Contacts of the helix formed by residues 643 - 657 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576D LYS* 4.4 14.8 - - - +
579D VAL* 3.9 6.5 - - - -
641D ARG 4.0 0.2 + - - -
642D VAL* 1.3 76.8 - - - +
644D ALA* 1.3 60.1 + - - +
645D ALA* 3.5 6.4 + - - +
646D GLU* 3.2 23.2 + - - +
647D LEU* 2.9 29.3 + - - +
628E GLN* 3.0 33.1 + - - -
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Residues in contact with ALA 644 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500D LEU* 3.8 29.6 - - + +
503D LEU* 4.2 2.5 - - + -
504D GLU* 4.0 21.6 - - - +
507D HIS* 3.7 33.0 + - + +
579D VAL* 3.8 9.9 - - + +
643D SER* 1.3 75.0 - - - +
645D ALA* 1.3 51.4 + - - +
647D LEU* 4.7 0.2 - - - -
648D GLY* 2.8 31.4 + - - -
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Residues in contact with ALA 645 (chain D).
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* 3.6 35.9 - - + +
643D SER* 3.2 7.7 + - - +
644D ALA* 1.3 77.7 - - - +
646D GLU* 1.3 65.6 + - + +
648D GLY* 3.2 1.3 + - - -
649D GLY 3.0 18.9 + - - -
624E PRO* 4.3 4.5 - - + -
625E LEU* 3.8 40.4 - - + +
628E GLN* 5.4 1.1 - - - +
657E GLN* 5.3 1.1 - - - +
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Residues in contact with GLU 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642D VAL* 3.3 29.5 - - + +
643D SER* 3.2 25.9 + - - +
645D ALA* 1.3 80.6 - - - +
647D LEU* 1.3 61.3 + - - +
649D GLY* 3.3 7.8 + - - -
650D LYS* 3.4 21.6 + - - +
625E LEU* 4.6 16.7 - - + +
628E GLN* 4.0 16.7 - - - +
650E LYS* 4.0 26.7 - - - +
653E ARG* 3.5 29.7 + - - +
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Residues in contact with LEU 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D LEU* 5.0 4.3 - - + -
500D LEU* 3.8 30.1 - - + -
579D VAL* 3.8 19.5 - - + -
582D SER* 3.9 9.2 - - - +
583D CYS* 3.9 15.7 - - - -
629D ALA* 3.2 42.4 - - + +
633D GLY* 4.7 0.2 - - - -
642D VAL* 3.9 15.9 - - + +
643D SER 2.9 16.0 + - - +
644D ALA 4.0 2.7 - - - +
646D GLU* 1.3 73.8 - - - +
648D GLY* 1.3 59.8 + - - +
650D LYS* 3.2 9.2 + - + +
651D VAL* 2.9 37.7 + - + +
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Residues in contact with GLY 648 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497D GLY* 5.5 4.1 - - - -
500D LEU* 3.9 19.0 - - - +
501D GLU* 6.5 0.9 - - - -
504D GLU* 5.7 2.7 - - - -
644D ALA 2.8 23.3 + - - -
645D ALA* 3.2 3.1 + - - -
647D LEU* 1.3 72.6 - - - +
649D GLY* 1.3 60.9 + - - +
651D VAL* 3.7 3.2 + - - +
652D ASN* 3.2 22.7 + - - +
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Residues in contact with GLY 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D ALA 3.0 12.9 + - - -
646D GLU 3.8 3.6 - - - -
647D LEU 3.2 0.2 - - - -
648D GLY* 1.3 77.0 - - - +
650D LYS* 1.3 56.8 + - - +
652D ASN* 3.3 10.0 + - - +
653D ARG* 2.9 29.8 + - - +
625E LEU* 5.2 7.9 - - - -
653E ARG* 6.0 6.1 - - - -
657E GLN* 6.3 4.0 - - - +
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Residues in contact with LYS 650 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625D LEU* 3.4 21.3 - - + +
