Contacts of the helix formed by residues 712 - 727 (chain B) in PDB entry 2WSF
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 HIS 712 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B VAL* 3.0 47.3 + - + +
659B THR* 3.5 22.9 - - + +
660B GLY* 4.3 6.3 - - - -
663B PHE* 4.6 10.4 - + - -
708B VAL* 2.5 46.2 - - + +
709B GLY* 4.1 2.9 - - - -
710B LEU 2.6 1.5 - - - +
711B VAL* 1.3 75.5 - - - +
713B PHE* 1.3 65.3 + - - +
714B SER* 3.0 3.2 + - - +
715B VAL* 4.0 5.6 - - - -
716B GLY 3.5 5.9 + - - -
841B CLA 3.1 64.7 + + + +
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Residues in contact with PHE 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 5.3 2.7 - - + -
694A PHE* 4.4 17.3 - + - -
850A CLA 3.9 22.0 - - + -
581B PHE* 3.4 40.6 - + + -
584B LEU* 3.5 28.0 - - + -
657B TRP* 3.3 59.7 - + - +
660B GLY* 4.5 1.0 - - - -
661B PHE* 5.1 4.9 - + - -
664B LEU* 4.6 6.5 - - + -
709B GLY 4.3 2.4 - - - -
710B LEU* 3.2 27.2 - - + +
712B HIS* 1.3 77.8 - - - +
714B SER* 1.3 57.3 + - - +
717B TYR* 3.1 29.3 + + - +
850B CLA 4.2 4.7 - - - -
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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
----------------------------------------------------------
381B PHE* 4.6 2.7 - - - -
580B VAL* 5.3 1.9 - - - +
584B LEU* 4.0 23.9 - - - +
710B LEU* 3.7 21.0 - - - +
711B VAL 4.1 4.0 - - - -
712B HIS 3.0 2.0 - - - +
713B PHE* 1.3 76.2 - - - +
715B VAL* 1.3 54.1 + - - -
717B TYR* 3.1 6.8 + - - +
718B ILE* 2.5 41.1 + - - +
848B LMG 3.8 34.1 - - - +
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Residues in contact with VAL 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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652B PHE* 4.2 13.0 - - + -
656B VAL* 3.6 21.8 - - + -
711B VAL 4.0 6.7 - - - +
712B HIS* 3.9 11.7 - - - +
714B SER* 1.3 69.2 - - - +
716B GLY* 1.3 62.7 + - - +
718B ILE* 2.8 12.2 + - + +
719B PHE* 2.3 71.0 + - + +
830B CLA 5.7 9.9 - - + -
841B CLA 3.9 17.3 - - + -
848B LMG 4.8 13.7 - - + +
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Residues in contact with GLY 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B GLY* 3.3 22.1 - - - -
656B VAL* 3.6 17.6 - - - +
657B TRP* 3.7 6.7 - - - -
712B HIS 3.5 5.0 + - - -
714B SER 3.4 0.6 - - - -
715B VAL* 1.3 86.6 - - - +
717B TYR* 1.3 49.8 + - - +
719B PHE* 3.5 1.9 - - - -
720B THR* 2.3 39.6 + - - -
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Residues in contact with TYR 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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850A CLA 4.8 3.1 - - + -
377B TYR* 2.9 30.4 + + - -
584B LEU* 2.4 58.8 + - + -
585B ASN* 4.1 1.9 + - - -
588B GLY* 4.1 10.9 - - - -
592B PHE* 5.6 0.5 - - - -
657B TRP* 3.7 13.9 - - + -
713B PHE* 3.1 23.4 + + - +
714B SER 3.1 4.9 + - - +
716B GLY* 1.3 73.9 - - - +
718B ILE* 1.3 62.5 + - - +
720B THR* 3.3 14.0 + - - -
721B TYR 3.5 2.1 + - - -
850B CLA 3.1 89.4 - - + +
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Residues in contact with ILE 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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377B TYR* 3.6 33.4 - - + -
381B PHE* 4.8 6.1 - - + -
584B LEU* 5.5 0.4 - - + -
714B SER* 2.5 36.4 + - - +
715B VAL* 3.5 15.3 - - - +
717B TYR* 1.3 75.2 - - + +
719B PHE* 1.3 59.0 + - + +
720B THR 3.3 1.1 - - - -
721B TYR* 5.0 1.3 - - - +
722B ALA* 3.2 20.0 + - - +
828B CLA 3.3 68.2 - - + +
848B LMG 3.8 16.2 - - + -
850B CLA 5.3 0.2 - - - -
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Residues in contact with PHE 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B MET* 3.5 37.3 - - - +
652B PHE* 4.0 20.6 - + + -
653B GLY* 4.7 1.8 - - - -
715B VAL* 2.3 60.9 + - + +
716B GLY* 3.5 3.4 - - - +
718B ILE* 1.3 72.5 - - + +
720B THR* 1.3 59.5 + - - +
722B ALA* 3.8 5.9 - - - +
723B ALA* 3.4 20.6 + - - +
810B CLA 3.9 26.0 - - + -
828B CLA 3.2 50.0 - - + -
830B CLA 5.2 7.6 - - + -
847B BCR 4.4 12.8 - - + -
848B LMG 5.2 3.1 - - + -
