Contacts of the helix formed by residues 639 - 656 (chain A) in PDB entry 3E7C
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 MET 639 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A 866 4.0 23.1 - - - -
556A THR* 3.2 44.6 - - + +
559A ILE* 4.1 30.7 - - + -
560A MET* 5.6 0.4 - - - -
629A ILE* 4.7 7.2 - - + -
633A ARG 3.7 13.9 - - - +
634A MET* 3.7 10.5 - - + +
636A LEU* 3.2 22.7 + - + +
637A PRO 3.1 0.2 + - - -
638A GLY* 1.3 76.8 - - - +
640A TYR* 1.3 66.2 - - - +
641A ASP 3.2 1.9 + - - -
642A GLN* 3.4 5.0 + - - +
643A CYS* 3.2 40.8 + - - -
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Residues in contact with TYR 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A MET* 3.4 40.2 + - + +
636A LEU 4.5 0.4 + - - -
639A MET* 1.3 74.4 - - - +
641A ASP* 1.3 58.6 + - - +
642A GLN 3.0 10.9 + - - -
644A LYS* 3.1 51.0 + - + +
647A LEU* 4.0 22.0 - - + +
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Residues in contact with ASP 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLY* 4.6 6.3 - - - +
639A MET 3.2 1.4 - - - +
640A TYR* 1.3 79.6 - - - +
642A GLN* 1.3 59.0 + - - +
644A LYS* 2.9 25.3 + - - +
645A HIS* 3.6 16.6 + - - -
735A TYR* 4.1 20.9 - - + +
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Residues in contact with GLN 642 (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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1A 866 2.7 62.8 + - + +
601A MET* 5.2 1.4 - - - +
623A PHE* 6.5 0.7 - - + -
639A MET 3.4 2.5 + - - +
640A TYR 3.0 0.2 - - - -
641A ASP* 1.3 80.8 - - - +
643A CYS* 1.3 68.4 + - - +
644A LYS 3.1 1.8 - - - -
645A HIS* 3.1 23.7 + - - +
646A MET* 3.6 8.0 + - + +
731A ASN 4.0 1.4 - - - +
732A LEU* 3.0 51.8 + - + +
735A TYR* 3.3 32.9 - - + +
736A CYS* 4.3 0.2 - - - +
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Residues in contact with CYS 643 (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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1A 866 5.3 3.6 - - - -
621A LEU* 3.4 27.4 - - + -
623A PHE* 4.8 6.5 - - - -
629A ILE* 4.4 10.5 - - - -
634A MET* 3.1 35.2 - - + -
639A MET* 3.2 28.3 + - - -
642A GLN* 1.3 83.5 - - - +
644A LYS* 1.3 50.6 + - - +
646A MET* 2.9 7.9 + - - +
647A LEU* 2.6 39.9 + - - +
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Residues in contact with LYS 644 (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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640A TYR* 3.1 56.1 + - + +
641A ASP* 2.9 33.3 + - - -
643A CYS* 1.3 77.2 - - - +
645A HIS* 1.3 89.6 + - - +
647A LEU* 3.7 14.8 - - - +
648A TYR* 3.1 25.5 + - - +
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Residues in contact with HIS 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ASP* 3.6 20.2 + - - -
642A GLN* 3.4 19.1 - - - +
643A CYS 3.0 0.4 - - - -
644A LYS* 1.3 111.7 + - + +
646A MET* 1.3 64.4 - - - +
648A TYR* 3.4 12.5 + - - +
649A VAL* 3.3 19.6 + - - +
728A VAL* 3.9 14.9 - - + +
731A ASN* 3.3 48.1 + - + +
732A LEU* 3.6 17.0 - - + -
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Residues in contact with MET 646 (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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1A 866 3.5 26.5 - - - +
601A MET* 4.2 6.1 - - + -
605A ALA* 3.6 30.1 - - - +
608A LEU* 3.5 22.7 - - + -
609A GLY* 4.8 2.8 + - - -
621A LEU* 3.5 27.1 - - + +
623A PHE* 4.6 4.3 - - + -
642A GLN* 4.3 7.6 - - + +
643A CYS* 2.9 9.9 + - - +
645A HIS* 1.3 79.7 - - - +
647A LEU* 1.3 60.6 + - - +
649A VAL* 3.1 16.1 + - - +
650A SER* 3.1 12.5 + - - -
732A LEU* 3.6 41.3 - - + -
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Residues in contact with LEU 647 (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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619A ASN* 4.1 28.7 - - - +
620A LEU 4.9 0.9 - - - -
621A LEU* 3.6 27.6 - - + +
634A MET* 4.3 15.3 - - + -
640A TYR* 4.0 21.3 - - + +
643A CYS* 2.6 28.4 + - + +
644A LYS* 3.8 16.2 - - - +
646A MET* 1.3 73.1 - - - +
648A TYR* 1.3 52.8 + - - +
650A SER* 3.2 10.6 + - - -
651A SER* 2.7 37.5 + - - -
