Contacts of the helix formed by residues 707 - 717 (chain A) in PDB entry 6WCW
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 ALA 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706A PRO* 1.3 72.9 - - - +
708A PRO* 1.3 72.2 - - + +
709A THR* 3.2 3.1 - - - +
710A ARG* 3.2 21.0 + - + +
711A LYS* 2.9 20.1 + - - +
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Residues in contact with PRO 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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706A PRO 3.6 8.1 - - - +
707A ALA* 1.3 85.9 - - + +
709A THR* 1.3 58.3 + - - +
711A LYS* 3.9 7.3 - - + +
712A ILE* 3.1 38.8 + - + +
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Residues in contact with THR 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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707A ALA* 3.2 2.8 - - - +
708A PRO* 1.3 77.4 - - - +
710A ARG* 1.3 64.4 + - - +
712A ILE* 3.4 12.4 + - + +
713A ALA* 3.2 21.6 + - + +
745A TYR* 6.1 0.4 - - - +
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Residues in contact with ARG 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A PRO* 5.9 0.2 - - - -
707A ALA* 3.2 21.2 + - + +
709A THR* 1.3 77.8 - - - +
711A LYS* 1.3 60.2 + - - +
712A ILE 3.1 0.2 - - - -
713A ALA* 3.0 5.4 + - - +
714A VAL* 2.8 37.0 + - + +
733A ILE* 2.6 53.5 + - + -
734A LYS* 3.3 17.8 + - - +
736A LEU 2.8 28.4 + - - -
737A ARG* 5.1 1.4 - - - +
738A TYR* 5.2 1.4 - - - +
745A TYR* 3.6 38.9 + - + +
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Residues in contact with LYS 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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704A VAL 5.4 1.3 - - - -
706A PRO* 3.3 33.3 - - + +
707A ALA 2.9 16.4 + - - +
708A PRO* 3.9 9.4 - - + +
710A ARG* 1.3 76.0 - - - +
712A ILE* 1.3 63.2 + - + +
714A VAL* 4.9 0.4 - - - -
715A ALA* 3.1 29.2 + - + +
719A TYR* 2.6 34.1 + - - +
730A PRO* 3.7 23.2 + - - +
733A ILE* 3.7 14.9 - - + +
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Residues in contact with ILE 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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708A PRO* 3.1 24.7 + - + +
709A THR* 3.5 10.8 - - + +
710A ARG 3.1 0.6 - - - -
711A LYS* 1.3 79.0 - - + +
713A ALA* 1.3 57.9 + - + +
715A ALA* 3.9 2.8 - - - +
716A LYS* 3.0 32.2 + - + +
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Residues in contact with ALA 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A THR 3.2 12.5 + - - +
710A ARG 3.0 4.7 + - - +
712A ILE* 1.3 76.9 - - + +
714A VAL* 1.3 66.6 + - - +
716A LYS* 3.0 21.6 + - - +
717A GLN* 3.4 15.0 + - - +
738A TYR* 5.5 3.8 - - + -
745A TYR* 3.7 28.5 - - + -
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Residues in contact with VAL 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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710A ARG* 2.8 39.5 + - + +
711A LYS 4.5 0.7 - - - +
713A ALA* 1.3 71.8 - - - +
715A ALA* 1.3 60.4 + - - +
717A GLN* 3.1 20.1 + - + +
719A TYR* 3.0 56.4 + - + -
720A ARG 5.1 0.4 - - - +
728A THR* 4.4 1.3 - - - +
733A ILE* 3.8 17.0 - - + -
736A LEU* 3.6 29.2 - - + -
745A TYR* 4.1 13.2 - - + -
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Residues in contact with ALA 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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711A LYS* 3.1 23.3 + - + +
712A ILE* 4.1 3.4 - - - +
714A VAL* 1.3 78.2 - - - +
716A LYS* 1.3 62.2 + - - +
718A ASN* 3.1 16.1 + - - -
719A TYR* 3.6 32.2 - - + +
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Residues in contact with LYS 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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712A ILE* 3.0 19.6 + - + +
713A ALA* 3.0 14.7 + - - +
715A ALA* 1.3 78.3 - - - +
717A GLN* 1.3 56.8 + - - +
718A ASN* 3.6 9.9 + - - -
744A LYS* 5.7 7.4 - - - +
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Residues in contact with GLN 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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713A ALA* 3.5 13.5 - - - +
714A VAL* 3.1 14.5 + - + +
716A LYS* 1.3 77.4 - - + +
718A ASN* 1.3 55.6 + - - +
719A TYR 3.0 2.7 - - - -
720A ARG* 2.7 55.8 + - - +
721A CYS* 4.7 0.2 - - - +
722A ALA* 3.8 9.1 - - - +
744A LYS* 3.4 36.4 - - - +
745A TYR* 3.0 52.0 + - - +
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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
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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