Contacts of the helix formed by residues 648 - 661 (chain C) in PDB entry 1JPW
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 ASN 648 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608C GLU* 3.5 40.9 + - - +
609C ASN* 5.3 2.0 + - - +
612C ARG* 4.8 7.6 - - - +
646C SER* 2.8 16.3 + - - +
647C ARG* 1.3 76.4 - - - +
649C GLU* 1.3 65.2 + - - +
650C GLY* 2.8 30.8 + - - -
651C VAL* 3.1 18.9 + - + +
652C ALA* 3.0 20.8 + - - +
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Residues in contact with GLU 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646C SER 5.2 0.2 - - - -
647C ARG 3.3 8.0 + - - +
648C ASN* 1.3 70.4 + - - +
650C GLY* 1.3 51.4 + - - +
652C ALA* 3.3 6.4 + - - +
653C THR* 2.6 47.4 + - - +
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Residues in contact with GLY 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612C ARG* 4.0 20.2 - - - -
648C ASN* 2.8 15.6 + - - -
649C GLU* 1.3 70.8 - - - +
651C VAL* 1.3 67.7 + - - +
653C THR* 3.1 7.7 + - - -
654C TYR* 3.1 25.6 + - - +
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Residues in contact with VAL 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C GLU* 3.8 15.5 - - + +
611C GLN* 3.5 28.9 - - + +
612C ARG* 4.0 15.7 - - + +
615C ALA* 4.7 2.8 - - + +
643C LEU* 3.6 43.1 - - + +
646C SER* 3.7 6.1 - - - +
648C ASN* 3.1 30.7 + - + +
650C GLY* 1.3 73.0 - - - +
652C ALA* 1.3 59.0 + - - +
654C TYR* 3.4 2.2 + - - +
655C ALA* 2.8 30.9 + - - +
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Residues in contact with ALA 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643C LEU 3.6 12.1 + - - +
644C LEU* 3.8 21.5 - - - +
646C SER* 3.9 13.0 - - - +
648C ASN 3.0 9.6 + - - +
649C GLU* 3.5 10.8 - - - +
651C VAL* 1.3 80.3 - - - +
653C THR* 1.3 63.2 + - - +
655C ALA* 3.5 1.1 - - - +
656C ALA* 2.9 26.2 + - - +
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Residues in contact with THR 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C GLU* 2.6 33.6 + - - +
650C GLY* 3.1 7.3 + - - -
652C ALA* 1.3 74.1 - - - +
654C TYR* 1.3 70.6 + - + +
656C ALA* 3.6 5.6 + - - +
657C ALA* 3.2 19.3 + - + +
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Residues in contact with TYR 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C HIS* 3.4 37.3 + + - -
582C ARG* 5.9 1.4 + - - -
612C ARG* 3.7 23.3 - - + +
615C ALA* 3.6 21.3 - - + +
616C GLY* 3.5 16.6 - - - -
619C CYS* 3.8 30.1 - - + -
620C GLU* 5.7 2.1 + - + +
650C GLY* 3.1 15.2 + - - +
651C VAL* 4.0 0.4 - - - +
653C THR* 1.3 85.7 - - + +
655C ALA* 1.3 67.8 + - - +
657C ALA* 2.9 5.7 + - + +
658C VAL* 2.8 27.2 + - - +
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Residues in contact with ALA 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C ALA* 4.1 2.6 - - + +
640C LEU* 3.7 34.0 - - + +
643C LEU* 4.0 24.5 - - + +
644C LEU* 4.2 4.3 - - - +
651C VAL* 2.8 19.5 + - + +
652C ALA 3.5 4.5 - - - +
654C TYR* 1.3 79.1 - - - +
656C ALA* 1.3 64.8 + - - +
658C VAL* 3.2 2.1 + - - +
659C LEU* 3.2 24.0 + - - +
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Residues in contact with ALA 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C LEU* 3.6 23.2 - - + +
652C ALA 2.9 17.0 + - - +
653C THR* 3.6 6.1 - - - +
655C ALA* 1.3 77.3 - - - +
657C ALA* 1.3 62.7 + - - +
659C LEU* 3.4 5.7 + - - +
660C PHE* 3.0 22.2 + - - +
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Residues in contact with ALA 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C CYS* 3.7 25.1 - - - -
653C THR* 3.2 12.3 + - + +
654C TYR* 2.9 14.8 + - + +
656C ALA* 1.3 75.7 - - - +
658C VAL* 1.3 67.0 + - - +
660C PHE* 2.8 20.4 + - - +
661C ARG* 3.0 20.6 + - + +
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Residues in contact with VAL 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C ALA 3.2 29.6 - - - +
618C LEU* 3.9 24.5 - - + +
619C CYS* 3.5 15.7 - - - +
622C ALA* 4.7 5.3 - - + +
631C ILE* 4.7 2.9 - - + -
640C LEU* 3.3 27.8 - - + -
654C TYR 2.8 19.1 + - - +
655C ALA 3.8 1.3 - - - +
657C ALA* 1.3 72.5 - - - +
659C LEU* 1.3 64.3 + - - +
661C ARG* 3.6 3.3 + - - +
662C MET* 3.0 49.7 + - + +
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Residues in contact with LEU 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637C THR* 4.0 29.6 - - + +
640C LEU* 3.4 32.5 - - + +
641C THR* 4.4 5.8 - - - +
644C LEU* 3.5 40.8 - - + -
655C ALA 3.2 11.1 + - - +
656C ALA* 3.5 7.2 - - - +
658C VAL* 1.3 79.1 - - - +
660C PHE* 1.3 64.9 + - - +
662C MET* 3.1 20.8 - - - +
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Residues in contact with PHE 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C ALA 3.0 13.6 + - - +
657C ALA* 2.8 12.4 + - - +
659C LEU* 1.3 73.6 - - - +
661C ARG* 1.3 75.5 + - + +
662C MET* 2.5 22.4 + - - -
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Residues in contact with ARG 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C CYS* 3.0 49.0 + - - +
620C GLU* 4.3 2.8 + - - -
622C ALA* 3.3 28.5 - - + +
623C GLN* 3.2 42.8 - - - +
624C ASP 4.7 0.9 - - - +
628C ALA* 3.4 7.3 - - - +
657C ALA* 3.0 18.5 + - + +
658C VAL* 3.8 3.6 - - - +
660C PHE* 1.3 90.5 - - + +
662C MET* 1.3 57.8 + - - +
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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
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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