Contacts of the helix formed by residues 716 - 725 (chain A) in PDB entry 4Z96
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 LEU 716 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A LEU* 4.5 5.4 - - + -
705A ILE* 4.3 26.5 - - + -
707A THR* 4.4 7.9 - - + +
711A CYS* 3.6 25.8 - - - -
713A ILE* 2.8 18.1 + - + +
715A ASP* 1.3 80.4 - - - +
717A LEU* 1.3 64.6 + - - +
718A PRO* 3.3 1.6 - - - -
719A VAL* 3.2 12.4 + - + +
720A MET* 2.9 47.0 + - + +
753A LEU* 3.8 37.7 - - + -
766A ILE* 4.8 1.1 - - + -
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Residues in contact with LEU 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 ILE 4.0 3.1 - - - +
714A ARG* 3.2 47.3 - - - +
716A LEU* 1.3 77.2 - - - +
718A PRO* 1.3 66.3 - - + +
720A MET* 3.4 5.0 + - - +
721A CYS* 2.9 30.3 + - - -
730A THR 6.1 0.9 - - - +
732A LEU* 4.1 18.3 - - + +
734A LEU* 3.7 39.5 - - + -
749A TYR* 4.2 18.4 - - + -
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Residues in contact with PRO 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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714A ARG 3.8 3.1 - - - +
715A ASP* 3.3 22.0 - - - +
716A LEU 3.5 0.7 - - - -
717A LEU* 1.3 93.6 - - + +
719A VAL* 1.3 58.1 + - + +
721A CYS* 3.2 0.8 + - - -
722A ASP* 2.9 32.0 + - - +
728A GLN* 3.1 37.1 + - - +
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Residues in contact with VAL 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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689A LEU* 4.6 3.4 - - + -
705A ILE* 3.9 26.5 - - + -
715A ASP 4.5 11.2 - - - +
716A LEU* 3.2 15.0 + - + +
718A PRO* 1.3 77.6 - - + +
720A MET* 1.3 64.0 + - - +
722A ASP* 3.1 8.2 + - + +
723A ARG* 3.0 46.1 + - - +
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Residues in contact with MET 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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689A LEU* 3.6 30.1 - - + -
705A ILE* 6.3 0.2 - - + -
716A LEU* 2.9 37.6 + - + +
717A LEU* 3.6 11.9 - - - +
719A VAL* 1.3 79.1 - - + +
721A CYS* 1.3 60.8 + - - +
723A ARG* 4.0 0.8 - - - -
724A ALA 3.1 11.6 + - - -
732A LEU* 4.0 5.8 - - + -
734A LEU* 3.5 44.2 - - + -
766A ILE* 3.9 18.2 - - + -
768A PHE* 3.0 51.4 - - + -
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Residues in contact with CYS 721 (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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717A LEU* 2.9 26.6 + - - +
718A PRO 3.7 3.8 - - - +
720A MET* 1.3 72.5 - - - +
722A ASP* 1.3 58.8 + - - +
724A ALA* 3.8 0.2 - - - -
725A GLY 2.8 27.4 + - - -
726A PHE* 2.8 24.5 + - + +
727A ILE 3.6 25.6 - - - +
728A GLN* 4.0 12.8 - - - +
730A THR* 4.0 22.2 - - - -
732A LEU* 3.8 18.4 - - - -
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Residues in contact with ASP 722 (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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718A PRO 2.9 17.5 + - - +
719A VAL* 3.7 5.8 - - - +
721A CYS* 1.3 77.4 - - - +
723A ARG* 1.3 66.8 + - - +
725A GLY* 4.0 7.3 + - - -
726A PHE 4.7 5.8 - - - +
728A GLN* 4.8 4.7 - - - +
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Residues in contact with ARG 723 (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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689A LEU* 4.2 4.9 - - - +
701A TYR 5.4 0.3 - - - +
702A CYS* 2.7 42.7 + - + +
703A GLY* 3.6 4.0 - - - -
704A HIS* 2.8 45.8 + - - +
705A ILE* 3.6 13.3 - - - +
719A VAL* 3.0 32.9 + - + +
720A MET* 4.2 2.7 - - - +
722A ASP* 1.3 85.4 - - - +
724A ALA* 1.3 65.7 + - - +
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Residues in contact with ALA 724 (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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691A MET* 3.7 17.3 - - + +
702A CYS* 3.8 9.0 - - - -
720A MET 3.1 18.1 + - - +
721A CYS 3.8 0.9 - - - +
723A ARG* 1.3 80.0 - - - +
725A GLY* 1.3 57.1 + - - +
726A PHE* 3.6 34.1 - - + -
768A PHE* 3.7 13.5 - - + -
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Residues in contact with GLY 725 (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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721A CYS 2.8 8.1 + - - -
722A ASP 4.0 7.2 + - - -
723A ARG 3.5 1.0 - - - -
724A ALA* 1.3 75.6 - - - +
726A PHE* 1.3 70.1 + - - +
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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