Contacts of the helix formed by residues 643 - 658 (chain E) in PDB entry 4G3D
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 SER 643 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576E LYS* 4.1 18.6 - - - +
579E VAL* 4.0 2.9 - - - -
641E ARG 3.8 1.2 + - - -
642E VAL* 1.3 76.1 - - - +
644E ALA* 1.3 64.9 + - - +
645E ALA* 3.6 8.7 + - - +
646E GLU* 3.0 32.2 + - - +
647E LEU* 2.9 22.7 + - - +
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Residues in contact with ALA 644 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E LEU* 3.9 26.4 - - + +
503E LEU* 4.2 4.0 - - + -
504E GLU* 3.8 21.1 - - - +
507E HIS* 3.7 31.8 + - + +
579E VAL* 3.7 10.6 - - + +
643E SER* 1.3 72.6 - - - +
645E ALA* 1.3 52.6 + - - +
647E LEU* 3.4 2.1 + - - +
648E GLY* 2.7 32.4 + - - -
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Residues in contact with ALA 645 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E GLU* 3.4 38.9 - - + +
643E SER* 3.3 7.2 + - - +
644E ALA* 1.3 75.7 - - - +
646E GLU* 1.3 66.2 + - + +
648E GLY* 3.6 1.8 - - - +
649E GLY* 3.0 20.3 + - - -
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Residues in contact with GLU 646 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642E VAL* 3.8 21.5 - - + +
643E SER* 3.0 40.8 + - - +
645E ALA* 1.3 76.5 - - + +
647E LEU* 1.3 57.4 + - - +
649E GLY* 3.1 4.7 + - - -
650E LYS* 3.1 41.7 + - - +
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Residues in contact with LEU 647 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E LEU* 5.4 2.2 - - + -
500E LEU* 3.7 28.5 - - + -
579E VAL* 4.1 16.8 - - + -
582E SER* 4.5 2.0 - - - +
583E CYS* 3.7 26.5 - - - -
629E ALA* 3.4 42.4 - - + +
633E GLY* 4.6 2.9 - - - -
642E VAL* 4.2 10.8 - - + -
643E SER 2.9 16.0 + - - +
644E ALA 3.9 2.7 - - - +
646E GLU* 1.3 73.8 - - - +
648E GLY* 1.3 57.7 + - - +
650E LYS* 4.3 8.1 - - + +
651E VAL* 2.8 46.0 + - + +
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Residues in contact with GLY 648 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497E GLY* 5.5 4.9 - - - -
500E LEU* 3.9 19.2 - - - +
501E GLU* 6.4 1.6 - - - -
504E GLU* 5.9 1.6 - - - -
644E ALA 2.7 21.2 + - - -
645E ALA* 3.3 4.2 + - - -
647E LEU* 1.3 72.0 - - - +
649E GLY* 1.3 60.9 + - - +
651E VAL* 4.3 3.2 - - - +
652E ASN* 3.5 22.0 + - - +
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Residues in contact with GLY 649 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645E ALA 3.0 13.0 + - - -
646E GLU 3.1 4.7 + - - -
648E GLY* 1.3 76.3 - - - +
650E LYS* 1.3 61.6 + - - +
652E ASN* 3.4 7.1 + - - +
653E ARG* 3.2 32.8 + - - +
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Residues in contact with LYS 650 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646D GLU* 4.0 25.1 - - - +
625E LEU* 3.4 16.4 - - + +
628E GLN* 5.9 0.7 - - + +
629E ALA* 4.4 17.5 - - + -
632E GLU* 2.7 30.4 + - - +
642E VAL* 3.5 22.1 - - + +
646E GLU* 3.1 28.4 + - - +
647E LEU* 3.3 12.3 + - + +
649E GLY* 1.3 71.7 - - - +
651E VAL* 1.3 61.0 + - - +
653E ARG* 3.4 17.2 + - - +
654E ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 651 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493E LEU* 3.4 40.4 - - + +
496E LEU* 3.7 24.2 - - + -
