Contacts of the helix formed by residues 637 - 652 (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 ASP 637 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ALA 4.2 0.4 + - - -
636A LEU* 1.3 74.8 - - - +
638A TYR* 1.3 62.5 + - - +
639A GLU* 3.6 11.4 + - - +
640A SER* 3.0 41.8 + - - -
641A GLU* 2.9 25.9 + - - +
502B GLY 4.4 5.8 - - - +
503B ARG* 3.7 25.8 - - + +
504B SER* 2.7 32.8 + - - +
662B ALA* 4.5 12.3 - - + +
701B LEU* 6.0 5.1 - - + +
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Residues in contact with TYR 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LEU 3.9 0.6 + - - -
637A ASP* 1.3 73.8 - - - +
639A GLU* 1.3 57.1 + - - +
641A GLU* 3.6 10.3 + - - +
642A HIS* 3.0 28.2 + - - +
663A ARG* 3.6 32.7 - - - +
665A SER* 4.2 10.1 - - - -
662B ALA 3.7 17.7 - - - -
663B ARG* 3.3 33.3 - - - +
664B LEU* 3.7 22.0 + - + +
665B SER* 4.9 2.1 + - - -
701B LEU* 4.4 13.5 - - + +
704B LEU* 3.9 27.8 - - + -
705B GLN* 3.6 43.2 + - + +
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Residues in contact with GLU 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ASP* 3.2 10.2 + - - +
638A TYR* 1.3 76.6 - - - +
640A SER* 1.3 63.4 + - - +
642A HIS* 3.6 5.5 + - - +
643A VAL* 3.3 32.9 + - + +
503B ARG* 3.1 39.0 + - + +
700B TYR* 3.2 29.5 + - - +
701B LEU* 4.4 4.6 - - + +
704B LEU* 3.9 12.9 - - + +
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Residues in contact with SER 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA 5.1 0.3 - - - +
583A GLY* 5.9 0.5 - - - -
613A ARG* 4.1 22.8 + - - +
636A LEU* 3.8 20.2 - - - -
637A ASP* 3.0 33.7 + - - -
639A GLU* 1.3 74.5 - - - +
641A GLU* 1.3 65.4 + - - +
643A VAL* 3.6 6.8 + - - +
644A ILE* 3.3 27.5 + - - +
503B ARG* 5.7 0.5 - - - +
504B SER* 4.5 0.3 - - - -
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Residues in contact with GLU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A THR* 2.4 40.8 + - + +
636A LEU* 4.0 10.0 - - + +
637A ASP 2.9 16.5 + - - +
638A TYR* 3.7 11.3 - - - +
640A SER* 1.3 75.2 - - - +
642A HIS* 1.3 59.8 + - - +
644A ILE* 3.3 5.5 + - - +
645A MET* 2.9 42.0 + - + +
663A ARG* 3.3 23.8 + - - +
665A SER* 5.0 1.2 + - - +
666A THR* 2.7 38.3 + - - -
705B GLN* 5.4 1.6 - - - +
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Residues in contact with HIS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR 3.0 17.8 + - - +
639A GLU* 3.8 7.9 - - - +
640A SER 3.3 0.2 - - - -
641A GLU* 1.3 74.9 - - - +
643A VAL* 1.3 58.3 + - + +
645A MET* 3.1 7.2 + - + +
646A ARG* 2.7 75.8 + - + +
669A ASN* 4.9 12.1 - - - -
704B LEU* 5.6 2.7 - - + -
705B GLN* 4.1 26.7 + - - +
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Residues in contact with VAL 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LYS 4.5 4.0 - - - +
583A GLY* 4.1 27.1 - - - +
639A GLU* 3.3 21.1 + - + +
640A SER* 3.9 7.4 - - - +
641A GLU 3.4 0.2 - - - -
642A HIS* 1.3 77.1 - - + +
644A ILE* 1.3 61.4 + - - +
646A ARG* 3.9 10.6 - - - +
647A ASN* 3.0 40.1 + - - +
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Residues in contact with ILE 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LEU 4.1 8.3 - - - +
582A ALA 3.4 31.0 - - - +
613A ARG* 4.2 3.8 - - + -
616A ILE* 3.8 36.3 - - + -
620A LEU* 5.9 0.2 - - + -
629A PHE* 4.2 8.7 - - + -
633A THR* 4.4 6.1 - - + -
636A LEU* 3.5 32.1 - - + -
640A SER 3.3 8.7 + - - +
641A GLU 3.3 7.1 + - - +
642A HIS 3.1 0.4 - - - -
643A VAL* 1.3 74.3 - - + +
645A MET* 1.3 64.3 + - - +
647A ASN* 3.2 14.0 + - - +
648A MET* 3.2 34.7 + - + +
651A ILE* 4.2 2.8 - - + +
