Contacts of the helix formed by residues 720 - 728 (chain A) in PDB entry 5E3H
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 ASN 720 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719A GLY* 1.3 75.9 - - - -
721A VAL* 1.3 65.6 + - + +
722A ILE* 3.0 16.9 + - + +
723A LYS* 2.6 62.9 + - - +
724A MET* 3.3 19.4 + - - +
754A ASN* 3.7 10.4 + - - +
6B C 3.2 25.6 + - - +
7B U 3.6 19.3 + - - +
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Residues in contact with VAL 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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411A SER* 5.5 0.2 - - - +
413A GLY* 4.1 26.9 - - - -
414A VAL* 4.4 7.4 - - + +
415A GLY 5.6 1.3 - - - +
720A ASN* 1.3 78.4 - - + +
722A ILE* 1.3 66.8 + - + +
724A MET* 3.5 5.8 + - - +
725A ILE* 3.1 32.4 + - + +
754A ASN* 3.5 36.3 + - + +
757A LYS* 4.3 14.5 - - + +
758A GLU* 3.8 26.9 - - + +
761A MET* 5.2 3.4 - - - -
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Residues in contact with ILE 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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375A HIS* 3.7 47.6 - - + +
409A THR* 5.2 0.2 - - - +
411A SER* 3.3 24.6 + - - +
412A VAL 4.3 14.4 - - - +
413A GLY* 4.2 8.7 - - - -
426A TYR* 5.7 3.8 - - - +
702A GLU* 4.6 0.9 - - - +
720A ASN* 3.0 16.7 + - + +
721A VAL* 1.3 85.9 - - + +
723A LYS* 1.3 72.3 + - + +
725A ILE* 3.3 3.8 + - - +
726A GLN* 3.0 36.4 + - - +
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Residues in contact with LYS 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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375A HIS* 5.4 2.6 + - - -
376A ASN* 5.9 1.0 + - - -
701A ASP* 3.0 44.6 - - - +
702A GLU* 4.4 11.6 + - - -
717A TYR* 5.4 7.2 - - + +
719A GLY* 5.1 6.1 - - - -
720A ASN* 2.6 53.1 + - - +
722A ILE* 1.3 77.6 - - + +
724A MET* 1.3 55.3 + - - +
726A GLN* 3.1 14.9 + - - +
727A THR* 2.8 39.4 + - + +
5B G 4.8 4.2 + - - -
6B C 3.8 29.7 + - - +
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Residues in contact with MET 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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458A LYS* 3.4 31.9 - - - +
720A ASN 3.3 12.0 + - - +
721A VAL* 3.5 11.4 - - - +
722A ILE 3.2 0.2 - - - -
723A LYS* 1.3 79.5 - - - +
725A ILE* 1.3 61.7 + - + +
727A THR* 2.7 21.2 + - - -
728A ARG* 3.4 39.0 + - - +
751A GLU* 4.1 11.9 - - - +
754A ASN* 3.9 29.2 - - - +
755A MET* 3.8 25.4 - - + -
758A GLU* 3.8 9.4 - - - +
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Residues in contact with ILE 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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265A PRO* 5.5 5.8 - - + -
266A THR* 4.1 6.9 + - - -
410A ALA* 3.8 28.9 - - + +
411A SER* 3.5 26.5 - - - +
721A VAL* 3.1 24.0 + - + +
722A ILE 3.3 4.4 + - - +
724A MET* 1.3 78.5 - - + +
726A GLN* 1.3 63.6 + - - +
728A ARG* 3.5 33.4 - - - +
729A GLY 4.4 0.3 + - - -
758A GLU* 3.9 38.8 - - + +
761A MET* 4.0 8.5 - - + -
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Residues in contact with GLN 726 (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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266A THR* 3.7 19.3 + - - +
373A GLU* 3.5 9.1 + - - -
375A HIS* 3.3 19.4 - - - -
409A THR* 5.4 0.6 + - - -
410A ALA* 4.7 10.3 - - + +
701A ASP* 5.6 1.3 - - - -
702A GLU* 2.9 60.7 + - - +
722A ILE* 3.0 19.2 + - + +
723A LYS* 3.1 26.4 + - - +
725A ILE* 1.3 75.4 - - - +
727A THR* 1.3 53.2 - - + +
728A ARG 3.0 4.7 - - - -
729A GLY* 2.7 29.8 + - - -
730A ARG* 5.5 1.0 + - - +
1007A BEF 4.8 4.2 - - - -
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Residues in contact with THR 727 (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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633A PHE* 4.7 25.1 - - + -
700A ALA* 5.8 4.0 - - + +
701A ASP* 4.9 12.3 - - - +
712A VAL* 4.9 12.6 - - - +
714A LEU* 5.3 12.7 - - + +
717A TYR* 5.6 6.5 - - + -
723A LYS* 2.8 20.9 + - + +
724A MET* 2.7 25.9 + - - +
726A GLN* 1.3 73.7 - - + +
728A ARG* 1.3 60.5 + - - +
729A GLY 3.0 1.0 + - - -
730A ARG* 3.3 26.6 + - - +
731A GLY 4.4 0.5 + - - -
738A CYS* 6.1 1.5 - - - -
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Residues in contact with ARG 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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266A THR* 6.1 0.2 - - - -
454A TYR 5.0 1.6 - - - +
455A LYS* 3.6 36.9 - - - +
456A PRO* 3.9 35.2 + - + +
458A LYS* 6.0 1.6 - - - +
724A MET* 3.4 33.3 + - - +
725A ILE* 3.5 29.1 - - - +
726A GLN 3.0 0.8 + - - -
727A THR* 1.3 74.4 - - - +
729A GLY* 1.3 53.3 + - - +
730A ARG 2.9 6.1 - - - -
731A GLY* 2.6 33.4 + - - +
732A ARG* 3.5 2.9 + - - +
758A GLU* 2.7 43.4 + - - -
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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