Contacts of the helix formed by residues 726 - 735 (chain A) in PDB entry 4IQJ
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 726 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A PHE* 3.5 13.6 + - + -
725A HIS* 1.3 74.7 - - - +
727A GLU* 1.3 66.8 + - - +
728A LYS 3.1 3.1 - - - -
729A TYR* 2.8 24.4 + - - +
730A LEU* 3.0 30.9 + - + +
754A VAL* 4.9 4.9 - - + -
793A VAL* 3.7 21.7 - - + +
797A GLU* 3.7 3.3 + - + +
801A LEU* 4.1 14.1 - - + -
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Residues in contact with GLU 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A TYR* 4.1 26.8 + - + +
723A PHE 2.9 15.3 + - - +
724A PRO* 3.3 24.2 - - + +
725A HIS 3.2 0.6 - - - -
726A ALA* 1.3 74.1 - - - +
728A LYS* 1.3 58.6 + - + +
730A LEU* 4.2 8.5 - - - -
731A ARG* 2.8 62.0 + - + +
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Residues in contact with LYS 728 (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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724A PRO 5.4 2.9 - - - +
725A HIS* 4.0 14.1 + - - +
726A ALA 2.9 3.0 + - - -
727A GLU* 1.3 77.0 - - + +
729A TYR* 1.3 74.6 + - + +
731A ARG* 5.4 0.9 - - - -
732A PRO* 3.2 23.4 - - - +
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Residues in contact with TYR 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A HIS 4.6 8.1 - - - -
726A ALA* 2.8 21.1 + - - +
728A LYS* 1.3 87.9 + - + +
730A LEU* 1.3 64.6 + - - +
731A ARG 3.5 0.4 - - - -
732A PRO* 3.6 5.9 - - - +
733A ILE* 3.5 26.4 - - + +
750A ILE* 5.7 0.2 - - - -
753A GLN* 3.8 35.1 - - + +
754A VAL* 3.7 35.9 - - + -
791A ARG* 3.4 61.1 + - + +
792A GLY* 5.5 2.9 - - - -
793A VAL* 5.8 3.1 - - + -
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Residues in contact with LEU 730 (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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720A TYR* 4.2 20.9 - - + -
723A PHE* 3.9 22.7 - - + +
726A ALA* 3.0 37.9 + - + +
727A GLU* 3.9 6.7 - - - +
729A TYR* 1.3 78.7 - - + +
731A ARG* 1.3 58.4 + - - +
733A ILE* 3.6 1.2 + - - +
734A LEU* 3.0 39.2 + - + +
750A ILE* 3.6 46.7 - - + -
754A VAL* 4.7 4.7 - - + -
801A LEU* 4.0 17.3 - - + -
804A MET* 4.9 4.3 - - + -
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Residues in contact with ARG 731 (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 VAL* 4.2 11.8 + - - +
719A SER* 5.7 0.4 - - - +
720A TYR* 3.6 30.4 - - + +
727A GLU* 2.8 46.9 + - + +
728A LYS* 5.1 0.9 - - - +
730A LEU* 1.3 70.8 - - - +
732A PRO* 1.3 67.4 - - + +
735A ASP* 2.8 64.8 + - - +
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Residues in contact with PRO 732 (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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728A LYS 3.2 26.0 - - - +
729A TYR* 3.6 8.5 - - - +
731A ARG* 1.3 95.7 - - + +
733A ILE* 1.3 62.3 + - + +
735A ASP* 4.3 8.3 + - + +
736A GLU* 4.8 3.5 + - - +
753A GLN* 5.9 2.0 - - - +
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Residues in contact with ILE 733 (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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729A TYR 3.5 17.5 - - - +
730A LEU 3.6 6.2 + - - +
731A ARG 3.2 0.6 - - - -
732A PRO* 1.3 80.2 - - + +
734A LEU* 1.3 66.9 + - + +
735A ASP 3.8 0.3 + - - -
736A GLU* 4.1 11.8 + - - +
746A GLN* 3.2 48.3 - - + +
749A GLN* 3.4 59.0 - - + +
750A ILE* 3.4 13.2 - - + +
753A GLN* 4.0 15.0 - - + +
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Residues in contact with LEU 734 (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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720A TYR* 3.6 21.8 - - + +
730A LEU* 3.0 25.9 + - + +
733A ILE* 1.3 77.7 - - + +
735A ASP* 1.3 62.4 + - - +
736A GLU 3.3 1.8 - - - -
737A THR* 3.4 5.5 + - - -
738A TYR 3.1 3.3 + - - -
739A GLY* 2.6 51.1 + - - +
740A ILE 4.0 2.0 - - - +
741A PRO* 3.9 22.2 - - + -
746A GLN* 3.8 28.0 - - + +
750A ILE* 3.9 30.3 - - + -
804A MET* 5.0 5.8 - - + -
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Residues in contact with ASP 735 (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 ARG* 5.0 1.6 + - - -
718A VAL* 4.9 5.7 - - - +
720A TYR* 3.4 15.5 + - - -
731A ARG* 2.8 55.7 + - - +
732A PRO* 4.7 5.9 - - + +
733A ILE 3.5 0.6 - - - -
734A LEU* 1.3 69.5 - - - +
736A GLU* 1.3 65.9 + - - +
737A THR 3.1 3.1 + - - -
738A TYR* 3.2 19.4 + - - +
739A GLY 4.8 0.4 - - - +
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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