Contacts of the helix formed by residues 637 - 656 (chain A) in PDB entry 5J3V
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
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Residue Dist Surf HB Arom Phob DC
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581A LYS* 3.2 33.1 + - - +
584A PHE* 3.7 13.9 - - - -
619A THR* 3.9 6.3 - - - +
635A ALA 4.1 0.4 + - - -
636A PRO* 1.3 69.9 - - - +
638A LYS* 1.3 63.2 + - - +
639A ASP* 3.0 30.5 + - - +
640A PHE* 3.1 34.5 + - + +
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Residues in contact with LYS 638 (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 THR* 4.2 11.9 - - + -
623A ALA* 5.7 10.1 - - + -
636A PRO* 3.3 14.3 + - + +
637A ASP* 1.3 71.4 + - - +
639A ASP* 1.3 60.2 + - - +
640A PHE 3.1 0.4 - - - -
641A MET* 2.9 16.3 + - + +
642A ILE* 2.8 31.0 + - - +
678A ASP* 3.3 39.5 - - - +
679A LYS* 4.6 19.4 - - - +
680A MET* 3.8 28.7 - - + +
683A VAL* 3.9 10.1 - - + -
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Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PHE* 3.6 27.0 - - + -
637A ASP* 3.0 18.0 - - - +
638A LYS* 1.3 79.1 + - - +
640A PHE* 1.3 55.7 + - - +
642A ILE* 4.1 6.9 - - - +
643A VAL* 3.0 36.0 + - + +
680A MET* 4.1 15.2 - - - +
18C LYS* 3.9 24.0 + - - +
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Residues in contact with PHE 640 (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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578A ASP 3.3 24.0 - - - -
579A GLU* 3.3 28.7 - - - -
580A ASP 3.4 22.9 - - - -
581A LYS* 4.0 11.9 - - + -
583A LEU* 4.0 14.1 - - + -
584A PHE* 3.6 31.9 - + - -
615A LEU* 4.4 19.1 - - + +
619A THR* 4.0 12.6 - - - +
637A ASP* 3.1 29.0 + - + +
638A LYS 3.1 0.6 - - - -
639A ASP* 1.3 79.9 - - - +
641A MET* 1.3 56.0 + - - +
643A VAL* 4.2 2.1 - - - +
644A ALA* 3.2 29.6 + - - +
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Residues in contact with MET 641 (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 VAL* 4.0 21.0 - - + +
619A THR* 3.7 24.6 + - + -
620A LEU* 3.6 31.9 - - + -
638A LYS* 2.9 27.4 + - + +
640A PHE* 1.3 78.3 - - - +
642A ILE* 1.3 63.2 + - - +
644A ALA* 3.4 4.8 + - - +
645A LEU* 3.0 40.4 + - + +
675A CYS* 3.7 13.2 - - - -
678A ASP* 4.0 8.3 - - - +
683A VAL* 3.7 31.2 - - + -
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Residues in contact with ILE 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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588A GLU* 5.8 0.4 - - - +
638A LYS 2.8 21.5 + - - +
639A ASP* 4.0 9.4 - - - +
641A MET* 1.3 73.2 - - - +
643A VAL* 1.3 63.9 + - + +
645A LEU* 3.4 7.7 + - - +
646A ASP* 3.1 35.9 + - - +
680A MET* 3.7 27.8 - - + -
682A GLU* 3.6 28.7 - - + +
683A VAL* 3.7 19.5 - - + +
685A GLN* 5.7 1.1 - - - +
686A SER* 3.4 20.5 + - - +
18C LYS* 4.0 25.1 - - + +
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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
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584A PHE* 4.0 38.4 - - + +
587A LEU* 3.4 37.6 - - + +
588A GLU* 4.1 19.4 - - + +
639A ASP* 3.0 23.8 + - + +
640A PHE* 4.2 2.7 - - - +
642A ILE* 1.3 80.7 - - + +
644A ALA* 1.3 63.1 + - - +
646A ASP* 3.2 10.0 + - - +
647A LEU* 3.2 20.8 + - - +
18C LYS* 6.3 3.1 - - - -
