Contacts of the helix formed by residues 707 - 720 (chain A) in PDB entry 2WXL
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 THR 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 THR* 1.3 83.8 + - - +
708A LYS* 1.3 60.1 + - - +
709A PRO* 3.8 14.2 - - - +
710A GLN* 2.7 50.7 + - - +
711A THR* 2.9 12.9 + - - -
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Residues in contact with LYS 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 THR 3.9 1.0 + - - -
707A THR* 1.3 70.5 - - - +
709A PRO* 1.4 69.0 - - + +
711A THR* 3.3 2.2 + - - +
712A LYS* 2.8 35.0 + - + +
750A THR* 4.1 8.9 + - - -
751A PHE* 2.8 57.6 + - + -
752A MET* 4.3 2.0 - - - +
753A ASP* 2.8 36.8 + - - +
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Residues in contact with PRO 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 THR* 3.8 13.5 - - - +
708A LYS* 1.4 95.4 - - + +
710A GLN* 1.3 58.8 + - + +
712A LYS* 3.5 7.6 + - + +
713A GLU* 3.1 37.0 + - + +
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Residues in contact with GLN 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 THR* 2.8 27.9 + - + +
707A THR* 2.7 36.6 + - - +
709A PRO* 1.3 79.6 - - + +
711A THR* 1.3 65.0 + - - +
713A GLU* 3.3 14.2 + - - +
714A MET* 3.0 32.7 + - + +
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Residues in contact with THR 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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698A PHE* 4.3 1.3 - - + -
699A VAL* 4.1 21.5 - - + +
702A SER* 2.8 48.9 + - - +
703A SER* 3.7 4.6 + - - +
706A THR* 3.5 7.9 + - - +
707A THR 2.9 9.7 + - - -
708A LYS* 3.8 5.6 - - - -
710A GLN* 1.3 75.3 - - - +
712A LYS* 1.3 57.1 + - - +
714A MET* 3.3 4.5 + - - +
715A MET* 2.8 27.2 + - - +
751A PHE* 3.4 28.0 - - + -
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Residues in contact with LYS 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 LYS* 2.8 26.3 + - + +
709A PRO* 3.8 7.0 - - + +
711A THR* 1.3 74.0 - - - +
713A GLU* 1.3 56.5 + - + +
715A MET* 3.3 7.8 + - - +
716A HIS* 3.0 52.6 + - + +
747A GLU 4.7 6.3 + - - -
748A GLN* 5.9 1.2 - - - +
749A CYS 3.6 19.9 + - - +
750A THR* 3.8 28.3 + - - +
751A PHE* 4.0 10.1 - - + -
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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 PRO* 3.1 24.3 + - - +
710A GLN* 3.6 14.3 - - - +
712A LYS* 1.3 77.0 - - + +
714A MET* 1.3 70.2 + - + +
716A HIS* 3.3 11.4 + - - +
717A MET* 2.9 31.5 + - + +
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Residues in contact with MET 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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698A PHE* 3.4 31.1 - - + -
702A SER* 5.0 2.2 - - - +
706A THR* 6.0 1.6 - - + -
710A GLN* 3.0 19.1 + - + +
711A THR* 3.3 4.7 + - - +
713A GLU* 1.3 87.6 - - + +
715A MET* 1.3 59.4 + - - +
717A MET* 3.3 30.9 + - - +
718A CYS* 2.9 29.6 + - - +
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Residues in contact with MET 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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695A LEU* 4.0 25.6 - - + -
698A PHE* 4.0 7.3 - - - -
699A VAL* 4.1 20.2 - - + -
711A THR 2.8 18.1 + - - +
712A LYS* 3.3 10.3 - - - +
714A MET* 1.3 72.7 - - - +
716A HIS* 1.3 59.2 + - - +
718A CYS* 3.3 4.5 + - - +
719A MET* 2.9 47.0 + - - +
749A CYS* 4.0 9.0 - - + +
750A THR* 3.3 40.6 - - - +
751A PHE* 4.5 5.8 - - - -
759A LEU* 4.2 8.7 - - + -
761A ILE* 3.9 25.4 - - + -
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Residues in contact with HIS 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 LYS* 3.0 36.3 + - + +
713A GLU* 3.5 12.2 - - - +
715A MET* 1.3 78.9 - - + +
717A MET* 1.3 60.1 + - + +
719A MET* 3.2 3.5 + - - +
720A ARG* 2.9 55.8 + - - +
746A VAL* 2.9 32.4 + - + -
747A GLU* 3.6 29.6 + - - -
749A CYS* 2.6 34.1 + - + -
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Residues in contact with MET 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 GLU* 2.9 20.0 + - + +
714A MET* 3.7 33.4 - - - +
716A HIS* 1.3 71.6 - - + +
718A CYS* 1.3 64.6 + - - +
720A ARG* 3.2 17.5 + - - +
721A GLN* 3.4 13.5 + - - +
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Residues in contact with CYS 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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695A LEU* 3.6 24.0 - - + -
698A PHE* 5.3 10.8 - - + -
714A MET 2.9 14.2 + - - +
715A MET* 3.4 9.4 - - - +
717A MET* 1.3 75.8 - - - +
719A MET* 1.3 61.8 + - - +
720A ARG 3.3 0.3 + - - -
721A GLN* 3.0 41.3 + - - +
724A TYR* 3.5 27.3 - - - -
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Residues in contact with MET 719 (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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695A LEU* 3.7 17.0 - - + -
715A MET* 2.9 35.5 + - - +
716A HIS* 3.2 6.9 + - - +
718A CYS* 1.3 76.1 - - - +
720A ARG* 1.3 60.0 + - - +
721A GLN 3.2 0.2 - - - -
724A TYR* 3.3 23.4 - - - +
725A MET* 3.3 18.4 + - - +
728A LEU* 3.5 27.7 - - + +
744A VAL* 3.7 25.6 - - + -
746A VAL* 4.1 18.2 - - + -
749A CYS* 3.9 28.7 - - - -
761A ILE* 4.1 12.1 - - + -
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Residues in contact with ARG 720 (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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716A HIS* 2.9 39.3 + - - +
717A MET* 3.2 11.0 + - - +
718A CYS 3.2 0.6 - - - -
719A MET* 1.3 74.1 - - - +
721A GLN* 1.3 64.4 + - - +
722A GLU* 3.6 1.7 + - - +
725A MET* 3.8 16.2 - - + +
746A VAL* 3.6 38.3 - - + +
747A GLU* 3.4 30.1 + - - +
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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