628D GLN* 4.2 10.6 + - - +
629D ALA* 4.4 17.6 - - + +
632D GLU* 2.7 37.4 + - + +
642D VAL* 4.6 13.9 - - + +
646D GLU* 3.4 15.0 + - - +
647D LEU* 3.2 11.3 + - + +
649D GLY* 1.3 73.5 - - - +
651D VAL* 1.3 57.3 + - - +
653D ARG* 3.3 10.7 - - - +
654D ALA* 3.1 21.7 + - - +
653E ARG* 3.5 43.9 - - - +
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Residues in contact with VAL 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D LEU* 3.4 47.5 - - + +
496D LEU* 3.8 24.5 - - + -
497D GLY* 3.8 15.7 - - - +
500D LEU* 4.0 9.9 - - + -
629D ALA* 4.9 7.0 - - + -
647D LEU* 2.9 27.1 + - + +
648D GLY 4.0 4.5 - - - +
650D LYS* 1.3 74.7 - - - +
652D ASN* 1.3 66.2 + - - +
653D ARG 3.1 1.3 - - - -
654D ALA* 3.2 3.0 + - - +
655D LEU* 3.0 25.4 + - + +
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Residues in contact with ASN 652 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648D GLY 3.2 13.0 + - - +
649D GLY* 3.3 11.1 + - - +
651D VAL* 1.3 80.2 - - - +
653D ARG* 1.3 65.8 + - - +
655D LEU* 3.8 17.6 + - - +
656D GLN* 3.8 12.0 + - - +
656E GLN* 3.8 28.7 + - - +
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Residues in contact with ARG 653 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625D LEU* 3.8 23.7 - - + +
649D GLY 2.9 14.2 + - - +
650D LYS* 3.3 16.6 - - - +
651D VAL 3.1 0.2 - - - -
652D ASN* 1.3 82.5 + - - +
654D ALA* 1.3 61.5 + - - +
655D LEU 3.5 0.3 + - - -
656D GLN* 3.6 11.9 + - - +
657D GLN* 3.6 11.6 + - - +
652E ASN* 5.3 6.7 + - - -
656E GLN* 4.4 28.8 + - - +
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Residues in contact with ALA 654 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493D LEU* 3.9 17.5 - - + +
623D ALA* 5.4 2.9 - - + +
625D LEU* 4.1 11.7 - - + +
626D THR* 3.7 35.9 + - - +
629D ALA* 6.0 0.4 - - + -
650D LYS 3.1 16.6 + - - +
651D VAL 3.2 4.6 + - - +
653D ARG* 1.3 75.2 - - - +
655D LEU* 1.3 65.7 + - - +
656D GLN 3.3 0.2 - - - -
657D GLN* 3.4 23.7 + - - +
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Residues in contact with LEU 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D ASP* 4.2 18.9 - - + +
493D LEU* 3.9 13.4 - - + +
494D TYR* 3.8 47.3 - - + +
651D VAL* 3.0 15.7 + - + +
652D ASN* 3.9 14.6 - - - +
653D ARG 3.3 0.4 - - - -
654D ALA* 1.3 78.0 - - - +
656D GLN* 1.3 69.7 + - - +
657D GLN 4.1 3.5 - - - -
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Residues in contact with GLN 656 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652D ASN 3.8 8.1 + - - +
653D ARG* 3.6 10.2 + - - +
654D ALA 3.3 0.2 - - - -
655D LEU* 1.3 88.6 - - + +
657D GLN* 1.3 60.4 + - - +
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Residues in contact with GLN 657 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623D ALA* 3.6 17.4 - - + +
624D PRO* 3.5 31.3 - - - +
625D LEU* 3.5 32.1 - - + +
653D ARG 3.6 8.7 + - - +
654D ALA* 3.4 17.0 + - - +
655D LEU 3.3 3.9 - - - -
656D GLN* 1.3 83.9 - - - +
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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