Contacts of the helix formed by residues 702 - 718 (chain A) in PDB entry 1WBB
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 TYR 702 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A SER* 4.8 0.6 - - - -
701A THR* 1.3 90.1 - - + +
703A ASP* 1.3 64.2 + - - +
704A GLY 3.2 2.9 - - - -
705A LEU* 3.1 23.9 + - + +
706A SER* 2.7 31.4 + - - -
731A GLU* 3.5 20.4 - - - -
701B THR* 3.9 9.2 - - + +
702B TYR* 3.8 24.5 + + - -
705B LEU* 5.9 0.9 - - - +
731B GLU* 3.5 23.2 + - - -
793B LEU* 3.4 15.9 - - + +
796B LEU* 3.7 46.6 + - + -
797B GLU* 4.0 22.0 + - + -
800B SER* 4.8 5.7 + - - -
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Residues in contact with ASP 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A GLY* 3.2 5.7 - - - -
699A THR* 2.7 27.9 + - - -
700A SER* 3.7 22.6 - - - +
702A TYR* 1.3 75.8 - - - +
704A GLY* 1.3 61.9 + - - +
706A SER* 3.5 9.2 + - - -
707A LEU* 3.6 9.1 + - - +
770B SER* 3.1 24.3 + - - +
772B GLY* 2.9 24.9 + - - -
773B LEU* 3.7 24.3 + - - +
793B LEU* 3.2 16.3 - - + +
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Residues in contact with GLY 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A GLY* 3.3 21.6 - - - -
697A ARG* 3.6 10.1 - - - -
698A GLY 3.4 25.3 - - - +
700A SER 4.6 2.6 + - - -
701A THR 4.9 0.8 + - - -
702A TYR 3.2 1.0 - - - -
703A ASP* 1.3 77.5 - - - +
705A LEU* 1.3 63.6 + - - +
707A LEU* 3.5 6.7 + - - +
708A ALA 3.3 15.4 + - - -
729A TYR* 4.3 2.5 - - - -
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Residues in contact with LEU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A THR 5.0 2.4 + - - +
702A TYR* 3.1 18.6 + - + +
704A GLY* 1.3 76.3 - - - +
706A SER* 1.3 59.0 + - - +
708A ALA* 3.2 1.8 + - - +
709A TRP* 2.9 28.1 + - + +
729A TYR* 3.8 44.9 + - + -
731A GLU* 3.5 41.3 - - + +
732A LEU* 3.6 26.0 - - + -
701B THR* 4.7 2.0 - - - +
796B LEU* 3.6 27.4 - - + -
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Residues in contact with SER 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A TYR 2.7 21.7 + - - -
703A ASP 3.7 6.1 - - - -
704A GLY 3.3 0.2 - - - -
705A LEU* 1.3 73.8 - - - +
707A LEU* 1.3 59.0 + - - +
709A TRP* 3.4 7.7 + - - +
710A ALA* 3.0 22.7 + - - +
773B LEU* 5.0 0.9 - - - -
789B ALA* 3.4 37.2 - - - +
792B LYS* 4.2 8.0 - - - +
793B LEU* 3.5 25.1 - - - +
796B LEU* 3.6 9.2 - - - +
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A MET* 3.9 25.4 - - + -
696A GLY* 5.1 0.9 - - - -
697A ARG 5.0 5.6 - - - +
703A ASP 3.6 6.2 + - - +
704A GLY* 3.5 10.0 + - - +
705A LEU 3.2 0.2 - - - -
706A SER* 1.3 76.1 - - - +
708A ALA* 1.3 54.4 + - - +
709A TRP 3.1 0.2 - - - -
710A ALA* 3.4 1.4 + - - +
711A CYS* 2.8 48.6 + - - -
772B GLY* 3.5 27.6 - - - +
773B LEU* 3.5 24.5 - - + -
776B ALA* 3.6 22.9 - - + -
781B VAL* 4.2 16.8 - - + -
785B VAL* 4.8 4.3 - - + -
786B ILE* 5.3 2.7 - - + -
789B ALA* 4.0 8.0 - - + +
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Residues in contact with ALA 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A ILE* 4.0 32.5 - - + +
696A GLY* 4.1 3.7 - - - -
704A GLY 3.3 10.3 + - - +
705A LEU* 3.2 12.2 + - - +
707A LEU* 1.3 79.5 - - - +
709A TRP* 1.3 57.8 + - - +
711A CYS* 3.7 5.6 - - - +
712A ALA* 3.1 27.7 + - - +
725A PHE* 3.6 12.6 - - + -
729A TYR* 4.7 2.9 - - + -
732A LEU* 4.4 13.0 - - + +
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Residues in contact with TRP 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU* 2.9 21.0 + - + +
706A SER* 3.6 8.1 - - - +
707A LEU 3.1 0.2 - - - -
708A ALA* 1.3 75.9 - - - +
710A ALA* 1.3 68.2 + - + +
712A ALA* 3.2 6.1 + - - +
713A GLU* 3.1 45.3 + - - +
731A GLU* 3.3 26.0 - - + -
732A LEU* 3.3 35.9 - - + -
734A GLN* 4.1 26.5 - - + -
735A LEU* 4.2 21.7 - - + +
738A LYS* 4.7 16.8 - - + -
739A MET* 6.0 0.7 - - + -
