Contacts of the helix formed by residues 467 - 479 (chain D) in PDB entry 2J2M
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 ASP 467 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D MET* 5.2 0.2 - - + -
425D GLY* 4.7 2.2 - - - -
428D TYR* 3.6 26.2 - - + -
429D ARG* 2.9 37.4 + - - +
463D PHE 2.9 11.8 + - - +
464D TYR 3.1 4.6 + - - +
466D ALA* 1.3 81.2 - - + +
468D ALA* 1.3 60.4 + - - +
469D SER* 3.0 14.4 + - - -
470D LEU* 2.7 33.6 + - + +
471D GLY 2.9 24.9 + - - -
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Residues in contact with ALA 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D TYR* 3.3 38.4 + - + +
467D ASP* 1.3 72.4 + - - +
469D SER* 1.3 58.0 + - - +
471D GLY* 3.4 0.9 + - - -
472D GLU* 2.8 40.4 + - - +
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Residues in contact with SER 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D TYR* 4.3 6.6 - - - -
467D ASP* 3.0 12.3 + - - -
468D ALA* 1.3 75.8 - - - +
470D LEU* 1.3 63.1 + - - +
472D GLU* 3.1 15.8 + - - +
473D LYS* 2.9 53.8 + - - +
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Residues in contact with LEU 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D MET* 3.7 37.7 - - + -
428D TYR* 3.6 40.4 - - + +
439D LEU* 4.1 6.5 - - + -
440D LEU* 4.2 16.4 - - + +
443D LEU* 4.3 8.5 - - + -
463D PHE* 4.2 17.5 - - + +
467D ASP* 2.7 19.3 + - + +
469D SER* 1.3 74.2 + - - +
471D GLY* 1.3 63.4 + - - +
473D LYS* 3.3 6.1 + - + +
474D LEU* 2.9 43.7 + - + +
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Residues in contact with GLY 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D ILE* 3.4 12.1 - - - +
463D PHE* 4.4 2.2 + - - -
464D TYR* 3.7 31.1 - - - +
467D ASP 2.9 15.3 + - - -
468D ALA 3.6 4.0 - - - -
470D LEU* 1.3 77.2 - - - +
472D GLU* 1.3 56.8 + - - +
474D LEU* 3.5 1.3 + - - -
475D SER* 3.0 29.2 + - - -
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Residues in contact with GLU 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D TYR* 4.1 18.8 + - + -
468D ALA* 2.8 29.2 + - - +
469D SER* 3.5 16.4 + - - +
471D GLY* 1.3 71.2 - - - +
473D LYS* 1.3 53.5 + - + +
475D SER* 3.1 7.8 + - - -
476D GLU* 2.6 48.4 + - + +
482D ILE* 4.5 6.5 - - + -
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Residues in contact with LYS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D TYR* 3.9 19.8 + - - +
436D GLN* 5.3 5.5 + - - +
440D LEU* 3.9 32.0 - - + +
469D SER* 2.9 37.8 + - - +
470D LEU* 3.7 5.4 - - + +
472D GLU* 1.3 71.6 - - + +
474D LEU* 1.3 57.5 + - - +
476D GLU* 3.4 17.1 + - - +
477D ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D LEU* 3.9 12.5 - - + +
443D LEU* 3.8 35.9 - - + -
444D VAL* 3.9 14.8 - - + +
447D LEU* 4.0 8.5 - - + -
460D ILE* 4.2 9.6 - - + -
463D PHE* 3.7 40.2 - - + -
470D LEU* 2.9 23.0 + - + +
471D GLY* 3.8 3.8 - - - +
473D LYS* 1.3 72.3 - - - +
475D SER* 1.3 64.9 + - - +
477D ALA* 3.4 2.9 + - - +
478D LEU* 3.0 52.2 + - + +
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Residues in contact with SER 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D ILE* 3.9 9.8 - - - +
471D GLY 3.0 14.8 + - - -
472D GLU* 3.2 11.0 - - - -
474D LEU* 1.3 78.3 - - - +
476D GLU* 1.3 64.7 + - - +
479D ASN* 3.3 2.8 - - - +
480D VAL 2.6 48.5 + - - +
481D ASP* 3.9 2.4 - - - -
482D ILE* 3.6 32.9 + - - +
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Residues in contact with GLU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D GLU* 2.6 26.7 + - + +
473D LYS* 3.6 23.2 + - - +
475D SER* 1.3 73.8 + - - +
477D ALA* 1.3 57.3 + - - +
479D ASN* 3.0 22.4 + - - +
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Residues in contact with ALA 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D LEU* 5.3 4.9 - - + -
444D VAL* 3.8 32.5 - - + +
448D GLN* 4.5 5.5 + - - -
473D LYS 3.0 17.7 + - - +
474D LEU 4.2 0.7 - - - +
475D SER 3.4 0.2 - - - -
476D GLU* 1.3 76.6 - - - +
478D LEU* 1.3 64.3 + - - +
479D ASN* 3.9 6.5 + - - +
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Residues in contact with LEU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D VAL* 3.8 37.7 - - + +
447D LEU* 4.1 17.3 - - + +
448D GLN* 4.1 16.5 + - + +
456D VAL* 4.3 12.3 - - + -
460D ILE* 3.8 24.9 - - + -
474D LEU* 3.0 42.9 + - + +
475D SER 4.1 1.6 - - - +
477D ALA* 1.3 79.1 - - - +
479D ASN* 1.3 58.3 + - - +
480D VAL* 4.2 9.9 - - + +
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Residues in contact with ASN 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D SER 3.3 2.5 - - - +
476D GLU 3.0 24.6 + - - +
477D ALA 4.3 5.1 + - - -
478D LEU* 1.3 75.5 + - - +
480D VAL* 1.3 63.1 + - - +
481D ASP 4.2 0.7 + - - -
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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