Contacts of the helix formed by residues 698 - 717 (chain B) in PDB entry 2XWU
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 ASP 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B LYS* 4.4 6.1 - - - +
695B TRP* 2.8 37.1 + - + +
697B ASN* 1.3 79.4 - - - +
699B ALA* 1.3 59.2 + - - +
700B GLN* 2.8 36.7 + - - +
701B VAL* 3.8 22.0 - - + +
702B VAL* 2.8 36.6 + - - +
738B ILE* 4.0 1.6 - - - -
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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
----------------------------------------------------------
697B ASN 3.8 1.6 + - - -
698B ASP* 1.3 74.4 + - - +
700B GLN* 1.3 70.9 + - + +
703B GLU* 3.4 22.4 + - - +
738B ILE* 3.3 26.1 - - + +
740B GLN* 3.5 13.6 + - - +
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Residues in contact with GLN 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B LYS* 6.4 1.6 - - + -
638B VAL* 4.1 13.6 - - + +
698B ASP* 2.8 14.5 + - - +
699B ALA* 1.3 84.0 - - + +
701B VAL* 1.3 59.8 + - + +
703B GLU* 3.7 5.5 + - - +
704B ALA* 3.5 19.6 + - - +
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Residues in contact with VAL 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B LYS* 4.8 7.2 - - + +
637B ILE* 5.3 5.2 - - + -
638B VAL* 3.9 22.2 - - + -
641B LEU* 4.6 7.2 - - + -
691B VAL* 4.2 15.3 - - + -
692B LEU* 6.3 0.9 - - + -
695B TRP* 3.7 48.9 - - + +
698B ASP* 3.5 20.0 + - + +
699B ALA 3.3 0.2 - - - -
700B GLN* 1.3 74.4 - - + +
702B VAL* 1.3 66.8 + - - +
703B GLU 3.0 3.5 + - - -
704B ALA* 3.2 10.5 + - - +
705B VAL* 3.2 22.1 + - + +
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Residues in contact with VAL 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LEU* 6.5 0.9 - - - -
695B TRP 4.6 4.0 + - - +
696B LEU* 4.6 8.3 - - + +
698B ASP 2.8 24.6 + - - +
699B ALA 4.2 2.2 - - - +
701B VAL* 1.3 74.0 - - - +
703B GLU* 1.3 58.9 + - - +
705B VAL* 4.0 7.7 - - - +
706B CYS* 3.5 17.8 + - - +
734B MET* 4.1 18.8 - - + +
738B ILE* 3.7 27.4 - - + -
740B GLN* 4.4 6.3 - - - +
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Residues in contact with GLU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B ALA 3.4 12.9 + - - +
700B GLN* 4.2 5.8 - - - +
701B VAL 3.0 1.0 - - - -
702B VAL* 1.3 78.8 - - - +
704B ALA* 1.3 54.8 + - - +
705B VAL 3.1 1.6 - - - -
706B CYS* 3.1 4.4 + - - +
707B ALA* 2.8 33.3 + - - +
740B GLN* 2.8 32.9 + - - +
742B SER* 3.4 29.7 + - - +
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Residues in contact with ALA 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B VAL* 4.3 18.2 - - + +
641B LEU* 3.8 25.9 - - + +
642B GLY* 5.4 2.6 - - - +
645B SER* 4.8 1.0 + - - -
700B GLN 3.5 13.1 + - - +
701B VAL 3.2 8.0 + - - +
703B GLU* 1.3 77.6 - - - +
705B VAL* 1.3 60.9 + - - +
707B ALA* 3.5 9.2 + - - +
708B ILE* 3.2 26.2 + - - +
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Residues in contact with VAL 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 3.7 23.1 - - + -
688B ILE* 5.2 6.5 - - + -
691B VAL* 5.4 3.8 - - + -
692B LEU* 3.9 20.9 - - + -
701B VAL* 3.2 24.0 + - + +
702B VAL* 4.0 7.0 - - - +
703B GLU 3.1 0.2 - - - -
704B ALA* 1.3 75.8 - - - +
706B CYS* 1.3 65.3 + - - +
708B ILE* 3.3 18.9 + - + +
709B PHE* 3.4 16.5 + - + -
730B MET* 3.4 33.2 - - + -
734B MET* 4.4 5.8 - - - -
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Residues in contact with CYS 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B VAL 3.5 14.3 + - - +
703B GLU* 3.1 13.4 + - + +
705B VAL* 1.3 80.8 - - - +
707B ALA* 1.3 57.3 + - - +
709B PHE* 3.0 9.9 + - - +
710B GLU* 2.9 29.1 + - - +
731B LEU* 4.9 4.9 - - - -
734B MET* 4.9 8.3 - - - -
740B GLN* 5.5 0.2 - - - +
742B SER* 3.4 44.2 - - - +
743B ALA* 3.9 11.0 - - - -
746B LEU* 4.1 13.9 - - - +
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B SER* 3.8 13.7 - - - +
703B GLU 2.8 16.3 + - - +
704B ALA* 3.5 10.3 - - - +
706B CYS* 1.3 73.4 - - - +
708B ILE* 1.3 65.1 + - - +
710B GLU* 3.7 18.6 - - - +
711B LYS* 3.1 33.9 + - + +
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Residues in contact with ILE 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 3.4 58.6 - - + +
644B LEU* 4.1 15.0 - - + -
645B SER* 3.6 13.9 - - - +
648B PHE* 4.7 15.2 - - + -
681B LEU* 4.9 6.1 - - + -
684B VAL* 6.1 6.1 - - + -
704B ALA 3.2 11.8 + - - +