20C LEU* 5.8 3.4 - - + -
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Residues in contact with ALA 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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587A LEU* 4.7 2.7 - - - -
612A CYS* 3.8 34.6 - - - +
615A LEU* 3.8 20.4 - - + -
616A VAL* 3.9 5.2 - - + -
640A PHE 3.2 20.6 + - - +
641A MET 3.8 3.4 - - - +
642A ILE 3.3 0.4 - - - -
643A VAL* 1.3 78.2 - - - +
645A LEU* 1.3 61.6 + - - +
647A LEU* 3.5 1.6 + - - -
648A LEU* 3.2 27.6 + - - +
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Residues in contact with LEU 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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616A VAL* 3.7 25.4 - - + -
641A MET* 3.0 30.1 + - + +
642A ILE* 3.7 4.7 - - - +
643A VAL 3.3 0.4 - - - -
644A ALA* 1.3 74.1 - - - +
646A ASP* 1.3 60.8 + - - +
648A LEU* 3.3 10.7 + - + +
649A SER* 3.1 29.5 + - - -
668A ILE* 5.9 1.1 - - + -
671A LEU* 6.4 0.4 - - + -
672A MET* 5.0 6.5 - - + -
675A CYS* 4.0 24.7 - - + -
683A VAL* 4.2 9.4 - - + +
686A SER* 4.0 14.4 - - - +
687A SER* 4.2 24.2 - - - +
690A LEU* 3.9 23.8 - - + +
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Residues in contact with ASP 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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588A GLU* 3.4 20.1 - - - +
591A SER* 3.1 12.1 + - - +
642A ILE* 3.1 22.5 + - - +
643A VAL 3.2 7.6 + - - +
645A LEU* 1.3 75.2 - - - +
647A LEU* 1.3 60.1 + - - +
649A SER* 3.2 10.2 + - - -
650A GLY 3.1 20.6 + - - -
686A SER* 3.0 28.9 + - - +
689A ALA* 5.8 1.2 - - - +
17C ARG* 3.6 36.5 + - - +
18C LYS* 5.1 2.4 + - - +
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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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573A TRP* 4.2 3.4 - - + -
587A LEU* 3.8 38.8 - - + +
590A LEU* 3.7 13.7 - - + +
591A SER* 3.6 33.6 - - - +
594A ALA* 4.7 8.1 - - + -
601A PHE* 5.8 0.4 - - + -
608A VAL* 3.7 23.1 - - + -
612A CYS* 3.5 24.0 - - - -
643A VAL 3.2 12.4 + - - +
644A ALA 3.8 7.9 - - - +
645A LEU 3.3 0.2 - - - -
646A ASP* 1.3 74.0 - - - +
648A LEU* 1.3 64.6 + - - +
650A GLY 3.2 1.0 + - - -
651A LEU* 3.1 23.1 + - + +
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Residues in contact with LEU 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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609A TYR* 3.6 40.2 - - + +
612A CYS* 3.7 31.9 - - + -
613A VAL* 4.7 4.9 - - + +
616A VAL* 4.7 3.4 - - + -
644A ALA 3.2 15.9 + - - +
645A LEU* 3.4 20.4 - - + +
647A LEU* 1.3 75.5 - - - +
649A SER* 1.3 59.5 + - - +
651A LEU* 3.3 8.1 + - + +
652A ALA* 3.0 28.1 + - - +
659A ILE* 4.5 3.2 - - + +
668A ILE* 3.9 21.3 - - + -
690A LEU* 3.6 21.5 - - + +
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Residues in contact with SER 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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645A LEU 3.1 14.6 + - - -
646A ASP* 3.4 12.6 + - - -
647A LEU 3.2 0.4 - - - -
648A LEU* 1.3 75.0 - - - +
650A GLY* 1.3 59.1 + - - +
652A ALA* 3.8 1.1 - - - -
653A GLU* 2.9 34.1 + - - +
686A SER 4.0 3.8 + - - -
689A ALA* 4.0 4.6 - - - +
690A LEU* 3.5 30.3 + - - +
693A ASP* 3.6 18.4 - - - +
