Contacts of the strand formed by residues 786 - 798 (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 VAL 786 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 3.8 29.8 - - + -
199A GLN* 3.3 27.4 - - - +
598A LEU* 3.8 37.5 - - + -
599A VAL 3.3 12.3 - - - +
600A ALA* 4.2 3.6 - - + +
785B ARG* 1.3 76.7 - - - +
787B GLU* 1.3 72.4 + - - +
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Residues in contact with GLU 787 (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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591A LEU* 4.9 4.9 - - + -
598A LEU* 3.6 2.2 - - - -
599A VAL* 2.8 37.4 + - - +
601A LEU* 5.3 1.8 - - + -
785B ARG* 2.6 53.6 + - + +
786B VAL* 1.3 82.5 - - - +
788B THR* 1.3 64.5 + - - +
789B VAL* 3.4 8.8 + - + +
793B GLN* 4.2 18.2 - - - +
795B LEU* 4.3 20.4 - - + +
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Residues in contact with THR 788 (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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597A ALA 3.6 5.8 - - - +
598A LEU* 3.6 24.9 - - + -
786B VAL 4.5 0.2 + - - -
787B GLU* 1.3 72.3 + - - +
789B VAL* 1.3 60.4 + - - +
790B ASP 4.2 0.5 + - - -
793B GLN* 2.8 21.1 + - - +
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Residues in contact with VAL 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A LEU* 3.8 33.9 - - + +
593A THR* 3.7 18.0 - - + +
595A SER 3.5 4.5 - - - +
596A LEU* 3.3 3.2 - - - -
597A ALA 2.9 31.4 + - - +
599A VAL* 3.7 27.4 - - + -
787B GLU 3.8 6.1 - - - +
788B THR* 1.3 77.7 - - - +
790B ASP* 1.3 60.6 + - - +
792B PHE* 3.9 6.5 - - - -
793B GLN* 3.7 35.9 - - + +
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Residues in contact with ASP 790 (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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595A SER 4.8 0.2 - - - -
596A LEU* 3.9 23.9 + - + +
788B THR 4.2 1.6 + - - -
789B VAL* 1.3 71.3 - - - +
791B ARG* 1.3 65.5 + - - +
792B PHE* 2.5 29.5 + - - +
793B GLN* 4.8 2.8 - - - +
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Residues in contact with ARG 791 (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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592A GLU* 3.5 1.2 - - - +
593A THR* 2.7 49.9 + - - +
594A ASP* 2.7 49.2 + - - +
595A SER* 3.7 14.3 + - - +
789B VAL 3.8 0.4 + - - -
790B ASP* 1.3 77.4 + - - +
792B PHE* 1.3 82.2 + - + +
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Residues in contact with PHE 792 (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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591A LEU 3.1 12.8 - - - +
592A GLU* 3.7 26.7 - - + +
789B VAL* 3.9 3.6 - - - -
790B ASP 2.5 18.0 + - - +
791B ARG* 1.3 96.8 - - + +
793B GLN* 1.3 66.8 + - - +
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Residues in contact with GLN 793 (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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590A HIS* 3.7 1.5 - - - +
591A LEU* 2.7 45.9 + - + +
787B GLU* 4.2 14.7 - - - +
788B THR 2.8 28.6 + - - +
789B VAL* 3.7 21.8 - - + +
790B ASP 4.8 1.8 - - - +
792B PHE* 1.3 78.6 - - - +
794B ILE* 1.3 68.1 + - - +
795B LEU* 3.3 24.6 - - + +
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Residues in contact with ILE 794 (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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588A LYS* 4.0 40.6 - - + +
589A LEU 3.4 11.4 - - - +
590A HIS* 3.5 32.3 - - + +
793B GLN* 1.3 82.0 - - - +
795B LEU* 1.3 69.8 + - - +
796B THR* 4.2 1.5 + - - +
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Residues in contact with LEU 795 (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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588A LYS* 3.3 4.2 - - - -
589A LEU* 2.9 39.3 + - + +
591A LEU* 3.7 29.8 - - + -
601A LEU* 4.0 17.9 - - + -
783B LEU* 4.7 12.1 - - + -
785B ARG* 5.0 8.3 - - - +
787B GLU* 4.3 21.3 - - + +
793B GLN* 3.3 24.5 - - - +
794B ILE* 1.3 79.5 - - - +
796B THR* 1.3 61.7 + - - +
797B LEU* 3.7 19.8 + - + +
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Residues in contact with THR 796 (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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586A SER* 4.7 8.0 + - - -
587A VAL 4.1 2.7 - - - -
588A LYS* 4.1 19.5 - - - +
794B ILE* 4.1 2.6 + - - +
795B LEU* 1.3 70.3 - - - +
797B LEU* 1.3 69.0 + - - +
798B TRP* 4.1 29.0 - - + -
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Residues in contact with LEU 797 (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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586A SER* 3.3 6.7 - - - -
587A VAL* 2.7 52.4 + - + +
589A LEU* 4.2 21.5 - - + -
782B TRP* 4.4 12.8 - - + -
783B LEU* 3.6 46.0 - - + -
785B ARG* 4.2 13.2 - - - +
795B LEU* 3.8 20.9 - - + +
796B THR* 1.3 84.0 + - - +
798B TRP* 1.3 67.8 + - - +
808B ILE* 5.6 1.6 - - + -
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Residues in contact with TRP 798 (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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584A GLY* 3.9 16.4 - - - +
586A SER* 3.1 28.2 + - - +
587A VAL* 4.8 0.2 - - - -
782B TRP* 4.9 4.9 - - - -
796B THR* 4.1 29.2 - - + -
797B LEU* 1.3 81.3 - - + +
799B LEU* 1.3 62.8 + - - +
800B PRO* 3.3 10.0 - - - +
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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