Contacts of the helix formed by residues 702 - 721 (chain B) in PDB entry 5WRZ
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 702 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B LYS 3.1 7.7 + - - -
701B LEU* 1.3 76.8 - - - +
703B LYS* 1.3 66.4 + - - +
704B ARG* 3.4 7.7 + - - +
705B GLN* 3.2 39.4 + - - +
706B ILE* 3.1 25.6 + - - +
772B GLU* 4.2 7.4 - - - -
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Residues in contact with LYS 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B SER* 1.3 73.7 - - - +
704B ARG* 1.3 60.7 + - + +
706B ILE* 3.2 9.5 + - - +
707B GLN* 3.0 49.0 + - - +
769B LEU* 4.2 18.8 - - + +
772B GLU* 4.0 30.6 + - - +
773B VAL* 5.7 4.7 - - - -
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Residues in contact with ARG 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B SER* 3.4 8.7 + - - +
703B LYS* 1.3 75.3 - - + +
705B GLN* 1.3 67.9 + - - +
707B GLN* 3.8 17.7 + - + +
708B ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B MET* 4.8 15.9 - - + -
700B LYS 4.9 4.3 - - - +
702B SER* 3.2 35.4 + - - +
704B ARG* 1.3 85.7 - - - +
706B ILE* 1.3 60.5 + - + +
708B ALA* 3.2 6.6 + - - +
709B ALA* 2.9 30.0 + - - +
739B LEU* 3.6 28.7 - - + +
740B ILE* 4.8 4.6 - - + +
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Residues in contact with ILE 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B LEU* 3.9 24.7 - - + -
702B SER 3.1 17.9 + - - +
703B LYS* 3.6 6.3 - - - +
705B GLN* 1.3 76.0 - - + +
707B GLN* 1.3 58.2 + - - +
709B ALA* 3.3 7.4 + - - +
710B TYR* 2.9 55.4 + - + -
740B ILE* 5.3 3.1 - - + -
765B LEU* 3.9 22.2 - - + +
768B LEU* 3.6 35.7 - - + +
769B LEU* 3.9 18.4 - - + +
772B GLU* 4.3 5.8 - - + -
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Residues in contact with GLN 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LYS* 3.0 44.4 + - - +
704B ARG* 3.8 17.0 + - + +
705B GLN 3.3 0.2 - - - -
706B ILE* 1.3 76.5 - - - +
708B ALA* 1.3 62.3 + - - +
710B TYR* 3.4 14.6 + - + +
711B SER* 3.0 25.7 + - - -
769B LEU* 5.4 4.7 - - + +
881B PRO* 5.3 7.4 - - + +
883B GLU* 3.7 34.2 - - + +
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Residues in contact with ALA 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B ARG 2.9 18.8 + - - +
705B GLN* 3.4 9.0 - - - +
707B GLN* 1.3 78.3 - - - +
709B ALA* 1.3 60.5 + - - +
711B SER* 3.3 10.3 + - - -
712B ILE* 3.2 25.8 + - - +
739B LEU* 4.0 17.0 - - + +
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Residues in contact with ALA 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B GLN 2.9 13.5 + - - +
706B ILE 3.5 8.5 - - - +
708B ALA* 1.3 74.5 - - - +
710B TYR* 1.3 64.5 + - - +
712B ILE* 3.4 5.6 + - - +
713B LEU* 3.1 17.8 + - - +
736B PHE* 3.8 22.8 - - + -
739B LEU* 3.8 13.8 - - + +
740B ILE* 4.0 13.9 - - + -
765B LEU* 3.7 22.4 - - + -
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Residues in contact with TYR 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B ILE* 2.9 41.9 + - + -
707B GLN* 3.4 11.4 - - + +
709B ALA* 1.3 73.6 - - - +
711B SER* 1.3 59.7 + - - +
713B LEU* 3.1 8.1 + - + +
714B SER* 2.9 24.1 + - - -
762B ALA* 4.0 5.2 - - - -
765B LEU* 3.4 24.3 + - + +
766B ASP* 2.5 44.2 + - - -
769B LEU* 4.5 8.2 - - + +
881B PRO* 3.7 33.9 - - + +
883B GLU* 3.3 20.7 - - + +
884B ALA* 3.5 26.2 - - + -
885B PRO* 4.0 7.2 - - + +
889B TYR* 3.7 4.7 - - - -
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Residues in contact with SER 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B GLN 3.0 15.8 + - - -
708B ALA* 3.5 11.4 - - - -
709B ALA 3.3 0.2 - - - -
710B TYR* 1.3 74.6 - - - +
712B ILE* 1.3 58.4 + - - +
714B SER* 3.3 5.3 + - - -
715B GLU* 2.8 30.5 + - - +
883B GLU* 3.5 24.1 + - - +
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Residues in contact with ILE 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B ALA 3.2 13.8 + - - +
709B ALA* 3.5 8.3 - - - +
711B SER* 1.3 75.3 - - - +
713B LEU* 1.3 61.9 + - + +
715B GLU* 3.1 9.0 + - + +
716B VAL* 2.9 29.5 + - + +
732B LEU* 3.5 45.5 - - + +
735B ARG* 4.3 24.5 - - + +
736B PHE* 4.1 18.4 - - + +
739B LEU* 4.1 17.3 - - + -
752B LEU* 5.5 0.4 - - + -
