Contacts of the helix formed by residues 663 - 678 (chain A) in PDB entry 2X7G
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 PRO 663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661A GLY 3.6 3.8 - - - +
662A TRP* 1.3 87.8 - - + +
664A HIS* 1.3 66.4 + - + +
665A GLU* 3.4 2.5 - - + +
666A ASP* 3.2 29.3 + - + +
667A ALA* 3.2 18.5 + - - +
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Residues in contact with HIS 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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653A PHE* 3.5 26.7 - + + -
657A VAL* 3.8 33.0 - - + +
662A TRP 4.2 2.5 - - - -
663A PRO* 1.3 73.0 - - + +
665A GLU* 1.3 64.3 + - - +
667A ALA 3.2 1.4 + - - -
668A ALA* 2.9 21.5 + - - +
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Residues in contact with GLU 665 (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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663A PRO* 3.4 2.1 - - + +
664A HIS* 1.3 78.1 - - - +
666A ASP* 1.3 67.1 + - - +
668A ALA* 3.3 12.4 + - - +
669A GLN* 3.1 55.3 + - - +
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Residues in contact with ASP 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 5.5 10.3 - - + +
662A TRP* 3.6 19.4 - - + -
663A PRO* 3.2 32.8 + - + +
665A GLU* 1.3 78.8 - - - +
667A ALA* 1.3 60.9 + - - +
669A GLN* 3.5 13.9 + - - +
670A PHE* 3.2 24.3 + - - +
696A TRP* 5.0 1.2 + - - -
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Residues in contact with ALA 667 (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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653A PHE* 4.0 7.4 - - + -
656A LEU* 3.7 22.0 - - + +
657A VAL* 3.8 24.5 - - + -
662A TRP* 3.7 13.2 - - + -
663A PRO 3.2 9.2 + - - +
664A HIS 3.2 7.8 + - - +
666A ASP* 1.3 76.6 - - - +
668A ALA* 1.3 61.1 + - - +
670A PHE 3.3 0.5 + - - -
671A THR* 2.8 35.6 + - - -
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Residues in contact with ALA 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A PHE* 3.7 16.7 - - + -
664A HIS 2.9 16.1 + - - +
665A GLU* 3.5 16.6 - - - +
667A ALA* 1.3 78.3 - - - +
669A GLN* 1.3 57.1 + - + +
671A THR* 3.7 2.2 - - - -
672A ASP* 2.9 41.6 + - - +
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Residues in contact with GLN 669 (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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202A LYS* 5.8 3.5 + - - -
665A GLU* 3.1 48.7 + - - +
666A ASP* 3.9 14.4 - - - +
667A ALA 3.2 0.2 - - - -
668A ALA* 1.3 77.2 - - + +
670A PHE* 1.3 61.6 + - - +
672A ASP* 3.6 8.6 + - - +
673A PHE* 3.2 16.1 + - - +
694A HIS* 4.7 1.7 - - - -
696A TRP* 3.5 26.2 - - + +
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Residues in contact with PHE 670 (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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585A ALA* 3.6 28.9 - - + -
586A PHE* 4.2 6.5 - + - -
589A ALA* 3.7 21.8 - - + -
656A LEU* 4.0 19.5 - - + -
662A TRP* 3.4 23.8 - + + -
666A ASP 3.2 17.9 + - - +
667A ALA 3.9 2.5 - - - +
668A ALA 3.2 0.2 - - - -
669A GLN* 1.3 76.0 - - - +
671A THR* 1.3 59.7 + - - +
673A PHE* 3.1 4.9 + + - +
674A LEU* 2.9 64.5 + - + +
696A TRP* 3.1 49.8 - + - +
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Residues in contact with THR 671 (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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652A LEU* 4.0 13.8 - - + +
653A PHE* 3.6 25.6 + - + +
656A LEU* 3.7 7.4 - - - +
667A ALA 2.8 24.8 + - - -
668A ALA* 3.7 6.1 - - - -
670A PHE* 1.3 75.0 - - - +
672A ASP* 1.3 68.7 + - - +
674A LEU 3.0 1.6 + - - +
675A ILE* 2.9 43.8 + - + +
1710A EDO 3.4 29.8 - - - +