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Residues in contact with MET 645 (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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629A PHE* 3.9 22.4 - - + -
633A THR* 3.8 28.5 - - + +
641A GLU* 2.9 28.4 + - + +
642A HIS* 3.8 9.2 - - + +
644A ILE* 1.3 69.2 - - + +
646A ARG* 1.3 59.9 + - - +
648A MET* 2.7 47.0 + - + +
649A HIS* 3.6 2.8 + - - +
659A ILE* 4.0 24.0 - - + -
666A THR* 4.0 28.9 - - + +
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Residues in contact with ARG 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A HIS* 2.7 56.3 + - + +
643A VAL* 3.9 10.5 - - - +
645A MET* 1.3 72.4 - - - +
647A ASN* 1.3 68.1 + - - +
648A MET 3.4 0.2 + - - -
649A HIS* 3.4 20.0 + - - +
650A LYS* 4.2 16.4 - - - +
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Residues in contact with ASN 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LYS 4.3 1.4 + - - -
581A LEU* 2.8 50.0 + - + +
643A VAL* 3.0 20.4 + - - +
644A ILE 3.2 4.6 + - - +
645A MET 3.1 0.8 - - - -
646A ARG* 1.3 80.4 + - - +
648A MET* 1.3 52.1 + - - +
649A HIS 3.2 1.6 - - - -
650A LYS* 2.9 22.6 + - + +
651A ILE* 2.6 54.6 + - + +
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Residues in contact with MET 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A VAL* 4.3 9.3 - - + +
620A LEU* 4.9 0.9 - - + -
627A LEU* 4.6 1.8 - - - -
629A PHE* 3.6 28.9 - - + -
644A ILE* 3.2 46.4 + - + +
645A MET* 2.7 29.7 + - + +
647A ASN* 1.3 72.9 - - - +
649A HIS* 1.3 54.9 + - - +
650A LYS 3.0 5.8 - - - -
651A ILE* 3.5 31.2 - - + -
652A CYS* 2.9 33.3 + - - +
657A VAL* 3.9 29.6 - - + -
659A ILE* 5.0 1.6 - - + -
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Residues in contact with HIS 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A VAL* 5.7 1.8 - - - -
645A MET 3.6 2.4 + - - +
646A ARG* 3.4 14.7 + - - +
648A MET* 1.3 77.6 - - - +
650A LYS* 1.3 79.2 + - + +
652A CYS* 4.3 7.3 - - - -
653A LYS* 3.3 37.2 + - + +
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Residues in contact with LYS 650 (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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581A LEU* 6.0 4.9 - - + -
646A ARG* 4.2 20.0 - - - +
647A ASN* 2.9 24.0 + - + +
649A HIS* 1.3 100.4 + - + +
651A ILE* 1.3 59.9 + - + +
652A CYS 3.3 1.6 - - - -
653A LYS* 3.4 24.9 - - + +
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Residues in contact with ILE 651 (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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581A LEU* 4.0 18.4 - - + +
620A LEU* 3.5 45.8 - - + -
627A LEU* 4.2 7.2 - - + -
644A ILE* 4.2 3.8 - - + +
647A ASN* 2.6 46.2 + - + +
648A MET* 3.4 27.7 + - + +
650A LYS* 1.3 75.1 - - - +
652A CYS* 1.3 56.0 + - - +
653A LYS 3.3 0.9 - - - -
655A ARG* 2.6 55.2 + - - +
657A VAL* 4.4 2.4 - - + +
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Residues in contact with CYS 652 (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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495A GLY* 3.4 24.6 - - - -
497A VAL* 3.9 18.2 - - + -
648A MET 2.9 18.1 + - - +
649A HIS* 4.3 11.4 - - - -
650A LYS 3.3 0.2 - - - -
651A ILE* 1.3 77.6 - - - +
653A LYS* 1.3 60.7 + - - +
654A GLY 2.7 5.2 + - - -
655A ARG* 2.6 46.7 + - - +
657A VAL* 3.6 16.6 - - + -
671A ASP* 5.4 0.7 - - - -
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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
------------------------------------------------------------
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