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Residues in contact with LEU 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B ALA 3.1 2.9 + - - +
710B TYR* 3.1 11.3 + - - +
712B ILE* 1.3 80.6 - - + +
714B SER* 1.3 57.0 + - - +
716B VAL* 3.2 8.4 + - + +
717B GLN* 3.0 26.3 + - - +
736B PHE* 3.5 29.8 - - + -
752B LEU* 3.7 19.7 - - + -
758B VAL* 3.9 23.2 - - + +
761B LYS* 3.7 14.4 - - + -
762B ALA* 3.6 36.6 - - + +
765B LEU* 3.9 18.8 - - + -
885B PRO* 4.1 13.8 - - + +
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Residues in contact with SER 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B TYR 2.9 8.6 + - - -
711B SER* 3.5 10.5 - - - -
712B ILE 3.2 0.2 - - - -
713B LEU* 1.3 74.6 - - - +
715B GLU* 1.3 59.9 + - - +
717B GLN* 3.4 11.7 + - - +
718B GLN* 2.9 29.1 + - - +
883B GLU 2.7 25.0 + - - -
884B ALA 3.5 0.9 + - - -
885B PRO* 3.3 25.6 - - - +
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Residues in contact with GLU 715 (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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711B SER 2.8 16.8 + - - +
712B ILE* 3.3 14.4 - - + +
714B SER* 1.3 73.4 - - - +
716B VAL* 1.3 61.2 + - - +
718B GLN* 3.3 11.7 + - - +
719B ALA* 2.9 30.5 + - - +
728B GLN* 3.4 24.8 + - - -
732B LEU* 3.8 21.4 - - + +
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Residues in contact with VAL 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B ILE* 2.9 21.5 + - + +
713B LEU* 3.4 12.1 - - + +
714B SER 3.2 0.2 - - - -
715B GLU* 1.3 73.6 - - - +
717B GLN* 1.3 66.7 + - - +
719B ALA* 3.1 4.6 + - - +
720B VAL* 2.8 30.7 + - + +
729B ILE* 4.3 12.8 - - + +
732B LEU* 3.5 34.8 - - + -
733B SER 4.9 0.7 - - - +
752B LEU* 3.6 28.9 - - + +
753B ASN 5.2 0.9 - - - -
758B VAL* 3.7 20.6 - - + -
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Residues in contact with GLN 717 (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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934A HIS* 3.6 25.2 + - + +
981A ASP* 5.2 4.0 + - - +
983A SER* 5.3 2.5 - - - +
713B LEU 3.0 12.6 + - - +
714B SER* 3.4 15.0 + - - +
716B VAL* 1.3 77.8 - - - +
718B GLN* 1.3 73.9 + - - +
720B VAL* 3.5 7.3 + - - +
721B SER* 3.2 22.7 + - - +
758B VAL* 4.9 6.9 - - + +
885B PRO* 3.2 23.0 - - + +
886B VAL* 3.4 3.6 + - - +
887B THR* 2.8 54.1 + - + +
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Residues in contact with GLN 718 (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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934A HIS* 4.7 1.0 - - - -
953A LYS* 4.3 20.1 - - - +
980A ASN 4.5 2.8 + - - -
981A ASP* 4.2 11.9 + - - +
982A THR 2.8 38.8 + - - +
983A SER* 4.8 2.8 - - - -
714B SER 2.9 16.4 + - - +
715B GLU* 3.6 14.1 - - - +
716B VAL 3.2 0.2 - - - -
717B GLN* 1.3 90.8 + - - +
719B ALA* 1.3 64.5 + - - +
721B SER* 3.2 9.7 + - - -
722B GLN* 3.2 32.0 + - - +
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Residues in contact with ALA 719 (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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715B GLU* 2.9 16.8 + - - +
716B VAL 3.6 0.2 - - - +
718B GLN* 1.3 74.0 - - - +
720B VAL* 1.3 66.4 + - - +
722B GLN* 3.0 29.6 + - - +
723B GLY 4.8 1.2 - - - +
725B SER* 5.2 3.0 + - - +
728B GLN* 3.5 23.1 - - + +
729B ILE* 3.2 27.1 - - + -
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Residues in contact with VAL 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B VAL* 2.8 30.3 + - + +
717B GLN* 3.7 7.2 - - - +
719B ALA* 1.3 71.7 - - - +
721B SER* 1.3 60.6 + - - +
722B GLN* 2.6 13.5 + - - -
723B GLY 4.0 8.4 + - - +
726B ASP* 5.9 0.2 - - - +
729B ILE* 3.9 12.7 - - + +
753B ASN 3.8 22.9 - - - +
754B ASN* 4.9 7.9 - - - -
755B ALA 6.0 1.3 - - - +
758B VAL* 6.1 0.9 - - + -
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Residues in contact with SER 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A MET* 5.6 0.3 - - - +
983A SER* 3.2 47.7 + - - +
717B GLN* 3.2 13.9 + - - +
718B GLN* 3.2 13.2 + - - -
719B ALA 3.2 2.0 + - - -
720B VAL* 1.3 75.1 - - - +
722B GLN* 1.4 67.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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