Contacts of the helix formed by residues 648 - 660 (chain j) in PDB entry 5JPQ
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 GLY 648 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646j SER* 3.4 4.0 + - - +
647j MET* 1.4 78.9 - - - +
649j TYR* 1.3 64.7 + - - +
650j GLY 3.1 4.0 - - - +
651j SER* 3.3 11.3 + - - -
652j LYS* 2.9 20.7 + - - +
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Residues in contact with TYR 649 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516j CYS* 5.0 13.0 - - + -
570j LEU* 4.9 9.0 - - + -
583j LEU* 5.8 2.9 - - + -
584j CYS* 4.7 17.5 - - + -
640j THR* 5.4 6.1 - - - -
644j TYR* 5.6 3.8 - - + +
647j MET* 3.3 14.0 - - + +
648j GLY* 1.3 79.7 - - - +
650j GLY* 1.3 56.9 + - - +
652j LYS* 3.0 10.6 + - + +
653j ALA* 2.7 29.6 + - - +
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Residues in contact with GLY 650 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638j ILE* 6.4 2.7 - - - -
640j THR* 5.4 9.9 - - - -
648j GLY* 3.1 2.0 - - - -
649j TYR* 1.3 78.1 - - - +
651j SER* 1.3 59.4 + - - +
653j ALA* 3.0 21.7 + - - +
654j LEU* 3.3 6.2 + - - +
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Residues in contact with SER 651 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648j GLY* 3.3 12.1 + - - -
650j GLY* 1.3 72.0 - - - +
652j LYS* 1.3 65.3 + - - +
654j LEU* 3.0 10.2 + - - +
655j GLN* 2.9 23.6 + - - +
739j ARG 5.9 2.0 - - - -
740j ALA* 5.8 9.9 - - - -
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Residues in contact with LYS 652 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518j LEU* 4.8 12.3 - - + +
648j GLY 2.9 14.1 + - - +
649j TYR* 3.1 17.0 - - - +
651j SER* 1.3 77.2 - - - +
653j ALA* 1.3 64.1 + - - +
655j GLN* 3.4 7.2 + - - +
656j LEU* 3.1 21.8 + - - +
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Residues in contact with ALA 653 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518j LEU* 5.9 1.6 - - - -
568j PHE* 4.5 11.3 - - + +
569j VAL 6.5 0.9 - - - -
570j LEU* 6.2 2.0 - - + -
584j CYS* 5.7 6.3 - - + -
585j VAL 5.1 5.4 - - - +
586j ILE* 4.0 25.4 - - + +
638j ILE* 6.1 2.9 - - + -
649j TYR 2.7 11.7 + - - +
650j GLY* 3.0 13.6 + - - +
652j LYS* 1.3 77.4 - - - +
654j LEU* 1.3 62.4 + - - +
656j LEU* 3.1 9.7 + - - +
657j LEU* 3.1 17.3 + - - +
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Residues in contact with LEU 654 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650j GLY 3.3 5.2 + - - +
651j SER* 3.0 13.5 + - - +
653j ALA* 1.3 76.2 - - - +
655j GLN* 1.3 57.7 + - - +
657j LEU* 2.7 34.2 + - - +
658j VAL* 3.1 7.2 + - - +
740j ALA* 5.1 17.7 - - + +
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Residues in contact with GLN 655 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651j SER 2.9 16.0 + - - +
652j LYS* 3.8 8.1 - - - +
654j LEU* 1.3 76.1 - - - +
656j LEU* 1.3 52.8 + - - +
658j VAL* 3.0 8.7 + - - +
659j ASP* 2.7 36.9 + - + +
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Residues in contact with LEU 656 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518j LEU* 4.4 18.4 - - + -
519j LEU* 5.3 6.1 - - - +
520j HIS* 6.0 4.1 - - + +
568j PHE* 4.8 12.1 - - + -
652j LYS 3.1 13.8 + - - +
653j ALA* 3.4 11.2 - - - +
654j LEU 3.1 0.4 - - - -
655j GLN* 1.3 79.1 - - - +
657j LEU* 1.3 61.2 + - - +
659j ASP* 3.2 20.9 + - + +
660j TYR 4.2 2.9 + - - -
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Residues in contact with LEU 657 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568j PHE* 5.4 6.2 - - + +
653j ALA 3.1 9.0 + - - +
654j LEU* 2.7 20.1 + - - +
656j LEU* 1.3 77.9 - - - +
658j VAL* 1.3 57.8 + - - +
660j TYR 4.9 1.4 + - - -
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Residues in contact with VAL 658 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654j LEU 3.1 7.7 + - - +
655j GLN* 3.0 10.3 + - - +
657j LEU* 1.3 76.9 - - - +
659j ASP* 1.4 65.4 + - - +
660j TYR* 3.4 4.1 + - - -
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Residues in contact with ASP 659 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655j GLN* 2.7 21.0 + - + +
656j LEU* 3.2 17.0 + - - +
658j VAL* 1.4 74.3 - - - +
660j TYR* 1.3 69.4 + - + +
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Residues in contact with TYR 660 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656j LEU 4.2 3.8 + - - -
657j LEU 4.9 1.2 + - - -
658j VAL 3.4 4.9 + - - -
659j ASP* 1.3 86.2 - - + +
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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