Contacts of the helix formed by residues 729 - 738 (chain A) in PDB entry 1FGR
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 729 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A HIS 4.7 5.8 + - - +
725A GLU* 2.7 26.7 + - + +
728A ASN* 1.3 78.2 - - + +
730A HIS* 1.3 65.0 + - - +
731A GLU* 4.0 6.2 + - - +
732A LYS* 3.2 34.0 + - + +
733A ALA 3.1 16.8 + - - -
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Residues in contact with HIS 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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286A PHE* 5.0 5.0 - + - -
341A MET* 5.2 6.1 - - + +
477A THR* 3.4 30.9 - - + +
480A LEU* 4.6 20.0 - - + +
725A GLU 3.8 0.8 + - - -
726A MET 3.7 11.5 + - - +
727A ILE 5.0 1.9 + - - +
728A ASN 4.0 0.6 - - - -
729A ASN* 1.3 71.2 - - - +
731A GLU* 1.3 92.3 + - + +
733A ALA* 3.5 6.7 - - - +
734A TYR* 3.0 24.3 + - - +
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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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284A HIS 5.2 0.2 - - - +
285A SER* 3.8 13.3 - - - -
286A PHE* 2.9 65.7 + - + +
287A GLN 4.5 1.0 + - - -
729A ASN* 3.3 6.3 + - - +
730A HIS* 1.3 100.9 + - + +
732A LYS* 1.3 57.4 + - - +
734A TYR* 3.3 2.6 + - - +
735A LEU* 2.9 35.1 + - - +
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Residues in contact with LYS 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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282A GLU* 3.7 15.4 + - - +
283A PHE 3.4 19.2 + - - +
284A HIS* 3.2 47.3 + - - +
725A GLU* 3.4 18.4 - - - +
729A ASN* 3.2 35.4 + - + +
731A GLU* 1.3 75.7 - - - +
733A ALA* 1.3 67.3 + - - +
735A LEU* 4.4 3.4 - - + +
736A ARG* 2.9 64.5 + - + +
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Residues in contact with ALA 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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477A THR* 4.7 4.7 - - + -
481A LEU* 4.4 5.4 - - + -
713A ARG* 2.9 21.3 + - - +
725A GLU* 3.7 8.4 + - - +
726A MET* 4.0 34.3 - - + +
729A ASN 3.1 13.4 + - - +
730A HIS* 3.5 9.9 - - - +
732A LYS* 1.3 75.9 - - - +
734A TYR* 1.3 60.2 + - - +
737A THR* 2.8 25.6 + - - -
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Residues in contact with TYR 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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286A PHE* 3.7 24.0 - + + -
340A TRP* 3.7 11.6 - + - -
477A THR* 6.4 0.7 - - + -
480A LEU* 3.6 40.3 - - + +
481A LEU* 3.8 21.0 - - + +
484A ALA* 3.7 32.1 + - + +
705A MET* 2.7 49.3 + - + -
708A PRO* 4.6 2.3 - - - +
730A HIS 3.0 12.9 + - - +
731A GLU 3.5 8.3 - - - +
733A ALA* 1.3 77.9 - - - +
735A LEU* 1.3 61.8 + - - +
737A THR* 3.1 12.0 + - - -
738A ILE* 3.1 26.4 + - + +
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Residues in contact with LEU 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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282A GLU* 4.1 2.5 - - - +
283A PHE* 3.8 30.4 - - + +
284A HIS 3.9 4.7 - - - -
285A SER* 3.5 44.6 - - - +
286A PHE* 4.0 15.9 - - + +
289A VAL* 4.1 22.4 - - + -
704A ILE* 5.4 0.2 - - + -
705A MET* 4.5 2.7 - - + -
712A ARG* 3.0 18.1 + - - -
731A GLU 2.9 21.7 + - - +
732A LYS* 4.0 4.7 - - + +
734A TYR* 1.3 76.0 - - - +
736A ARG* 1.3 58.3 + - - +
737A THR 3.3 0.7 + - - -
738A ILE* 3.4 30.0 - - + +
739A THR 4.5 2.1 - - - +
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Residues in contact with ARG 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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282A GLU* 4.5 7.5 - - - +
712A ARG* 3.4 29.0 + - - +
713A ARG* 3.1 34.7 + - - +
725A GLU* 2.7 41.0 + - - -
732A LYS* 2.9 47.3 + - - +
735A LEU* 1.3 77.1 - - - +
737A THR* 1.3 59.2 + - - +
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Residues in contact with THR 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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481A LEU* 3.9 19.9 - - + +
484A ALA* 5.5 3.4 - - + -
485A TYR* 3.6 37.1 + - + +
711A SER* 3.1 9.6 - - - -
712A ARG 2.7 28.8 + - - -
713A ARG* 3.2 26.4 + - - +
733A ALA 2.8 16.9 + - - -
734A TYR 3.1 9.3 + - - -
736A ARG* 1.3 80.3 - - - +
738A ILE* 1.3 64.4 + - + +
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Residues in contact with ILE 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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484A ALA* 4.2 16.4 - - + -
488A VAL* 5.3 1.8 - - + -
704A ILE* 4.1 41.7 - - + +
705A MET* 4.2 2.2 - - - -
708A PRO* 3.7 21.1 - - + -
710A ALA 3.4 8.1 - - - +
711A SER* 5.7 0.4 - - - -
712A ARG* 2.9 25.1 + - - -
734A TYR* 3.1 44.5 + - + +
735A LEU* 3.4 19.5 + - + +
737A THR* 1.3 80.8 - - + +
739A THR* 1.3 72.7 + - - +
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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