A ARG* 2.7 48.5 + - - +
700A TYR* 2.7 30.7 + - - +
701A LEU* 4.4 11.2 - - + +
704A LEU* 3.9 15.3 - - + +
637B ASP* 3.1 9.7 + - - +
638B TYR* 1.3 76.6 - - - +
640B SER* 1.3 58.7 + - - +
642B HIS* 3.4 4.8 - - + +
643B VAL* 2.9 41.8 + - + +
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Residues in contact with SER 640 (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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503A ARG* 5.9 0.5 - - - +
504A SER* 4.2 1.2 + - - -
582B ALA 5.0 0.3 - - - +
583B GLY* 6.0 0.8 - - - -
613B ARG* 3.9 26.1 + - - -
636B LEU* 3.8 21.8 - - - -
637B ASP* 2.7 32.2 + - - -
639B GLU* 1.3 74.9 + - - +
641B GLU* 1.3 63.9 + - - +
643B VAL* 3.9 7.3 - - - +
644B ILE* 3.4 29.3 + - - +
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Residues in contact with GLU 641 (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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705A GLN* 4.0 19.9 - - - +
633B THR* 3.1 41.0 + - + +
634B SER* 5.0 0.5 - - - -
636B LEU* 4.4 9.6 - - + +
637B ASP 2.9 15.9 + - - +
638B TYR* 3.7 7.3 - - - +
640B SER* 1.3 73.4 - - - +
642B HIS* 1.3 56.4 + - - +
644B ILE* 3.2 6.3 + - - +
645B MET* 2.8 45.4 + - + +
663B ARG* 4.1 18.8 + - - +
666B THR* 2.9 36.2 + - - +
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Residues in contact with HIS 642 (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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700A TYR* 5.8 1.3 - - - -
704A LEU* 3.6 28.5 - - + +
705A GLN* 3.2 30.0 + - - +
707A ASP* 5.6 3.6 - - - -
638B TYR 2.8 19.7 + - - +
639B GLU* 3.4 11.2 - - + +
641B GLU* 1.3 74.1 - - - +
643B VAL* 1.3 59.4 + - + +
645B MET* 3.0 5.4 + - - +
646B ARG* 2.6 73.0 + - + +
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Residues in contact with VAL 643 (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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580B LYS 4.7 1.6 - - - +
583B GLY* 3.9 26.7 - - - +
639B GLU* 2.9 29.8 + - + +
640B SER* 3.9 7.9 - - - +
641B GLU 3.3 0.2 - - - -
642B HIS* 1.3 80.5 - - + +
644B ILE* 1.3 59.4 + - - +
646B ARG* 3.3 6.9 + - - +
647B ASN* 2.9 47.8 + - - +
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Residues in contact with ILE 644 (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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581B LEU 4.1 7.4 - - - +
582B ALA* 3.3 35.0 - - - +
613B ARG* 4.3 1.6 - - + -
616B ILE* 3.8 21.5 - - + -
629B PHE* 4.3 23.8 - - + -
633B THR* 4.3 6.5 - - + -
636B LEU* 3.6 24.2 - - + -
640B SER 3.4 15.7 + - - +
641B GLU* 3.2 9.2 + - - +
643B VAL* 1.3 76.2 - - + +
645B MET* 1.3 62.7 + - - +
647B ASN* 3.0 18.4 + - - +
648B MET* 3.2 13.4 + - + +
651B ILE* 3.7 14.3 - - + +
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Residues in contact with MET 645 (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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705A GLN* 5.9 3.8 - - - +
497B VAL* 5.4 3.1 - - + -
629B PHE* 5.7 2.9 - - - -
633B THR* 5.6 2.9 - - - -
641B GLU* 2.8 38.3 + - + +
642B HIS* 3.8 4.9 - - - +
644B ILE* 1.3 79.0 - - + +
646B ARG* 1.3 60.6 + - - +
648B MET* 3.3 46.5 - - + +
649B HIS 5.0 0.2 + - - -
659B ILE* 3.7 26.2 - - + -
666B THR* 3.5 34.1 - - + +
667B VAL* 5.4 1.1 - - - -
669B ASN* 6.4 2.5 - - + +
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Residues in contact with ARG 646 (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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642B HIS* 2.6 55.2 + - + +
643B VAL* 3.7 6.5 - - - +
645B MET* 1.3 72.7 - - - +
647B ASN* 1.3 59.6 + - - +
648B MET 3.2 1.6 + - - -
649B HIS* 4.6 6.9 + - - +
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Residues in contact with ASN 647 (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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580B LYS 3.6 7.9 + - - -
581B LEU* 2.9 45.0 + - + +
643B VAL* 2.9 28.5 + - - +
644B ILE 3.0 10.9 + - - +
646B ARG* 1.3 77.2 - - - +
648B MET* 1.3 56.8 + - - +
649B HIS 3.3 2.5 - - - -
650B LYS* 3.1 26.2 + - + +
651B ILE* 3.0 28.8 + - + +
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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