Contacts of the helix formed by residues 432 - 448 (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 THR 432 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430D ARG 3.9 1.5 + - - +
431D MET* 1.3 77.1 - - - +
433D GLU* 1.3 64.9 + - - +
434D GLU* 3.6 19.2 - - - +
435D GLU* 2.8 40.0 + - - +
436D GLN* 3.1 23.6 + - - +
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Residues in contact with GLU 433 (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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432D THR* 1.3 71.2 - - - +
434D GLU* 1.3 72.1 + - - +
436D GLN* 3.9 13.8 + - - +
437D MET* 3.0 42.1 + - + +
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Residues in contact with GLU 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D THR* 3.6 16.0 - - - +
433D GLU* 1.3 89.0 + - - +
435D GLU* 1.3 59.4 + - + +
437D MET* 3.2 12.2 + - - +
438D ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 435 (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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182D THR* 4.5 14.3 - - + +
430D ARG 4.6 1.0 - - - +
431D MET* 3.3 30.4 - - + +
432D THR* 2.8 40.7 + - - +
433D GLU 3.4 0.2 - - - -
434D GLU* 1.3 79.6 - - + +
436D GLN* 1.3 57.7 + - - +
438D ALA* 3.2 6.5 + - - +
439D LEU* 2.8 31.4 + - - +
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Residues in contact with GLN 436 (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* 3.0 69.8 + - + +
429D ARG* 4.2 8.1 + - - +
431D MET* 3.7 16.6 + - + -
432D THR 3.1 18.4 + - - +
433D GLU* 3.9 15.0 - - + +
435D GLU* 1.3 75.0 - - - +
437D MET* 1.3 57.2 + - - +
439D LEU* 3.8 4.3 - - - +
440D LEU* 3.2 26.7 + - - +
470D LEU* 5.5 0.2 - - - +
473D LYS* 5.3 5.5 + - - +
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Residues in contact with MET 437 (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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433D GLU* 3.0 34.5 + - + +
434D GLU* 3.2 12.5 + - - +
436D GLN* 1.3 76.0 - - - +
438D ALA* 1.3 60.3 + - - +
440D LEU* 3.3 10.7 + - + +
441D ASN* 3.1 31.6 + - - +
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Residues in contact with ALA 438 (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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181D PHE 4.0 0.2 - - - -
183D ASP* 3.6 38.1 - - + +
434D GLU 2.9 15.9 + - - +
435D GLU* 3.2 8.0 + - - +
437D MET* 1.3 73.7 - - - +
439D LEU* 1.3 63.9 + - - +
441D ASN* 3.3 5.5 + - - +
442D ASN* 3.0 33.2 + - - -
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Residues in contact with LEU 439 (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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177D LEU 4.0 4.0 - - - +
178D MET* 3.7 29.4 - - - +
181D PHE* 3.3 39.6 + - + +
182D THR* 4.5 5.8 - - + +
428D TYR* 3.5 35.4 - - + -
431D MET* 4.2 9.2 - - + -
435D GLU 2.8 17.7 + - - +
436D GLN 3.8 4.3 - - - +
438D ALA* 1.3 76.6 - - - +
440D LEU* 1.3 57.0 + - - +
443D LEU* 2.9 51.5 + - + +
470D LEU* 4.1 7.9 - - + -
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Residues in contact with LEU 440 (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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436D GLN 3.2 16.4 + - - +
437D MET* 3.6 10.5 - - + +
438D ALA 3.3 0.4 - - - -
439D LEU* 1.3 78.8 - - - +
441D ASN* 1.3 62.1 + - - +
443D LEU* 3.8 4.3 - - - +
444D VAL* 2.9 44.6 + - + +
470D LEU* 4.2 9.9 - - + -
473D LYS* 3.9 32.8 - - + +
474D LEU* 3.9 39.9 - - + +
477D ALA* 5.3 3.4 - - + -