14C LYS* 4.7 9.2 - - - -
17C ARG* 6.1 1.1 - - - -
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Residues in contact with GLY 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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591A SER* 4.0 11.2 - - - -
594A ALA* 3.9 7.9 - - - -
595A THR* 3.4 29.0 + - - -
646A ASP 3.1 12.8 + - - -
647A LEU 3.2 6.6 + - - -
649A SER* 1.3 78.0 - - - +
651A LEU* 1.3 56.6 + - - +
653A GLU* 4.7 1.1 - - - -
654A GLY* 2.9 25.6 + - - -
17C ARG* 5.5 1.5 - - - +
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Residues in contact with LEU 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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594A ALA* 4.0 8.7 - - + +
601A PHE* 3.5 38.4 - - + -
605A CYS* 4.2 9.0 - - + +
608A VAL* 4.0 19.7 - - + -
609A TYR* 4.0 35.9 - - + +
647A LEU* 3.1 14.5 + - + +
648A LEU* 3.7 11.0 - - + +
649A SER 3.3 0.2 - - - -
650A GLY* 1.3 75.5 - - - +
652A ALA* 1.3 59.0 + - - +
655A LEU* 2.6 52.4 + - + +
659A ILE* 3.8 13.7 - - + -
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Residues in contact with ALA 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 LEU 3.0 17.2 + - - +
649A SER* 3.9 1.6 - - - +
651A LEU* 1.3 76.2 - - - +
653A GLU* 1.3 58.7 + - - +
656A GLY* 3.2 23.4 + - - -
659A ILE* 3.8 14.1 - - + +
690A LEU* 4.5 1.1 - - + -
693A ASP* 3.7 31.0 - - + +
694A LEU* 3.7 29.4 - - + -
697A ALA* 4.2 1.6 - - + +
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Residues in contact with GLU 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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595A THR* 3.7 28.9 + - + +
598A GLN* 5.4 1.6 - - - +
649A SER 2.9 18.3 + - - +
650A GLY* 4.1 2.6 - - - +
652A ALA* 1.3 76.6 - - - +
654A GLY* 1.3 63.1 + - - +
656A GLY* 4.5 1.4 + - - -
693A ASP* 4.3 12.3 - - - +
14C LYS* 2.9 33.7 + - - +
17C ARG* 5.6 2.6 + - - -
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Residues in contact with GLY 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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594A ALA 3.8 15.7 - - - -
595A THR 4.2 7.2 - - - -
598A GLN* 3.3 32.7 - - - +
599A SER* 4.0 1.9 + - - -
650A GLY 2.9 18.3 + - - -
653A GLU* 1.3 79.6 - - - +
655A LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 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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598A GLN 3.4 22.4 - - - +
599A SER* 4.5 3.9 + - - +
601A PHE* 4.2 4.0 - - + -
602A LEU* 3.7 37.2 - - + +
605A CYS* 3.6 29.6 - - + -
651A LEU* 2.6 39.9 + - + +
654A GLY* 1.3 73.8 - - - +
656A GLY* 1.3 61.4 + - - +
657A GLY 3.4 2.9 + - - -
658A ASN* 3.5 28.2 + - + +
659A ILE* 4.3 22.9 - - + +
662A LEU* 5.3 0.4 - - + -
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Residues in contact with GLY 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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651A LEU 3.8 0.4 + - - -
652A ALA 3.2 20.1 + - - -
653A GLU 5.2 1.3 - - - -
654A GLY 3.5 1.6 - - - -
655A LEU* 1.3 76.4 - - - +
657A GLY* 1.3 61.6 + - - -
658A ASN 3.1 1.9 + - - -
659A ILE* 3.2 14.7 - - - +
697A ALA* 3.2 24.6 - - - +
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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