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Residues in contact with TYR 648 (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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644A LYS 3.1 18.3 + - - +
645A HIS* 3.6 6.3 - - - +
646A MET 3.2 0.4 - - - -
647A LEU* 1.3 76.5 - - - +
649A VAL* 1.3 60.1 + - + +
651A SER* 3.2 7.8 + - - -
652A GLU* 2.8 66.9 + - + +
721A LEU* 4.2 6.1 - - + +
724A SER* 3.1 34.0 + - - -
725A MET* 5.7 0.4 - - - -
728A VAL* 3.8 28.0 - - + -
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Residues in contact with VAL 649 (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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605A ALA* 4.0 22.7 - - + +
606A PHE* 4.0 18.2 - - + -
609A GLY* 4.3 6.5 - - - -
645A HIS 3.3 16.6 - - - +
646A MET* 3.1 10.7 + - - +
648A TYR* 1.3 79.0 - - - +
650A SER* 1.3 65.6 + - - +
652A GLU* 3.7 3.6 - - - +
653A LEU* 3.0 31.8 + - + +
721A LEU* 5.5 2.5 - - + -
725A MET* 3.9 27.8 - - + -
728A VAL* 3.8 23.6 - - + -
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Residues in contact with SER 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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609A GLY* 3.9 21.2 - - - -
612A SER* 3.8 14.5 + - - -
613A TYR* 3.7 21.8 + - - +
619A ASN 6.0 1.7 - - - -
620A LEU 5.2 0.3 + - - -
621A LEU* 5.0 2.7 - - - -
646A MET 3.1 8.5 + - - -
647A LEU* 3.4 14.1 - - - -
649A VAL* 1.3 81.1 - - - +
651A SER* 1.3 60.4 + - - +
653A LEU* 3.6 3.3 + - - +
654A HIS* 3.1 24.0 + - - +
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Residues in contact with SER 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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647A LEU 2.7 20.9 + - - -
648A TYR* 3.2 9.8 + - - -
650A SER* 1.3 73.8 - - - +
652A GLU* 1.3 62.0 + - - +
654A HIS* 3.3 9.7 + - - +
655A ARG* 2.8 30.7 + - - +
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Residues in contact with GLU 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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648A TYR* 2.8 60.3 + - + +
649A VAL 3.7 2.7 - - - +
651A SER* 1.3 77.7 + - - +
653A LEU* 1.3 67.1 + - - +
655A ARG* 2.8 46.5 + - - +
656A LEU* 3.0 30.1 + - + +
721A LEU* 3.6 27.3 - - + +
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Residues in contact with LEU 653 (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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606A PHE* 4.0 28.0 - - + +
609A GLY* 3.5 9.9 - - - -
610A TRP* 3.3 44.2 - - + +
613A TYR* 4.1 15.2 - - + -
649A VAL* 3.0 23.6 + - + +
650A SER 3.7 4.3 - - - +
652A GLU* 1.3 75.8 - - - +
654A HIS* 1.3 58.4 + - - +
656A LEU 3.5 0.3 + - - -
657A GLN* 2.9 22.2 + - - -
658A VAL* 3.0 42.1 + - + +
666A MET* 5.1 0.2 - - + -
721A LEU* 3.9 15.3 - - + -
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Residues in contact with HIS 654 (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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613A TYR* 3.5 27.3 - + + -
650A SER 3.1 15.6 + - - +
651A SER* 3.6 8.5 + - - +
652A GLU 3.1 0.2 - - - -
653A LEU* 1.3 78.6 - - - +
655A ARG* 1.3 72.1 + - - +
657A GLN* 3.0 40.4 + - - +
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Residues in contact with ARG 655 (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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651A SER* 2.8 21.2 + - - +
652A GLU* 2.8 43.1 + - - +
654A HIS* 1.3 83.1 + - - +
656A LEU* 1.3 96.3 + - - +
657A GLN* 3.2 4.7 + - - +
717A GLN* 4.7 7.3 - - - +
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Residues in contact with LEU 656 (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 GLU* 3.0 20.0 + - + +
655A ARG* 1.3 113.6 - - - +
657A GLN* 1.3 71.2 + - - +
658A VAL* 3.8 11.4 - - + -
704A ARG* 4.1 0.3 + - - -
714A ARG* 2.9 30.8 + - - +
717A GLN* 3.9 44.2 - - + +
718A LEU* 4.0 19.1 - - + -
721A LEU* 4.0 21.8 - - + -
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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
------------------------------------------------------------
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