Contacts of the helix formed by residues 752 - 756 (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 ALA 752 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489N SER* 6.0 0.7 - - - -
493N SER* 5.0 1.8 - - - +
526N GLU* 2.9 43.1 + - + +
750N GLY 2.8 3.2 + - - -
751N VAL* 1.3 80.3 - - - +
753N ALA* 1.3 65.7 + - - +
755N ILE* 3.2 27.1 + - - +
756N ILE* 4.2 4.1 - - - +
770N GLN 5.5 1.3 - - - +
771N SER* 4.0 19.7 - - - +
775N LYS* 4.9 4.5 - - + -
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Residues in contact with ALA 753 (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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523N CYS* 4.1 13.0 - - - -
525N ALA* 5.1 5.4 - - + -
749N LEU* 4.1 31.2 - - + +
750N GLY 2.9 10.1 + - - +
752N ALA* 1.3 77.4 - - - +
754N SER* 1.3 51.6 + - - +
755N ILE 2.6 1.2 + - - -
756N ILE* 2.5 58.4 + - + +
759N PRO* 5.4 2.0 - - + +
767N ASN* 5.9 0.4 - - + -
771N SER* 4.1 6.4 + - - +
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Residues in contact with SER 754 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541N LEU* 3.4 21.4 - - - +
746N SER 4.9 0.9 + - - -
749N LEU* 3.9 19.8 - - - +
750N GLY 3.3 8.9 + - - -
751N VAL 3.1 13.1 + - - -
753N ALA* 1.3 76.1 - - - +
755N ILE* 1.3 57.0 + - - +
756N ILE 4.6 1.6 - - - -
806N THR* 3.3 30.0 + - - +
808N ALA* 3.8 15.1 - - - +
809N MET* 4.2 3.1 - - - +
812N LEU* 3.7 18.4 - - - -
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Residues in contact with ILE 755 (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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489N SER* 4.0 28.0 - - - +
751N VAL 3.9 9.4 - - - +
752N ALA* 3.2 22.4 - - - +
753N ALA 2.6 2.8 + - - -
754N SER* 1.3 75.0 - - - +
756N ILE* 1.3 62.8 + - + +
757N PRO* 3.0 15.1 - - - +
770N GLN* 6.0 6.3 - - - +
774N GLY* 5.9 6.7 - - - -
806N THR* 4.7 0.2 - - - -
809N MET* 3.7 17.5 - - + +
812N LEU* 4.7 9.4 - - + -
814N PHE* 3.8 39.9 - - + -
983N ARG* 3.1 22.1 + - + +
1091N TYR* 5.9 0.4 - - + -
1093N GLN* 6.1 4.0 - - - +
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Residues in contact with ILE 756 (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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752N ALA 4.2 3.6 - - - +
753N ALA* 2.5 36.6 + - + +
754N SER 4.6 0.9 - - - +
755N ILE* 1.3 71.3 - - + +
757N PRO* 1.3 72.1 - - + +
759N PRO* 3.0 26.7 - - + +
762N ASN* 4.1 5.2 - - - +
767N ASN* 3.4 40.8 - - + +
770N GLN* 3.9 20.0 - - + -
771N SER* 3.4 25.4 - - - +
806N THR* 4.0 8.4 + - - -
983N ARG* 3.6 19.3 - - - +
984N HIS* 4.5 0.7 - - - +
1046N PRO* 5.6 0.9 - - - +
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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