Contacts of the helix formed by residues 744 - 749 (chain N) in PDB entry 2JA7
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 HIS 744 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27N ALA* 6.0 6.7 - - + -
30N SER* 4.5 10.5 + - - -
31N TRP* 3.7 30.6 + + + -
34N ILE* 4.2 17.7 - - + +
705N MET 5.4 0.2 - - - -
742N GLU* 3.1 11.8 + - - +
743N ILE* 1.3 81.5 + - - +
745N PRO* 1.3 79.4 - - + +
746N SER* 2.8 44.9 - - - +
747N MET* 3.3 17.2 + - - +
1045N SER* 5.9 0.2 - - - -
1046N PRO* 5.4 1.8 - - - +
1047N PHE* 3.9 21.4 + - - -
1048N THR* 4.9 8.7 - - + +
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Residues in contact with PRO 745 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810M PRO* 3.4 30.7 - - + -
519N TRP* 5.0 3.4 - - + -
705N MET* 3.6 32.8 - - + +
706N GLN* 5.9 4.9 - - + -
730N ARG* 5.9 1.1 - - - +
742N GLU* 4.5 4.2 - - + -
744N HIS* 1.3 95.6 - - + +
746N SER* 1.3 53.7 + - - +
747N MET 2.4 20.2 + - - -
748N ILE* 2.7 26.1 + - + +
1047N PHE* 3.5 27.1 - - + +
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Residues in contact with SER 746 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N TRP* 3.5 16.2 - - - -
541N LEU* 5.1 0.5 - - - +
744N HIS* 2.8 27.7 - - - -
745N PRO* 1.3 79.1 - - - +
747N MET* 1.3 68.6 + - - +
748N ILE* 3.3 1.6 - - - -
749N LEU* 3.4 23.8 - - - +
754N SER* 4.9 2.4 + - - -
808N ALA* 5.5 3.6 - - - +
1046N PRO* 3.5 32.8 - - - -
1047N PHE* 3.4 10.9 - - - -
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Residues in contact with MET 747 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N TRP* 4.7 5.6 - - + -
34N ILE* 3.8 34.3 - - + -
38N PHE* 3.9 8.3 - - + -
520N GLY* 4.2 2.9 - - - +
540N SER* 3.2 19.2 - - - -
541N LEU* 3.7 33.7 + - + -
542N MET* 3.1 53.7 + - + +
635N ARG* 6.3 1.1 - - - +
742N GLU* 6.3 0.4 - - + -
743N ILE* 5.3 0.7 - - + -
744N HIS 3.5 17.5 - - - +
745N PRO 2.4 16.4 + - - -
746N SER* 1.3 83.7 - - - +
748N ILE* 1.3 57.8 + - - -
749N LEU 2.9 9.0 + - - +
808N ALA* 5.6 2.7 - - + -
811N TYR* 6.2 0.7 - - + -
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Residues in contact with ILE 748 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810M PRO 4.6 1.1 - - - +
813M PHE* 4.2 18.4 - - + -
814M PHE* 4.9 6.1 - - + -
519N TRP* 3.3 53.2 - - + +
520N GLY* 3.3 31.6 - - - +
522N VAL 3.5 2.6 - - - +
523N CYS* 3.5 1.7 - - - -
524N PRO* 3.5 19.1 - - + +
540N SER* 2.7 19.0 + - - -
635N ARG* 5.7 0.7 - - - +
742N GLU* 6.0 0.4 - - - -
745N PRO 2.7 18.0 + - - +
746N SER 4.5 1.3 - - - -
747N MET* 1.3 78.3 - - - +
749N LEU* 1.3 66.1 + - + +
1047N PHE* 4.0 20.0 - - + -
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Residues in contact with LEU 749 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813M PHE* 3.8 30.7 - - + -
523N CYS* 4.2 2.2 - - - -
524N PRO* 4.2 11.7 - - + -
525N ALA* 5.8 0.7 - - + -
540N SER* 3.2 3.5 - - - -
541N LEU* 3.0 28.1 + - - +
746N SER* 3.4 20.0 - - - +
747N MET 2.9 2.6 - - - +
748N ILE* 1.3 86.6 - - + +
750N GLY* 1.3 60.1 + - - +
753N ALA* 4.1 27.1 - - + -
754N SER* 3.9 20.0 - - - +
759N PRO* 4.5 14.8 - - + -
1046N PRO* 4.3 21.3 - - + -
1047N PHE* 5.9 2.5 - - + -
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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