705B VAL* 3.5 11.7 - - + +
706B CYS 3.3 0.4 - - - -
707B ALA* 1.3 76.6 - - - +
709B PHE* 1.3 65.5 + - + +
711B LYS* 4.3 1.2 - - - +
712B SER* 2.5 40.8 + - - +
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Residues in contact with PHE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B LEU* 4.3 21.1 - - + -
685B PHE* 4.1 24.9 - + + -
688B ILE* 5.3 5.8 - - + -
705B VAL* 3.4 19.2 + - + -
706B CYS* 3.0 8.7 + - - +
708B ILE* 1.3 87.2 - - + +
710B GLU* 1.3 59.3 + - - +
712B SER* 3.7 1.5 - - - -
713B VAL* 2.9 34.7 + - - +
720B PHE* 4.1 21.3 - + - -
723B MET* 4.5 9.6 - - + -
727B LEU* 3.3 28.9 - - + -
730B MET* 3.3 31.2 - - + -
734B MET* 5.1 2.9 - - + -
746B LEU* 3.8 16.6 - - + -
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Residues in contact with GLU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B CYS* 2.9 17.2 + - - +
707B ALA* 3.6 18.8 - - - +
709B PHE* 1.3 78.7 - - - +
711B LYS* 1.3 88.5 + - + +
713B VAL* 3.3 2.6 + - - +
714B LYS* 3.1 59.2 + - - +
742B SER* 6.2 0.3 - - - -
746B LEU* 4.0 19.2 - - + +
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Residues in contact with LYS 711 (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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645B SER* 3.5 25.1 - - - +
648B PHE* 3.4 5.6 - - + +
649B THR* 3.3 38.0 + - + +
707B ALA* 3.1 18.9 + - - +
708B ILE 4.5 1.6 - - - +
710B GLU* 1.3 102.5 + - + +
712B SER* 1.3 61.4 + - - +
714B LYS* 3.9 15.5 - - + +
715B THR* 3.1 28.4 + - - -
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Residues in contact with SER 712 (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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648B PHE* 3.7 19.2 - - - -
677B VAL* 4.8 2.2 - - - +
681B LEU* 3.7 24.5 - - - +
708B ILE 2.5 23.3 + - - -
709B PHE* 3.7 7.6 - - - -
710B GLU 3.2 0.2 - - - -
711B LYS* 1.3 77.4 - - - +
713B VAL* 1.3 55.6 + - - +
715B THR* 2.9 3.9 + - - -
716B LEU* 2.6 43.4 + - - +
720B PHE* 4.2 15.0 - - - -
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Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B PHE 2.9 19.2 + - - +
710B GLU 3.8 2.9 - - - +
712B SER* 1.3 76.7 - - - +
714B LYS* 1.3 60.0 + - + +
717B LEU* 2.7 32.4 + - - +
720B PHE* 3.5 41.5 - - + -
727B LEU* 4.5 1.3 - - + -
746B LEU* 4.1 9.4 - - + -
749B GLN* 4.3 17.3 - - + -
750B LEU* 4.0 15.5 - - + -
753B ILE* 3.4 27.8 - - + +
754B PHE* 5.6 0.4 - - + -
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Residues in contact with LYS 714 (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 ASP* 5.7 0.2 - - - +
710B GLU* 3.1 49.1 + - + +
711B LYS* 4.0 16.7 - - + +
712B SER 3.2 0.2 - - - -
713B VAL* 1.3 79.8 - - + +
715B THR* 1.3 61.3 + - - +
717B LEU* 4.0 17.2 - - - +
749B GLN* 6.0 6.7 - - + -
753B ILE* 5.6 0.4 - - - -
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Residues in contact with THR 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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648B PHE* 2.5 27.0 + - - +
649B THR* 3.9 9.2 + - - -
651B LEU 2.8 29.5 + - - +
652B ASP* 3.2 24.8 - - - +
653B ILE 4.4 2.2 + - - +
654B SER* 4.7 12.0 + - - -
677B VAL* 5.3 5.6 - - + -
711B LYS 3.1 9.2 + - - -
712B SER* 2.9 5.6 + - - -
714B LYS* 1.3 81.4 - - - +
716B LEU* 1.3 71.6 + - + +
717B LEU* 4.3 6.6 - - - +
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Residues in contact with LEU 716 (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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653B ILE* 6.2 1.8 - - + -
675B ASN* 5.4 3.1 - - + -
677B VAL* 3.7 34.1 - - + -
678B VAL* 4.0 19.3 - - + -
681B LEU* 3.3 21.5 - - + -
712B SER 2.6 20.4 + - - +
715B THR* 1.3 76.6 - - + +
717B LEU* 1.3 71.8 + - - +
718B ASP 3.2 0.2 + - - -
719B ASP* 3.2 27.6 + - + +
720B PHE* 3.1 48.0 - - + +
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Residues in contact with LEU 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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654B SER* 5.4 9.6 - - - -
713B VAL* 2.7 27.0 + - - +
714B LYS* 4.0 22.0 - - - +
715B THR 4.3 4.5 - - - +
716B LEU* 1.3 75.8 - - - +
718B ASP* 1.3 70.2 + - + +
720B PHE* 3.1 23.0 - - - +
753B ILE* 3.9 24.3 - - + +
754B PHE* 3.5 9.5 - - - -
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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