Contacts of the helix formed by residues 727 - 741 (chain A) in PDB entry 5I0H
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 ARG 727 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A ARG 4.3 6.7 - - - -
670A LYS 3.3 22.4 + - - -
671A ALA* 3.1 20.8 + - - +
672A GLY 2.8 24.1 + - - +
673A TYR* 3.9 15.2 + - + +
674A ALA 4.7 0.2 - - - +
675A VAL* 4.7 0.7 - - - -
715A SER* 2.8 34.8 + - - -
716A GLU* 2.9 41.3 + - + +
726A LEU* 1.3 75.7 - - - +
728A GLU* 1.3 68.6 + - - +
729A SER* 4.0 15.5 - - - +
730A LEU* 3.1 5.2 + - - +
731A GLU* 3.1 18.9 + - - +
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Residues in contact with GLU 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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97A GLY* 3.4 12.0 - - - -
98A SER* 3.0 29.5 + - - +
669A ARG* 2.7 47.7 + - - +
672A GLY 5.5 0.7 - - - +
674A ALA* 3.6 25.8 + - + +
675A VAL* 4.1 16.6 - - + -
727A ARG* 1.3 74.6 - - - +
729A SER* 1.3 57.1 + - - +
731A GLU* 3.2 5.9 + - - +
732A GLN* 2.9 47.1 + - - +
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Residues in contact with SER 729 (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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67A ASP* 5.8 4.3 - - - -
716A GLU* 4.6 12.9 + - - -
727A ARG* 4.0 12.8 - - - +
728A GLU* 1.3 77.4 - - - +
730A LEU* 1.3 62.7 + - - +
732A GLN* 3.6 16.1 + - - +
733A LYS* 3.2 22.4 + - - +
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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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707A LEU* 3.7 27.1 - - + +
710A TYR* 3.8 39.5 - - + +
711A ASP* 4.2 2.5 - - + -
716A GLU* 3.9 36.1 + - + +
717A TRP* 3.9 20.4 - - + -
726A LEU* 4.1 11.7 - - + -
727A ARG 3.1 10.3 + - - +
729A SER* 1.3 77.4 + - - +
731A GLU* 1.3 61.4 + - - +
733A LYS* 3.3 13.5 + - + +
734A LEU* 2.9 32.3 + - + +
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Residues in contact with GLU 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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139A GLU* 4.6 4.7 - - - +
146A LYS* 2.8 38.4 + - - +
675A VAL* 3.7 36.9 - - + +
677A ARG* 5.6 1.7 + - - +
686A TYR* 4.1 13.5 - - - +
726A LEU* 3.7 20.1 - - + +
727A ARG 3.1 10.3 + - - +
728A GLU* 3.2 13.5 + - - +
730A LEU* 1.3 77.8 - - - +
732A GLN* 1.4 57.2 + - - +
734A LEU* 3.2 5.3 + - - +
735A GLU* 2.8 41.9 + - - +
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Residues in contact with GLN 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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97A GLY 5.4 2.8 - - - +
125A HIS* 5.2 5.3 - - + +
126A LEU* 3.3 57.5 + - + +
127A GLY* 4.1 8.5 - - - -
139A GLU* 5.9 1.8 - - - +
146A LYS* 6.3 0.9 - - - +
728A GLU* 2.9 36.5 + - - +
729A SER* 3.8 13.5 - - - +
730A LEU 3.3 0.2 - - - -
731A GLU* 1.4 80.7 - - - +
733A LYS* 1.3 57.3 + - - +
735A GLU* 3.9 6.2 - - - +
736A LYS* 3.0 31.5 + - - +
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Residues in contact with LYS 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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709A LEU 5.4 0.4 + - - -
710A TYR* 2.9 53.2 + - + +
716A GLU* 5.9 0.9 - - - +
729A SER 3.2 11.0 + - - +
730A LEU* 3.4 15.9 - - + +
732A GLN* 1.3 79.2 - - - +
734A LEU* 1.4 59.7 + - - +
736A LYS* 4.0 4.9 - - - +
737A ARG* 3.4 27.8 + - + +