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Residues in contact with ASN 441 (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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437D MET* 3.1 15.2 + - - +
438D ALA* 3.6 10.1 - - - +
439D LEU 3.3 0.2 - - - -
440D LEU* 1.3 79.8 - - - +
442D ASN* 1.3 60.9 + - - +
444D VAL* 3.9 3.7 - - - +
445D ASN* 3.0 31.0 + - - +
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Residues in contact with ASN 442 (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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108D ARG* 3.5 25.0 + - - +
181D PHE* 2.9 43.6 + - + +
182D THR 3.6 4.4 + - - -
183D ASP* 3.3 24.3 + - - +
228D ALA* 4.2 15.8 + - - +
438D ALA* 3.0 15.5 + - - +
441D ASN* 1.3 76.4 - - - +
443D LEU* 1.3 56.5 + - - +
445D ASN* 3.4 6.6 + - - +
446D ASP* 2.8 35.5 + - - +
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Residues in contact with LEU 443 (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* 4.0 8.5 - - + -
177D LEU 4.8 0.2 - - - +
181D PHE* 3.8 28.9 - - + -
439D LEU* 2.9 50.9 + - + +
440D LEU* 3.8 1.6 - - - +
442D ASN* 1.3 75.0 - - - +
444D VAL* 1.3 53.4 + - - +
446D ASP* 3.0 4.6 + - - +
447D LEU* 2.6 41.0 + - + +
463D PHE* 3.6 35.9 - - + -
470D LEU* 4.3 6.7 - - + -
474D LEU* 3.8 35.2 - - + -
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Residues in contact with VAL 444 (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* 2.9 37.3 + - + +
441D ASN* 3.9 5.2 - - - +
443D LEU* 1.3 70.8 - - - +
445D ASN* 1.3 54.3 + - - +
447D LEU* 3.1 1.3 + - - +
448D GLN* 2.8 66.7 + - - +
474D LEU* 3.9 18.4 - - + -
477D ALA* 3.8 30.7 - - + +
478D LEU* 3.8 18.6 - - + +
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Residues in contact with ASN 445 (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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228D ALA* 5.8 3.9 - - - +
441D ASN* 3.0 19.2 + - - +
442D ASN* 3.7 7.1 - - - +
444D VAL* 1.3 76.3 - - - +
446D ASP* 1.3 60.9 + - - +
448D GLN* 3.7 23.1 + - - +
449D GLN* 3.0 31.5 + - - +
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Residues in contact with ASP 446 (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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160D PRO* 3.9 9.7 - - - +
163D TYR* 2.7 29.5 + - - -
164D TRP* 3.0 19.4 + - + +
181D PHE* 2.9 32.7 - - + -
442D ASN 2.8 18.2 + - - +
443D LEU* 3.5 3.6 - - - +
445D ASN* 1.3 76.5 + - - +
447D LEU* 1.3 60.8 - - - +
448D GLN 3.1 0.2 - - - -
449D GLN* 3.1 35.7 + - - +
450D VAL* 3.9 3.6 + - - +
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Residues in contact with LEU 447 (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* 3.6 45.5 - - + +
443D LEU* 2.6 22.2 + - + +
444D VAL 4.0 2.9 - - - +
446D ASP* 1.3 72.5 - - - +
448D GLN* 1.3 61.2 + - - +
449D GLN 3.2 0.9 + - - -
450D VAL* 3.5 24.8 + - + +
456D VAL* 4.1 19.8 - - + +
459D ALA* 3.8 26.9 - - + -
460D ILE* 4.9 4.0 - - + -
463D PHE* 4.8 5.8 - - + -
474D LEU* 4.0 27.4 - - + -
478D LEU* 4.1 22.9 - - + +
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Residues in contact with GLN 448 (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* 2.8 44.9 + - + +
445D ASN* 3.8 20.5 + - - +
446D ASP 3.1 0.6 - - - -
447D LEU* 1.3 78.2 - - - +
449D GLN* 1.3 58.2 + - + +
450D VAL 3.4 5.5 + - - +
477D ALA 4.5 8.3 + - - -
478D LEU* 4.1 14.2 + - + +
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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