788B ARG* 5.7 1.6 - - + -
792B LYS* 3.1 53.6 - - + +
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Residues in contact with ALA 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A SER 3.0 17.2 + - - +
707A LEU 3.9 1.8 - - - +
709A TRP* 1.3 81.7 - - + +
711A CYS* 1.3 62.0 + - - +
713A GLU* 3.4 8.2 - - - +
714A ASN* 3.1 22.3 + - - +
785B VAL* 3.3 38.6 - - + +
788B ARG* 3.9 11.0 - - + -
789B ALA* 3.8 12.3 - - + +
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Residues in contact with CYS 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A MET* 6.0 1.1 - - - -
677A THR* 3.6 30.1 - - + -
681A LEU* 3.8 18.4 - - + +
692A MET* 5.3 2.9 - - + -
695A ILE* 4.5 12.1 - - + -
707A LEU* 2.8 33.7 + - - +
708A ALA* 3.7 8.1 - - - +
709A TRP 3.2 0.2 - - - -
710A ALA* 1.3 74.4 - - - +
712A ALA* 1.3 66.6 + - - +
714A ASN* 3.2 7.0 + - - +
715A LEU* 3.0 27.9 + - - +
725A PHE* 5.1 1.8 - - + -
781B VAL* 5.2 1.1 - - - -
785B VAL* 4.3 11.0 - - - -
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Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 3.3 24.1 - - - +
611A ILE* 5.1 0.9 - - + -
708A ALA 3.1 18.1 + - - +
709A TRP 3.2 5.6 + - - +
711A CYS* 1.3 77.3 - - - +
713A GLU* 1.3 51.7 + - - +
715A LEU* 3.1 1.3 + - - -
716A ALA* 2.8 34.0 + - - +
725A PHE* 4.0 21.1 - - + -
732A LEU* 5.4 0.4 - - + -
735A LEU* 3.7 23.8 - - + -
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Residues in contact with GLU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A TRP* 3.1 37.2 + - - +
710A ALA* 3.4 11.0 - - - +
712A ALA* 1.3 78.3 - - - +
714A ASN* 1.3 58.3 + - - +
716A ALA* 4.5 4.7 - - - -
717A ASN* 2.8 41.8 + - - +
735A LEU* 4.5 5.6 - - + +
739A MET* 3.4 35.1 - - + +
788B ARG* 2.9 46.8 + - - +
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Residues in contact with ASN 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A LEU* 3.5 12.5 - - + +
710A ALA 3.1 10.7 + - - +
711A CYS 3.2 8.0 + - - +
713A GLU* 1.3 80.3 - - - +
715A LEU* 1.3 59.0 + - - +
717A ASN* 4.9 2.0 - - - +
718A LYS* 3.1 41.3 + - - +
719A ILE* 2.9 47.6 + - - +
782B PRO* 5.8 2.6 - - - +
784B GLU* 5.6 2.0 - - - +
785B VAL* 3.5 28.0 - - + +
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 3.4 17.9 - - + -
680A ILE* 4.4 9.6 - - + -
681A LEU* 4.3 7.9 - - + -
684A ALA* 4.9 0.7 - - + -
690A VAL* 4.0 27.8 - - + -
692A MET* 4.1 21.5 - - + -
711A CYS 3.0 16.8 + - - +
712A ALA 3.1 2.2 + - - +
714A ASN* 1.3 77.4 - - - +
716A ALA* 1.3 56.8 - - - +
719A ILE* 3.7 27.9 - - + -
720A LYS* 2.8 29.3 + - - -
721A ALA* 3.6 7.9 + - + +
723A THR* 3.8 32.1 - - + +
725A PHE* 4.3 6.1 - - + -
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Residues in contact with ALA 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ARG* 2.7 33.9 + - - +
609A MET* 3.7 11.9 - - + +
712A ALA 2.8 16.2 + - - +
713A GLU 3.9 2.2 - - - +
715A LEU* 1.3 79.6 - - - +
717A ASN* 1.3 59.1 + - - +
720A LYS* 3.7 8.1 - - - +
721A ALA 5.7 0.2 - - - -
739A MET* 4.1 10.3 - - + -
740A GLU 4.2 3.4 - - - +
742A VAL* 3.6 31.6 - - + -
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Residues in contact with ASN 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ARG* 4.8 1.8 - - - +
713A GLU* 2.8 27.8 + - - +
714A ASN* 4.9 0.6 - - - +
716A ALA* 1.3 74.2 - - - +
718A LYS* 1.3 79.0 + - - +
720A LYS* 3.5 20.8 - - - +
739A MET* 3.9 23.0 - - + -
740A GLU 5.5 1.1 - - - +
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Residues in contact with LYS 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A GLU* 5.6 0.2 - - - +
714A ASN* 3.1 38.8 + - - +
717A ASN* 1.3 94.3 - - - +
719A ILE* 1.3 66.4 + - + +
720A LYS* 3.6 6.0 - - - +
784B GLU* 4.8 20.6 - - + +
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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