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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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682A PHE* 4.0 19.7 - - + -
686A TYR* 3.7 18.3 - - + -
689A LEU* 3.6 18.7 - - + +
706A LEU* 3.8 26.7 - - + -
707A LEU* 4.6 3.4 - - + -
710A TYR* 3.8 31.0 - - + -
726A LEU* 3.7 30.5 - - + -
730A LEU* 2.9 21.4 + - + +
731A GLU* 3.2 5.4 + - - +
733A LYS* 1.4 75.1 - - - +
735A GLU* 1.3 59.0 + - - +
737A ARG 3.5 0.7 + - - -
738A ARG* 3.0 28.4 + - - +
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Residues in contact with GLU 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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125A HIS* 4.2 13.5 - - + +
146A LYS* 3.5 23.1 - - + +
685A ARG* 2.8 38.3 + - - -
686A TYR* 2.7 26.6 + - - +
731A GLU* 2.8 41.2 + - - +
732A GLN* 3.9 6.5 - - - +
734A LEU* 1.3 69.5 - - - +
736A LYS* 1.3 66.3 + - - +
738A ARG* 3.3 6.9 + - - +
739A GLU* 3.1 23.7 + - - +
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Residues in contact with LYS 736 (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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125A HIS* 3.7 30.9 + - + -
128A GLU* 3.1 31.0 + - + +
732A GLN 3.0 18.1 + - - +
733A LYS* 4.0 6.5 - - - +
735A GLU* 1.3 77.0 - - - +
737A ARG* 1.3 63.1 + - + +
739A GLU* 3.5 3.8 + - - +
740A GLU* 3.3 49.0 + - - +
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Residues in contact with ARG 737 (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 13.1 + - + +
710A TYR* 3.2 37.4 + - + +
733A LYS* 3.4 19.9 + - + +
734A LEU 3.9 2.7 - - - +
735A GLU 3.3 0.6 - - - -
736A LYS* 1.3 75.0 - - + +
738A ARG* 1.3 63.7 + - - +
740A GLU* 3.5 23.7 + - - +
741A GLU* 2.9 59.4 + - - +
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Residues in contact with ARG 738 (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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684A LYS 5.5 0.8 + - - -
685A ARG* 2.8 81.6 + - - +
686A TYR* 4.1 11.9 - - + -
688A VAL* 4.3 15.2 - - + +
689A LEU* 3.8 9.4 - - + +
734A LEU 3.0 17.0 + - - +
735A GLU* 3.3 8.7 + - - +
737A ARG* 1.3 75.2 - - - +
739A GLU* 1.4 64.5 + - - +
741A GLU* 3.3 18.7 + - - +
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Residues in contact with GLU 739 (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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123A ARG 5.8 0.2 - - - +
125A HIS* 3.3 31.0 + - + +
142A ARG* 5.5 7.6 + - - -
735A GLU 3.1 16.6 + - - +
736A LYS 3.7 4.7 - - - +
738A ARG* 1.4 79.0 - - - +
740A GLU* 1.4 62.7 + - - +
741A GLU 3.4 5.4 + - - -
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Residues in contact with GLU 740 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A LYS* 3.3 44.5 + - + +
737A ARG* 3.5 38.2 + - - +
738A ARG 3.4 0.2 - - - -
739A GLU* 1.4 76.5 - - + +
741A GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 741 (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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688A VAL* 4.1 22.2 - - + +
689A LEU* 3.8 12.1 - - + -
691A ARG* 3.0 35.7 + - - +
737A ARG* 2.9 47.5 + - - +
738A ARG 3.3 14.2 + - - +
739A GLU 3.3 5.5 - - - -
740A GLU* 1.3 81.4 - - - +
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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