Contacts of the helix formed by residues 452 - 467 (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 HIS 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A ARG* 3.1 54.2 + - - +
388A TYR* 3.7 15.9 + - - -
161D ASP* 3.0 24.0 + - - +
450D VAL* 3.5 3.3 - - - +
451D ARG* 1.3 89.2 - - + +
453D GLU* 1.3 69.5 + - - +
454D ASN 3.5 0.9 - - - +
455D THR* 3.4 11.1 + - - +
456D VAL* 3.5 16.6 + - - +
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Residues in contact with GLU 453 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451D ARG 4.2 1.0 + - - -
452D HIS* 1.3 71.5 - - - +
454D ASN* 1.3 69.2 + - - +
456D VAL* 3.1 11.2 + - - +
457D LEU* 3.1 38.7 + - + +
480D VAL* 6.0 8.3 - - + -
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Residues in contact with ASN 454 (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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452D HIS* 3.5 1.0 - - - +
453D GLU* 1.3 81.7 + - - +
455D THR* 1.3 59.2 + - - +
457D LEU* 3.8 22.8 - - + +
458D LEU* 3.1 32.7 + - - +
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Residues in contact with THR 455 (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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387A ARG* 3.2 31.1 + - - +
164D TRP* 3.7 42.8 - - + +
165D ASP* 3.6 11.5 + - - +
168D THR* 3.4 9.4 + - + +
447D LEU* 6.0 0.2 - - + -
450D VAL* 3.8 11.7 - - + -
452D HIS* 3.4 10.1 + - - +
453D GLU 3.2 1.0 - - - -
454D ASN* 1.3 75.3 - - - +
456D VAL* 1.3 61.6 + - - +
458D LEU* 3.2 8.2 + - - +
459D ALA* 2.9 25.6 + - + +
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Residues in contact with VAL 456 (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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447D LEU* 4.1 17.9 - - + +
450D VAL* 3.6 30.5 - - + +
452D HIS 3.5 15.4 + - - +
453D GLU* 3.1 7.8 + - - +
455D THR* 1.3 74.4 - - - +
457D LEU* 1.3 65.2 + - - +
459D ALA* 3.1 8.7 + - - +
460D ILE* 3.0 45.4 + - + +
478D LEU* 4.3 17.9 - - + -
480D VAL* 4.9 10.5 - - + -
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Residues in contact with LEU 457 (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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453D GLU* 3.1 29.4 + - + +
454D ASN* 3.8 23.8 - - - +
456D VAL* 1.3 73.9 - - - +
458D LEU* 1.3 57.1 + - - +
460D ILE* 3.2 12.9 + - + +
461D CYS* 3.0 42.9 + - - -
480D VAL* 4.9 21.5 - - + +
481D ASP 5.6 3.1 - - - +
482D ILE* 5.2 12.9 - - + +
485D PHE* 4.0 31.6 - - - +
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Residues in contact with LEU 458 (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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168D THR* 3.8 30.1 - - - +
169D LEU* 3.8 22.4 - - + -
454D ASN 3.1 18.9 + - - +
455D THR* 3.2 5.8 + - - +
457D LEU* 1.3 75.2 - - - +
459D ALA* 1.3 61.8 + - - +
461D CYS* 3.3 9.5 + - + +
462D ASN* 2.8 47.4 + - - +
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Residues in contact with ALA 459 (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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164D TRP* 4.1 11.9 - - + -
168D THR* 3.6 16.1 - - + +
447D LEU* 3.8 29.8 - - + -
455D THR* 2.9 13.4 + - + +
456D VAL 3.4 8.7 - - - +
458D LEU* 1.3 76.6 - - - +
460D ILE* 1.3 58.6 + - - +
462D ASN* 3.3 5.2 + - - +
463D PHE* 2.9 37.1 + - + -
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Residues in contact with ILE 460 (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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447D LEU* 4.9 4.5 - - + -
456D VAL* 3.0 27.4 + - + +
457D LEU* 3.7 8.3 - - + +
459D ALA* 1.3 75.3 - - - +
461D CYS* 1.3 51.1 + - - +
463D PHE* 3.3 7.1 + - - +
464D TYR* 2.7 35.9 + - - +
471D GLY* 3.4 25.9 - - - +
474D LEU* 4.2 8.1 - - + -
475D SER* 3.9 20.4 - - - +
478D LEU* 3.8 37.2 - - + -
480D VAL* 4.6 13.0 - - + -
482D ILE* 4.0 17.0 - - + -
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Residues in contact with CYS 461 (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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457D LEU* 3.0 32.8 + - - +
458D LEU* 3.7 15.5 - - + +
460D ILE* 1.3 73.4 - - - +
462D ASN* 1.3 60.9 + - - +
464D TYR* 3.1 8.2 + - - +
465D ARG* 2.8 44.7 + - + +
482D ILE* 5.3 11.0 - - - -
485D PHE* 5.2 13.0 - - - -
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Residues in contact with ASN 462 (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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167D MET 4.6 0.2 + - - -
168D THR* 3.4 38.6 + - - +
171D PRO* 4.0 12.0 - - - +
174D THR* 3.8 13.0 + - + +
421D PHE* 3.4 42.5 - - + -
458D LEU* 2.8 34.1 + - - +
459D ALA* 3.6 5.1 - - - +
461D CYS* 1.3 73.0 - - - +
463D PHE* 1.3 64.0 + - + +
465D ARG* 4.9 2.3 - - - -
466D ALA* 3.3 17.5 + - - +
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Residues in contact with PHE 463 (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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164D TRP* 3.8 19.7 - + - -
174D THR* 4.1 14.8 - - + -
177D LEU* 3.6 28.9 - - + -
178D MET* 3.8 35.7 - - + -
443D LEU* 3.6 32.5 - - + -
447D LEU* 4.8 4.0 - - + -
459D ALA* 2.9 28.2 + - + +
460D ILE 3.8 3.4 - - - +
462D ASN* 1.3 76.7 - - + +
464D TYR* 1.3 57.8 + - - +
466D ALA* 3.1 6.4 + - - +
467D ASP* 2.9 29.4 + - - +
470D LEU* 4.2 11.1 - - + +
471D GLY* 4.4 2.0 + - - -
474D LEU* 3.7 29.8 - - + -
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Residues in contact with TYR 464 (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 2.7 22.5 + - - +
461D CYS* 3.4 10.5 - - - +
463D PHE* 1.3 71.8 - - - +
465D ARG* 1.3 69.0 + - + +
467D ASP 3.1 24.3 - - - -
468D ALA* 3.3 44.7 + - + +
471D GLY* 3.7 8.4 - - - -
472D GLU* 4.3 13.8 + - + -
482D ILE* 3.6 31.2 - - + -
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Residues in contact with ARG 465 (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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421D PHE* 3.8 47.7 - - + +
461D CYS* 2.8 29.7 + - + +
462D ASN* 3.8 6.5 - - - +
464D TYR* 1.3 80.5 - - + +
466D ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 466 (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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174D THR* 4.3 3.8 - - + -
178D MET* 3.6 25.1 - - + -
421D PHE* 3.5 25.0 - - + +
422D GLY* 5.0 0.5 - - - +
424D ALA* 4.1 5.8 - - + -
425D GLY* 3.3 11.5 - - - +
429D ARG* 3.2 18.4 + - - -
462D ASN 3.3 10.5 + - - +
463D PHE 3.1 10.2 + - - +
465D ARG* 1.3 81.5 - - - +
467D ASP* 1.3 58.9 + - - +
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Residues in contact with ASP 467 (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* 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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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