Contacts of the helix formed by residues 696 - 708 (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 SER 696 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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694B TYR 3.5 0.2 - - - -
695B ALA* 1.3 77.9 - - - +
697B PRO* 1.3 71.4 - - - +
698B THR* 3.4 15.6 + - - -
699B ALA* 3.2 15.9 + - - +
700B LYS* 2.9 30.0 + - - +
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Residues in contact with PRO 697 (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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695B ALA 3.7 4.2 - - - +
696B SER* 1.3 86.7 - - - +
698B THR* 1.3 62.1 + - - +
700B LYS* 3.8 11.6 - - + +
701B ARG* 3.0 29.8 + - - +
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Residues in contact with THR 698 (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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696B SER* 3.2 10.6 + - - -
697B PRO* 1.3 81.6 - - - +
699B ALA* 1.3 58.6 + - - +
701B ARG* 3.4 4.5 + - - +
702B CYS* 3.0 41.7 + - - -
727B ASP* 5.6 5.4 - - + +
728B CYS* 5.4 3.8 - - + -
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Residues in contact with ALA 699 (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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694B TYR* 3.6 33.2 - - + +
696B SER* 3.2 18.7 + - - +
698B THR* 1.3 78.1 - - - +
700B LYS* 1.3 60.8 + - - +
702B CYS* 3.5 1.6 + - - +
703B CYS* 2.8 31.0 + - - +
727B ASP 6.0 0.7 - - - +
731B PRO* 4.2 17.2 - - + +
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Residues in contact with LYS 700 (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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691B LEU* 3.1 34.4 + - + +
692B GLY* 4.3 5.7 + - - -
694B TYR* 2.8 30.1 + - + +
695B ALA* 4.0 13.9 - - - +
696B SER 2.9 17.5 + - - +
697B PRO* 3.8 10.5 - - + +
698B THR 3.3 0.2 - - - -
699B ALA* 1.3 77.0 - - - +
701B ARG* 1.3 53.0 + - - +
703B CYS* 3.2 6.1 + - - +
704B GLN* 2.7 39.5 + - - +
769B GLU* 6.1 0.7 - - - +
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Residues in contact with ARG 701 (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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697B PRO 3.0 17.4 + - - +
698B THR* 3.9 5.2 - - - +
700B LYS* 1.3 76.3 - - - +
702B CYS* 1.3 60.9 + - - +
704B GLN* 3.4 23.7 + - - +
705B ASP* 3.0 51.5 + - - +
770B ASP* 3.1 40.0 + - - -
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Residues in contact with CYS 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B THR* 3.0 29.8 + - - +
699B ALA 3.9 3.6 - - - +
701B ARG* 1.3 79.8 - - - +
703B CYS* 1.3 60.2 + - - +
705B ASP* 3.7 5.6 + - - -
706B GLY 3.4 2.3 + - - -
728B CYS* 2.0 64.4 - - - +
731B PRO* 4.1 7.6 - - + -
732B PHE* 3.1 32.6 - - - -
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Residues in contact with CYS 703 (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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690B LYS* 4.5 5.6 - - - -
691B LEU* 3.5 24.5 - - + -
694B TYR* 4.1 14.4 - - + -
699B ALA 2.8 19.6 + - - +
700B LYS* 3.6 3.8 - - - +
702B CYS* 1.3 75.3 - - - +
704B GLN* 1.3 60.1 + - - +
706B GLY* 3.0 16.1 + - - -
707B VAL* 3.2 16.2 + - - +
731B PRO* 4.3 4.7 - - + +
732B PHE 4.8 0.4 - - - +
735B CYS* 2.0 50.8 - - - +
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Residues in contact with GLN 704 (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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691B LEU* 4.1 11.8 - - + +
700B LYS* 2.7 23.2 + - - +
701B ARG* 3.7 26.1 + - - +
703B CYS* 1.3 73.8 - - - +
705B ASP* 1.3 61.9 + - - +
707B VAL* 3.2 15.2 - - - +
708B THR* 3.0 24.0 + - - +
766B LEU* 4.2 19.3 - - + -
768B ASP* 3.3 27.1 + - - +
769B GLU* 5.4 4.5 + - - +
770B ASP* 3.2 26.6 + - - +
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Residues in contact with ASP 705 (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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701B ARG* 3.0 37.5 + - - +
702B CYS* 3.9 5.2 - - - +
703B CYS 3.2 0.2 - - - -
704B GLN* 1.3 79.4 - - - +
706B GLY* 1.3 55.7 + - - +
708B THR* 3.5 11.9 + - - +
719B ARG* 2.7 31.3 + - - +
728B CYS* 6.1 0.3 - - - -
732B PHE* 3.5 16.6 - - + -
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Residues in contact with GLY 706 (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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702B CYS 3.4 5.2 + - - -
703B CYS 3.0 8.6 + - - -
705B ASP* 1.3 80.3 - - - +
707B VAL* 1.3 60.8 + - - +
708B THR 3.4 0.7 + - - +
719B ARG* 3.5 15.9 + - - -
732B PHE* 3.4 26.0 - - - -
736B CYS* 3.6 27.4 - - - +
739B ALA* 4.7 1.0 - - - +
743B ARG* 5.3 0.7 + - - -
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Residues in contact with VAL 707 (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* 6.1 1.1 - - + -
687B ILE* 4.1 24.0 - - + -
690B LYS* 5.8 2.7 - - + -
691B LEU* 5.8 0.4 - - + -
703B CYS* 3.5 15.9 - - - +
704B GLN* 3.2 20.2 - - - +
706B GLY* 1.3 73.4 - - - +
708B THR* 1.3 61.0 + - - +
709B ARG 3.4 0.2 + - - -
735B CYS* 3.9 23.1 - - + +
738B PHE* 6.0 0.2 - - + -
739B ALA* 3.7 16.6 - - + -
743B ARG* 2.8 32.8 + - - +
766B LEU* 3.8 35.3 + - + -
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Residues in contact with THR 708 (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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704B GLN* 3.0 17.5 + - - +
705B ASP* 3.7 12.8 - - - -
706B GLY 3.2 1.0 - - - +
707B VAL* 1.3 81.2 - - - +
709B ARG* 1.3 71.3 + - + +
719B ARG* 2.8 34.9 + - - +
743B ARG* 4.5 0.4 - - - +
766B LEU* 5.9 2.9 - - - +
768B ASP* 5.6 1.4 + - - -
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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