Contacts of the helix formed by residues 682 - 692 (chain B) in PDB entry 5JPM
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 682 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681B VAL* 1.3 80.1 - - - +
683B PHE* 1.3 62.3 + - - +
685B LYS* 3.6 19.1 + - - +
686B ALA* 3.2 25.8 + - - +
742B LEU* 4.9 10.9 - - - +
746B SER* 5.6 5.4 - - - -
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Residues in contact with PHE 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681B VAL 3.2 1.2 - - - +
682B ASN* 1.3 79.3 + - - +
684B GLN* 1.3 75.7 + - - +
686B ALA* 3.5 1.2 + - - +
687B ILE* 3.1 50.7 + - + +
707B VAL* 5.6 1.1 - - + -
739B ALA* 4.4 3.1 - - + -
742B LEU* 3.6 37.0 - - + -
743B ARG* 3.4 45.8 - - + -
746B SER* 4.7 12.8 - - - +
764B GLU* 3.4 54.7 + - + +
765B ASP 4.2 9.2 - - - -
766B LEU* 4.3 3.8 - - + -
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Residues in contact with GLN 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TYR* 3.6 31.7 + - + +
300A GLU* 4.7 0.4 - - - +
681B VAL* 3.0 18.3 + - - +
683B PHE* 1.3 88.9 - - - +
685B LYS* 1.3 62.3 + - - +
687B ILE* 3.5 3.1 + - - +
688B ASN* 3.0 36.3 + - - +
764B GLU* 4.2 10.6 + - - +
765B ASP 2.9 27.5 + - - -
766B LEU* 3.5 11.9 - - - +
767B ILE* 3.1 38.6 + - + +
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Residues in contact with LYS 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ARG* 5.4 10.2 - - - +
300A GLU* 5.4 4.7 + - - +
681B VAL* 3.0 17.0 + - + +
682B ASN* 3.9 17.9 - - - +
683B PHE 3.4 0.2 - - - -
684B GLN* 1.3 77.9 - - - +
686B ALA* 1.3 59.4 + - + +
688B ASN* 3.7 5.8 - - - +
689B GLU* 2.8 51.0 + - + +
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Residues in contact with ALA 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682B ASN* 3.2 19.6 + - - +
685B LYS* 1.3 82.2 - - + +
687B ILE* 1.3 58.7 + - - +
689B GLU* 3.3 10.3 + - - +
690B LYS* 2.9 27.4 + - - +
738B PHE* 3.6 15.9 - - + -
742B LEU* 3.6 27.6 - - + -
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Residues in contact with ILE 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B PHE* 3.1 46.6 + - + +
684B GLN 4.0 2.9 - - - +
686B ALA* 1.3 77.3 - - - +
688B ASN* 1.3 57.0 + - - +
690B LYS* 3.1 6.2 + - + +
691B LEU* 2.8 30.5 + - + +
707B VAL* 4.1 20.6 - - + -
738B PHE* 4.0 13.0 - - + -
739B ALA* 4.2 19.3 - - + -
742B LEU* 3.9 17.9 - - + -
766B LEU* 3.7 35.4 - - + -
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Residues in contact with ASN 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ARG* 5.9 3.0 - - - +
297A ARG* 3.5 47.0 + - - +
300A GLU* 3.5 16.6 + - - -
684B GLN* 3.0 28.6 + - - +
685B LYS* 3.9 4.4 - - - +
687B ILE* 1.3 75.2 - - - +
689B GLU* 1.3 57.3 + - - +
691B LEU* 3.3 17.7 + - - +
692B GLY* 2.9 24.6 + - - -
766B LEU* 3.6 19.8 - - - +
767B ILE 5.2 1.5 + - - +
769B GLU* 4.2 12.1 + - - +
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Residues in contact with GLU 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ARG* 5.3 3.1 - - - +
685B LYS* 2.8 45.4 + - + +
686B ALA* 3.5 9.8 - - - +
687B ILE 3.2 0.2 - - - -
688B ASN* 1.3 77.7 - - - +
690B LYS* 1.3 61.8 + - - +
692B GLY* 3.4 9.4 + - - +
693B GLN* 3.7 17.5 + - - +
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Residues in contact with LYS 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B ALA 2.9 13.3 + - - +
687B ILE* 3.1 10.3 + - + +
689B GLU* 1.3 74.8 - - - +
691B LEU* 1.3 63.4 + - - +
693B GLN* 3.2 52.2 + - - +
694B TYR* 3.6 13.9 + - - -
703B CYS* 4.5 1.3 - - - -
707B VAL* 5.8 1.8 - - + -
734B SER* 2.9 37.5 + - - -
735B CYS* 3.9 30.1 - - + +
738B PHE* 3.8 35.1 - - + +
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Residues in contact with LEU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B ILE* 2.8 21.4 + - + +
688B ASN* 3.3 25.3 + - - +
690B LYS* 1.3 76.0 - - - +
692B GLY* 1.3 62.8 + - - +
694B TYR* 3.1 16.4 + - - +
700B LYS* 3.1 49.3 + - + +
703B CYS* 3.5 28.7 - - + -
704B GLN* 4.1 13.9 - - + +
707B VAL* 5.8 0.7 - - + -
766B LEU* 4.1 22.2 - - + -
769B GLU* 5.3 10.5 - - + +
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Residues in contact with GLY 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688B ASN 2.9 15.9 + - - -
689B GLU* 3.4 5.8 + - - -
690B LYS 3.2 0.8 - - - -
691B LEU* 1.3 75.9 - - - +
693B GLN* 1.3 60.3 + - - +
694B TYR 3.2 4.6 + - - +
695B ALA* 5.5 0.9 - - - +
700B LYS* 4.3 6.9 + - - -
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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