Contacts of the helix formed by residues 720 - 729 (chain A) in PDB entry 1N4M
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 LYS 720 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A TYR* 4.0 5.8 - - - -
718A ASP* 5.3 8.7 - - + +
719A LEU* 1.3 78.4 - - - +
721A PHE* 1.3 65.2 + - - +
722A LYS* 3.0 46.9 - - + +
723A ILE* 3.1 32.2 + - + +
724A ILE* 3.2 12.3 + - - +
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Residues in contact with PHE 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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705A MET* 4.1 14.6 - - + -
706A CYS* 4.0 22.7 - - - -
709A TYR* 3.5 55.3 - + + -
720A LYS* 1.3 74.6 - - - +
722A LYS* 1.3 54.9 + - - +
724A ILE* 3.6 10.0 - - + +
725A VAL* 2.7 45.8 + - + +
752A ILE* 3.7 39.3 - - + -
753A ILE* 3.7 39.3 - - + -
756A TYR* 3.8 18.2 - + + -
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Residues in contact with LYS 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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720A LYS* 3.0 45.1 - - + +
721A PHE* 1.3 79.4 - - - +
723A ILE* 1.3 63.6 + - + +
725A VAL* 4.0 6.7 - - - +
726A THR* 2.7 36.0 + - - +
753A ILE* 5.4 1.0 - - - +
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Residues in contact with ILE 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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669A LEU* 3.7 25.8 - - + -
719A LEU* 3.9 11.9 - - + -
720A LYS* 3.1 36.2 + - + +
722A LYS* 1.3 88.2 - - + +
724A ILE* 1.3 67.9 + - - +
726A THR* 2.7 19.8 + - - +
727A ALA* 3.1 10.7 + - + +
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Residues in contact with ILE 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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665A LEU* 4.6 3.8 - - + +
669A LEU* 3.5 13.5 - - + -
705A MET* 3.5 39.5 - - + +
708A MET* 4.2 11.9 - - + -
709A TYR* 3.9 34.8 - - + +
719A LEU* 3.5 40.6 - - + -
720A LYS 3.2 7.3 + - - +
721A PHE* 3.6 12.1 - - + +
723A ILE* 1.3 76.8 - - - +
725A VAL* 1.3 65.3 + - - +
727A ALA* 3.1 4.2 + - - +
728A TYR* 2.9 22.0 + - - +
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Residues in contact with VAL 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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705A MET* 4.4 7.0 - - - -
721A PHE* 2.7 26.3 + - + +
722A LYS* 4.0 7.6 - - - +
724A ILE* 1.3 73.6 - - - +
726A THR* 1.3 65.3 + - - +
728A TYR* 3.6 11.6 - - - +
729A LYS* 3.2 19.5 - - + +
739A PHE* 3.3 61.3 - - + -
752A ILE* 4.4 11.0 - - + -
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Residues in contact with THR 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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722A LYS* 2.7 21.7 + - - +
723A ILE* 2.7 18.5 + - - -
725A VAL* 1.3 74.9 - - - +
727A ALA* 1.3 63.5 + - - +
729A LYS* 3.5 28.3 - - + +
730A ASP* 4.4 4.5 + - - +
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Residues in contact with ALA 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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665A LEU* 3.7 11.8 - - + +
668A ARG* 3.6 14.9 - - - +
669A LEU* 3.1 37.0 - - + -
723A ILE* 3.1 7.8 + - + +
724A ILE 3.1 5.4 + - - +
726A THR* 1.3 74.0 - - - +
728A TYR* 1.3 57.2 + - - +
729A LYS 3.0 2.5 - - - -
730A ASP* 2.6 43.3 + - - +
731A LEU 4.2 0.5 + - - -
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Residues in contact with TYR 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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665A LEU* 3.5 12.0 - - + +
699A HIS* 4.2 1.9 + - - -
701A ASP* 2.8 45.7 + - + -
704A MET* 4.3 6.1 - - + -
705A MET* 3.7 24.9 - - + -
724A ILE 2.9 17.1 + - - +
725A VAL 3.6 5.4 - - - +
727A ALA* 1.3 77.2 - - - +
729A LYS* 1.3 54.0 + - - +
731A LEU* 2.8 44.2 + - + +
733A HIS* 4.2 1.9 - + - +
734A ALA* 2.9 35.0 + - + +
735A VAL 3.5 21.9 + - - -
738A THR* 3.5 19.0 + - + +
739A PHE* 3.7 25.8 - + - -
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Residues in contact with LYS 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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725A VAL* 3.2 21.0 - - + +
726A THR* 3.5 22.7 - - + +
727A ALA 2.9 0.2 + - - -
728A TYR* 1.3 75.9 - - + +
730A ASP* 1.3 61.2 + - - +
731A LEU 3.2 3.9 + - - +
734A ALA* 3.7 16.0 - - - +
735A VAL 6.4 1.1 - - - -
736A GLN* 2.5 49.0 - - - +
739A PHE* 3.6 13.3 - - + -
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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