Contacts of the helix formed by residues 456 - 464 (chain A) in PDB entry 1J07
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 GLY 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PHE* 3.6 9.4 - - - -
452A GLU 3.3 1.6 + - - -
453A PHE 3.1 16.3 + - - -
454A ILE 3.2 0.8 - - - -
455A PHE* 1.3 79.3 - - - +
457A LEU* 1.3 64.9 + - - +
458A PRO* 3.2 6.1 - - - -
459A LEU* 2.9 23.8 + - - +
473A ALA* 4.3 4.3 - - - -
477A MET* 3.7 20.2 - - - -
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Residues in contact with LEU 457 (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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131A ASP* 3.8 30.3 - - + +
132A VAL* 4.0 25.6 - - + +
134A ASP* 4.8 2.0 - - + -
137A PHE* 4.0 22.2 - - + -
452A GLU* 3.0 21.7 + - + +
455A PHE* 3.9 19.3 - - + -
456A GLY* 1.3 75.0 - - - +
458A PRO* 1.3 70.2 - - + +
459A LEU 2.8 2.1 + - - -
460A ASP* 2.8 20.8 + - - +
463A LEU* 3.6 25.6 - - + +
465A TYR* 4.2 8.7 - - + +
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Residues in contact with PRO 458 (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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452A GLU 3.3 12.6 - - - +
453A PHE* 3.7 26.2 - - + -
456A GLY* 3.2 8.3 - - - -
457A LEU* 1.3 90.0 - - + +
459A LEU* 1.3 58.6 + - - +
460A ASP 3.1 7.1 + - - +
461A PRO* 4.8 0.7 - - - +
465A TYR* 3.3 49.0 - - + +
469A GLU 4.0 15.9 - - - +
470A ARG* 3.6 19.5 - - - +
473A ALA* 3.9 6.7 - - + -
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Residues in contact with LEU 459 (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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25A PRO* 3.3 20.4 - - + +
137A PHE* 4.2 12.8 - - + -
141A VAL* 3.6 31.6 - - + -
456A GLY* 2.9 18.6 + - - +
457A LEU 2.8 4.4 + - - -
458A PRO* 1.3 74.2 - - - +
460A ASP* 1.3 57.7 + - - +
461A PRO* 3.1 15.0 - - - +
470A ARG* 3.8 26.2 - - + +
473A ALA* 3.9 13.0 - - + -
474A GLN* 3.8 33.7 - - + +
477A MET* 4.3 13.5 - - - -
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Residues in contact with ASP 460 (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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25A PRO* 4.0 6.5 - - - +
137A PHE* 4.1 21.1 - - + -
457A LEU 2.8 13.2 + - - +
458A PRO 4.0 5.6 - - - +
459A LEU* 1.3 76.8 - - - +
461A PRO* 1.3 70.5 - - - +
462A SER* 2.6 32.7 + - - -
463A LEU* 2.9 32.5 + - + +
464A ASN 4.4 1.2 + - - -
465A TYR* 5.1 1.0 + - - -
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Residues in contact with PRO 461 (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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25A PRO* 4.5 10.5 - - + -
458A PRO 5.3 0.7 - - - +
459A LEU 3.1 11.4 - - - +
460A ASP* 1.3 89.4 - - - +
462A SER* 1.3 61.0 + - - +
463A LEU 3.0 1.7 + - - -
464A ASN* 3.3 16.3 + - - +
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Residues in contact with SER 462 (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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460A ASP* 2.6 28.3 + - - -
461A PRO* 1.3 78.5 - - - +
463A LEU* 1.3 64.9 + - - +
464A ASN* 3.3 4.9 + - - +
701A NAG 3.6 20.4 + - - +
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Residues in contact with LEU 463 (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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137A PHE* 5.7 1.1 - - + -
436A THR* 4.0 9.9 - - - +
457A LEU* 3.6 46.0 - - + +
460A ASP* 2.9 29.3 + - + +
462A SER* 1.3 85.2 - - - +
464A ASN* 1.3 69.9 + - - +
465A TYR* 3.4 22.8 + - + -
701A NAG 3.8 17.9 - - + +
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Residues in contact with ASN 464 (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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435A SER* 4.2 3.6 + - - -
436A THR* 3.9 12.4 - - + +
460A ASP 4.4 0.6 + - - -
461A PRO 3.3 14.4 + - - +
462A SER* 4.1 2.3 - - - +
463A LEU* 1.3 78.7 - - - +
465A TYR* 1.3 63.0 + - - +
466A THR* 4.0 0.9 + - - +
701A NAG 1.5 69.7 + - + +
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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