Contacts of the helix formed by residues 698 - 712 (chain A) in PDB entry 3BWT
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 LYS 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A ASP* 3.4 29.9 + - - -
697A LEU* 1.3 69.4 - - - +
699A PRO* 1.3 66.7 - - + +
700A GLU* 3.9 17.9 - - + +
701A ASN* 2.7 44.6 + - - +
702A PHE* 2.8 15.1 + - - -
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Residues in contact with PRO 699 (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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697A LEU 4.1 0.9 - - - +
698A LYS* 1.3 87.4 - - + -
700A GLU* 1.3 69.5 + - - +
702A PHE* 2.7 31.4 - - + -
703A GLN* 3.0 24.7 + - - +
732A HIS 4.8 4.7 - - - +
734A THR* 3.8 22.9 - - - +
737A GLN* 3.1 20.5 + - - +
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Residues in contact with GLU 700 (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 LYS* 2.9 23.6 + - + +
699A PRO* 1.3 91.8 - - - +
701A ASN* 1.3 64.5 + - - +
703A GLN* 3.6 18.5 - - - +
734A THR* 5.2 1.7 + - - -
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Residues in contact with ASN 701 (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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663A ASP* 4.8 6.5 + - - +
666A ALA* 3.8 23.4 - - - +
667A GLN* 3.2 21.7 - - - +
670A VAL* 3.2 16.8 - - + +
697A LEU* 3.9 19.3 - - + +
698A LYS* 2.7 42.3 + - - +
700A GLU* 1.3 76.7 - - - +
702A PHE* 1.3 55.1 + - - +
703A GLN 3.4 2.0 - - - -
704A PHE* 3.1 21.0 + - - -
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Residues in contact with PHE 702 (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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693A CYS 4.0 14.8 - - - +
694A LEU* 3.1 42.2 - - + -
697A LEU* 3.0 26.0 - - + -
698A LYS 2.8 25.8 + - - -
699A PRO* 2.7 38.8 - - + -
701A ASN* 1.3 75.6 - - - +
703A GLN* 1.3 63.9 + - - +
704A PHE* 3.2 7.4 - - - -
705A ILE* 3.1 27.6 + - + +
706A PHE* 3.8 20.2 + + - -
732A HIS* 3.6 30.3 - - + -
737A GLN* 4.1 4.9 - - - -
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Residues in contact with GLN 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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699A PRO 3.0 9.7 + - - +
700A GLU* 3.6 18.6 - - - +
701A ASN 3.4 0.8 - - - -
702A PHE* 1.3 77.3 - - - +
704A PHE* 1.3 64.1 + - - +
706A PHE* 2.9 27.1 + - - +
707A ASP* 2.9 41.8 + - - +
737A GLN* 3.2 29.6 + - - +
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Residues in contact with PHE 704 (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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670A VAL* 4.0 21.3 - - + -
673A LEU* 4.2 16.6 - - + -
674A ARG* 3.8 46.8 - - + +
677A THR* 3.3 24.2 - - + -
690A ILE* 4.9 3.1 - - + -
693A CYS* 4.5 9.9 - - - -
697A LEU* 4.9 5.2 - - + -
701A ASN 3.1 28.2 + - - -
702A PHE* 4.0 3.6 - - + -
703A GLN* 1.3 78.6 - - - +
705A ILE* 1.3 91.5 + - + +
707A ASP* 3.6 11.7 - - - +
708A ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 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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677A THR* 4.1 10.8 - - + -
681A SER* 5.2 0.2 - - - +
690A ILE* 3.7 44.0 - - + +
693A CYS* 3.7 13.9 - - + -
694A LEU* 4.0 16.2 - - + -
702A PHE* 3.1 8.7 + - + +
703A GLN 2.9 0.8 + - - -
704A PHE* 1.3 111.9 - - + +
706A PHE* 1.3 59.9 + - - +
708A ALA* 3.4 1.9 + - - +
709A ILE* 3.0 46.5 + - + +
725A VAL* 4.4 1.6 - - + -
729A CYS* 4.1 13.0 - - - -
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Residues in contact with PHE 706 (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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694A LEU* 4.1 2.0 - - + -
702A PHE* 3.9 36.1 - + - -
703A GLN* 2.9 19.6 + - - +
705A ILE* 1.3 78.6 - - - +
707A ASP* 1.3 57.5 + - - +
709A ILE* 3.4 6.3 + - - +
710A SER* 2.8 33.7 + - - +
729A CYS* 3.4 41.5 - - + -
733A GLY* 3.7 10.1 - - - -
737A GLN* 3.6 46.0 - - + -
738A CYS* 4.1 2.0 - - - -
741A LEU* 3.6 32.9 - - + +
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Residues in contact with ASP 707 (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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703A GLN* 2.9 45.5 + - - +
704A PHE* 3.6 13.3 - - - +
706A PHE* 1.3 77.1 - - - +
708A ALA* 1.3 63.8 + - - +
710A SER* 3.2 21.1 + - - -
711A ASP* 3.5 14.9 + - - +
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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
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674A ARG 5.5 1.6 - - - +
677A THR* 3.6 32.5 - - + -
678A VAL* 4.2 12.5 - - + +
704A PHE 2.9 17.9 + - - +
705A ILE 3.9 0.2 - - - +
707A ASP* 1.3 76.2 - - - +
709A ILE* 1.3 62.7 + - + +
711A ASP* 3.3 13.5 + - - +
712A SER* 3.4 18.4 + - - -
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Residues in contact with ILE 709 (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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677A THR* 5.6 1.3 - - + -
681A SER* 5.2 1.6 - - - +
705A ILE* 3.0 27.4 + - + +
706A PHE* 3.8 4.7 - - - +
708A ALA* 1.3 73.9 - - + +
710A SER* 1.3 67.5 + - - +
711A ASP 2.9 4.0 + - - -
712A SER 3.1 0.2 + - - -
713A CYS* 3.0 30.3 + - - -
716A ILE* 4.0 34.8 - - + -
725A VAL* 4.1 7.4 - - + -
726A LEU* 3.8 21.8 - - + -
729A CYS* 3.6 31.0 - - - -
741A LEU* 3.9 26.5 - - + -
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Residues in contact with SER 710 (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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706A PHE* 2.8 22.8 + - - +
707A ASP* 3.3 13.1 + - - -
709A ILE* 1.3 78.4 - - - +
711A ASP* 1.3 63.9 + - - +
713A CYS* 4.2 6.9 - - - +
740A ASN* 5.5 4.0 + - - +
741A LEU* 5.7 6.2 - - - +
744A LYS* 3.2 51.4 + - - +
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Residues in contact with ASP 711 (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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707A ASP* 3.5 13.5 + - - +
708A ALA* 3.3 9.3 + - - +
709A ILE 3.0 1.0 - - - -
710A SER* 1.3 87.9 - - - +
712A SER* 1.3 62.4 + - - +
713A CYS 3.6 1.3 + - - -
744A LYS* 4.4 4.9 + - - -
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Residues in contact with SER 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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678A VAL* 3.4 31.8 - - - +
708A ALA 3.4 5.8 + - - -
709A ILE 3.1 5.5 + - - -
711A ASP* 1.3 81.2 + - - +
713A CYS* 1.3 60.7 + - - +
714A ILE* 3.4 0.9 - - - -
715A ASP* 2.8 35.4 - - - +
716A ILE* 3.0 19.2 + - - +
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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