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Residues in contact with ASP 672 (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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668A ALA* 2.9 27.4 + - - +
669A GLN* 3.7 8.7 - - - +
670A PHE 3.3 0.2 - - - -
671A THR* 1.3 81.0 - - - +
673A PHE* 1.3 56.2 + - - +
675A ILE* 5.1 1.8 - - - -
676A PRO* 3.1 22.0 - - - +
694A HIS* 3.2 22.1 + - + +
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Residues in contact with PHE 673 (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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205A ILE* 4.2 10.3 - - + -
209A LEU* 4.0 11.4 - - + -
585A ALA* 5.1 2.2 - - + -
669A GLN 3.2 6.7 + - - +
670A PHE* 3.1 10.5 + + - +
672A ASP* 1.3 75.3 - - - +
674A LEU* 1.3 78.4 + - + +
676A PRO* 3.7 6.2 - - - +
677A MET* 3.5 40.1 - - + +
691A CYS* 3.7 15.9 - - + -
694A HIS* 3.7 20.6 - + + -
696A TRP* 3.5 55.0 - + + -
697A LEU* 3.7 33.9 - - + -
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Residues in contact with LEU 674 (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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582A ALA* 3.7 33.2 - - + +
585A ALA* 4.2 6.1 - - + -
586A PHE* 4.6 14.6 - - + -
594A LEU* 5.8 1.3 - - + -
652A LEU* 3.8 31.0 - - + -
656A LEU* 5.6 0.2 - - + -
670A PHE* 2.9 55.3 + - + +
671A THR 3.9 0.2 - - - +
673A PHE* 1.3 93.6 - - + +
675A ILE* 1.3 65.9 + - - +
677A MET* 3.0 16.4 + - - +
678A LEU* 3.0 20.9 + - + +
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Residues in contact with ILE 675 (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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616A LEU 5.5 0.2 - - - +
617A LEU* 3.6 30.1 - - + -
652A LEU* 4.4 14.1 - - + -
671A THR* 2.9 33.7 + - + +
672A ASP* 4.9 1.8 - - - +
674A LEU* 1.3 74.6 - - - +
676A PRO* 1.3 66.4 - - + +
678A LEU* 2.9 19.7 + - + +
679A GLU* 3.0 16.4 + - - +
1710A EDO 3.9 25.4 - - - +
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Residues in contact with PRO 676 (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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672A ASP 3.1 24.2 - - - +
673A PHE 3.7 6.5 - - - +
674A LEU 3.5 2.9 - - - -
675A ILE* 1.3 98.5 - - + +
677A MET* 1.3 57.3 - - + +
679A GLU* 3.6 12.9 + - + +
684A LYS 4.8 0.2 - - - +
685A ARG* 3.4 8.3 - - - +
686A ALA* 3.0 37.0 + - + +
691A CYS* 6.1 0.2 - - - -
694A HIS* 4.9 10.1 - - + +
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Residues in contact with MET 677 (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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205A ILE* 5.2 0.2 - - + -
209A LEU* 4.3 10.3 - - + -
578A ILE* 3.8 29.4 - - + +
579A TRP* 3.6 15.9 + - - -
581A THR* 3.9 24.5 - - + -
582A ALA* 3.7 19.5 - - + +
585A ALA* 6.0 0.2 - - + -
673A PHE* 3.5 48.7 - - + +
674A LEU* 3.0 10.1 + - - +
676A PRO* 1.3 74.8 - - + +
678A LEU* 1.3 58.4 + - - +
679A GLU 3.5 0.7 - - - -
685A ARG* 3.3 19.2 - - - -
686A ALA* 4.6 1.6 - - + -
691A CYS* 3.4 30.7 - - - -
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Residues in contact with LEU 678 (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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579A TRP* 3.4 51.4 - - + +
582A ALA* 3.8 22.9 - - + -
583A CYS* 4.4 8.3 - - - -
594A LEU* 4.0 19.5 - - + -
595A PHE* 4.5 4.0 - - + -
616A LEU* 4.7 1.8 - - + -
617A LEU* 3.6 37.9 - - + +
652A LEU* 4.5 8.5 - - + -
674A LEU* 3.0 26.0 + - + +
675A ILE 2.9 7.5 + - - +
677A MET* 1.3 77.4 - - - +
679A GLU* 1.3 65.8 + - - +
680A MET* 3.2 3.1 + - - +
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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