497E GLY* 4.0 17.3 - - - +
500E LEU* 3.9 10.1 - - + -
629E ALA* 4.7 6.5 - - + -
647E LEU* 2.8 36.0 + - + +
648E GLY* 4.3 2.9 - - - +
650E LYS* 1.3 70.7 - - - +
652E ASN* 1.3 62.1 + - + +
654E ALA* 3.1 8.8 + - - +
655E LEU* 2.8 27.3 + - + +
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Residues in contact with ASN 652 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653D ARG* 5.3 6.6 + - - -
648E GLY 3.5 16.8 + - - +
649E GLY* 3.4 6.8 + - - +
651E VAL* 1.3 77.0 - - - +
653E ARG* 1.3 67.0 + - - +
655E LEU* 3.2 18.7 + - - +
656E GLN* 3.1 22.2 + - - +
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Residues in contact with ARG 653 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646D GLU* 3.5 32.2 + - - +
649D GLY* 6.0 5.9 - - - -
650D LYS* 3.5 40.2 - - - +
625E LEU* 4.1 20.1 - - + +
649E GLY* 3.2 18.6 + - - +
650E LYS* 3.5 22.4 - - - +
652E ASN* 1.3 78.3 - - - +
654E ALA* 1.3 62.2 + - - +
656E GLN* 3.2 9.3 + - - +
657E GLN* 3.2 21.1 + - - +
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Residues in contact with ALA 654 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493E LEU* 3.6 12.9 - - + +
623E ALA* 5.7 0.3 - - - +
625E LEU* 3.8 22.6 - - + +
626E THR* 3.8 29.7 + - - +
629E ALA* 5.5 0.4 - - + -
650E LYS 3.0 14.5 + - - +
651E VAL* 3.1 10.1 + - - +
653E ARG* 1.3 75.4 - - - +
655E LEU* 1.3 60.7 + - - +
657E GLN* 3.6 4.9 + - - +
658E VAL* 3.4 24.1 + - - +
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Residues in contact with LEU 655 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490E ASP 4.2 10.8 - - - +
493E LEU* 3.8 21.7 - - + +
494E TYR* 3.5 39.9 - - + +
497E GLY* 6.0 1.1 - - - -
651E VAL* 2.8 13.5 + - + +
652E ASN* 3.4 23.3 - - - +
653E ARG 3.2 0.4 - - - -
654E ALA* 1.3 76.1 - - - +
656E GLN* 1.3 64.5 + - - +
658E VAL* 3.2 17.3 - - + +
660E GLY* 3.5 12.1 + - - +
661E LEU* 4.0 27.8 - - + +
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Residues in contact with GLN 656 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652D ASN* 3.8 23.1 + - - +
653D ARG* 4.4 26.1 + - - +
652E ASN* 3.1 13.4 + - - +
653E ARG* 3.2 11.9 + - - +
655E LEU* 1.3 77.2 - - - +
657E GLN* 1.3 61.7 + - - +
659E GLY* 3.4 12.0 + - - -
660E GLY* 3.6 11.3 + - - +
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Residues in contact with GLN 657 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D GLU* 2.7 34.1 + - - +
645D ALA* 5.4 1.1 - - - -
649D GLY* 6.3 4.3 - - - +
623E ALA* 4.2 19.1 - - - +
624E PRO* 4.4 1.6 - - - +
625E LEU* 3.2 37.2 + - + +
653E ARG 3.2 12.0 + - - +
654E ALA* 3.8 9.6 - - - +
655E LEU 3.3 0.4 - - - -
656E GLN* 1.3 74.5 - - - +
658E VAL* 1.3 56.8 + - + +
659E GLY* 2.9 11.2 + - - -
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Residues in contact with VAL 658 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489E GLU* 4.1 30.1 - - + +
490E ASP* 3.9 29.5 - - + +
493E LEU* 4.3 4.0 - - + -
623E ALA* 4.2 15.5 - - + -
654E ALA 3.4 14.1 - - - +
655E LEU* 3.2 23.1 - - + +
656E GLN 3.3 0.2 - - - -
657E GLN* 1.3 74.6 - - - +
659E GLY* 1.3 57.6 + - - +
660E GLY 3.1 14.8 - - - +
662E LYS* 3.8 8.5 - - - +
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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