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Residues in contact with THR 720 (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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650B PHE* 3.4 35.2 - - + +
653B GLY* 2.9 20.5 + - - -
654B HIS* 3.7 18.6 - - + +
716B GLY 2.3 27.7 + - - -
717B TYR* 3.3 5.7 + - - -
719B PHE* 1.3 76.6 - - - +
721B TYR* 1.3 51.9 + - - +
723B ALA* 3.1 5.1 + - - +
724B PHE* 2.5 34.8 + - - +
850B CLA 3.0 28.2 - - + +
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Residues in contact with TYR 721 (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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373B THR* 4.9 8.5 - - + -
377B TYR* 5.1 7.0 - + + +
591B THR* 3.8 30.6 - - + -
592B PHE* 3.0 37.7 + + - -
595B HIS* 3.6 9.7 - + - -
623B TYR* 2.7 24.0 + - - -
717B TYR 3.5 4.6 + - - +
718B ILE* 4.9 2.7 - - - +
720B THR* 1.3 70.3 - - - +
722B ALA* 1.3 67.7 + - - +
724B PHE* 3.7 18.6 - + - -
725B LEU* 2.8 47.9 + - + +
828B CLA 4.8 5.4 - - + -
850B CLA 2.5 55.5 + + - +
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Residues in contact with ALA 722 (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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646B TRP* 4.6 1.3 - - - -
649B MET* 4.8 1.8 - - + -
718B ILE 3.2 22.6 + - - +
719B PHE* 3.8 8.5 - - - +
721B TYR* 1.3 80.6 - - - +
723B ALA* 1.3 60.4 + - - +
725B LEU* 3.8 4.8 - - - +
726B ILE* 3.2 31.9 - - - +
828B CLA 3.7 48.7 - - + +
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Residues in contact with ALA 723 (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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646B TRP* 3.4 36.4 - - + +
649B MET* 3.5 21.3 - - + +
650B PHE* 4.0 9.2 - - + +
719B PHE 3.4 11.1 + - - +
720B THR 3.1 4.7 + - - +
722B ALA* 1.3 78.4 - - - +
724B PHE* 1.3 62.4 + - - +
727B ALA* 2.8 33.1 + - - +
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Residues in contact with PHE 724 (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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595B HIS* 4.4 5.8 - - - -
623B TYR* 3.6 37.0 - + - -
624B LEU* 4.5 6.3 - - - -
627B ASN* 3.1 27.6 - - + -
628B SER* 3.5 6.3 - - - -
631B LEU* 4.4 7.4 - - + -
650B PHE* 4.0 17.0 - + + -
720B THR 2.5 25.6 + - - +
721B TYR* 3.0 21.7 + + - +
723B ALA* 1.3 71.0 - - - +
725B LEU* 1.3 70.4 + - - +
727B ALA* 2.9 13.5 + - - +
728B SER* 3.1 29.6 + - - -
850B CLA 3.1 47.6 - - + -
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Residues in contact with LEU 725 (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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366B THR* 5.3 1.6 - - + +
369B ALA* 2.6 45.1 - - + +
370B ALA* 4.0 10.5 - - + +
373B THR* 5.3 2.5 - - + +
595B HIS* 3.6 36.1 - - + +
721B TYR* 2.8 47.0 + - + +
722B ALA 3.8 7.4 - - - +
724B PHE* 1.3 74.2 - - - +
726B ILE* 1.3 65.8 + - + +
728B SER* 2.8 8.1 + - - -
729B THR* 2.6 40.1 + - - +
828B CLA 4.4 12.6 - - + -
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Residues in contact with ILE 726 (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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117B TYR* 4.1 20.0 - - + +
366B THR* 5.0 4.0 - - + -
370B ALA* 4.1 20.4 - - + -
643B LEU* 4.9 0.6 - - + +
646B TRP* 3.3 53.2 - - + +
722B ALA* 3.2 21.5 - - - +
724B PHE 3.4 0.6 - - - -
725B LEU* 1.3 81.5 - - + +
727B ALA* 1.3 53.4 + - - +
728B SER 2.7 15.1 + - - -
729B THR* 3.6 5.4 + - - +
730B SER* 2.5 36.0 + - - +
828B CLA 3.6 21.3 - - + +
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Residues in contact with ALA 727 (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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630B GLN* 4.1 3.6 - - - +
631B LEU* 3.6 42.1 + - + +
643B LEU* 4.0 18.5 - - + +
646B TRP* 3.7 20.6 - - + -
723B ALA 2.8 23.1 + - - +
724B PHE 2.9 5.1 + - - +
726B ILE* 1.3 76.1 - - - +
728B SER* 1.3 63.2 + - - +
730B SER* 4.9 2.0 - - - -
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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
------------------------------------------------------------
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