Contacts of the helix formed by residues 432 - 450 (chain B) in PDB entry 1W1J
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 SER 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 3.6 23.9 + - - -
293B VAL* 3.6 3.1 - - - -
294B ASP* 4.1 6.1 - - - -
297B ARG* 4.8 4.3 - - - +
430B LYS* 3.0 16.1 - - - +
431B VAL* 1.3 79.1 - - - +
433B GLY* 1.3 64.6 + - - +
434B GLU* 3.7 9.8 + - - +
435B ASP* 3.3 22.2 + - - +
436B ALA* 3.1 22.2 + - - +
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Residues in contact with GLY 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LYS* 3.1 33.4 - - - -
293B VAL* 3.7 16.1 - - - +
294B ASP* 2.9 14.5 + - - -
432B SER* 1.3 71.8 - - - +
434B GLU* 1.3 63.1 + - - +
436B ALA* 3.5 1.9 + - - +
437B MET* 3.1 28.1 + - - +
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LYS* 3.7 21.7 - - - +
294B ASP* 4.3 0.6 + - - -
432B SER* 3.2 8.4 + - - +
433B GLY* 1.3 77.3 - - - +
435B ASP* 1.3 63.1 + - + +
437B MET* 3.4 6.0 + - - +
438B MET* 3.2 23.2 + - + +
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LYS* 3.2 31.4 + - - +
429B ALA* 3.6 3.1 - - - +
430B LYS* 3.0 42.8 + - + +
432B SER* 3.3 18.4 + - - +
434B GLU* 1.3 77.7 - - + +
436B ALA* 1.3 61.7 + - - +
438B MET* 3.2 12.0 + - - +
439B GLN* 2.9 24.4 + - - +
500B TRP* 3.1 22.8 + - - -
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 4.4 6.3 - - + -
293B VAL* 4.2 12.8 - - + -
429B ALA* 4.8 4.7 - - - +
430B LYS 4.9 0.2 - - - +
432B SER 3.1 13.9 + - - +
433B GLY 3.8 4.0 - - - +
434B GLU 3.3 0.2 - - - -
435B ASP* 1.3 77.5 + - - +
437B MET* 1.3 58.6 + - - +
439B GLN* 3.4 6.5 + - - +
440B TYR* 2.9 28.8 + - - +
458B PHE* 4.1 15.3 - - + -
465B MET* 3.8 26.9 - - + -
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Residues in contact with MET 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP 4.6 2.7 - - - +
287B GLY* 3.8 26.9 - - - +
289B LEU* 4.2 15.5 - - - +
290B LYS* 3.5 36.8 - - + -
433B GLY 3.1 10.2 + - - +
434B GLU* 3.5 9.6 - - - +
436B ALA* 1.3 74.5 - - - +
438B MET* 1.3 54.2 - - - +
440B TYR* 3.2 20.9 + - + +
441B ALA* 2.8 37.0 + - - +
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Residues in contact with MET 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LYS* 3.2 32.8 - - - +
434B GLU* 3.2 13.8 + - + +
435B ASP* 3.2 16.1 + - - +
437B MET* 1.3 78.9 - - - +
439B GLN* 1.3 62.5 + - - +
441B ALA* 3.5 4.6 + - - +
442B VAL* 3.0 36.6 + - + +
498B ASN* 3.6 21.8 - - + +
500B TRP* 3.6 16.4 - - + -
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PRO* 3.6 19.7 - - + +
428B ILE 3.3 15.4 + - - -
429B ALA* 3.3 15.4 + - + +
435B ASP 2.9 13.7 + - - +
436B ALA* 3.7 8.5 - - - +
438B MET* 1.3 74.6 - - - +
440B TYR* 1.3 55.5 + - - +
442B VAL* 3.7 1.6 - - - +
443B THR* 2.7 40.4 + - - +
458B PHE* 4.3 0.2 - - - -
467B HIS* 3.0 41.2 - - + +
495B CYS* 4.7 2.0 - - - -
500B TRP* 3.1 54.5 - - + -
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Residues in contact with TYR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 2.7 43.4 + - - -
289B LEU* 4.5 4.7 - - + -
313B HIS* 3.5 12.6 + - - -
350B ARG* 4.1 3.3 + - - -
351B TRP* 3.8 20.6 - + - -
436B ALA 2.9 14.4 + - - +
437B MET* 3.2 28.0 - - + +
439B GLN* 1.3 75.6 - - - +
441B ALA* 1.3 53.4 + - + +
443B THR* 3.1 2.2 + - - -
444B LYS* 2.5 68.7 + - + +
454B PHE* 3.5 42.3 - + - +
458B PHE* 5.0 0.2 - - + -
467B HIS* 4.4 10.4 + - - +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B MET 2.8 19.1 + - - +
438B MET* 4.0 5.4 - - - +
440B TYR* 1.3 73.0 - - + +
442B VAL* 1.3 64.0 + - + +
444B LYS* 4.3 9.4 - - - +
445B LYS* 3.2 27.2 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B MET* 3.0 28.3 + - + +
439B GLN 3.7 3.4 - - - +
441B ALA* 1.3 79.3 - - + +
443B THR* 1.3 63.4 - - - +
445B LYS* 3.8 4.2 - - - +
446B ARG* 3.7 22.3 + - - +
491B LEU* 4.8 1.3 - - + -
494B ASP* 4.0 31.2 - - + +
495B CYS* 4.4 18.4 - - - -
498B ASN* 4.2 19.5 - - - +
500B TRP* 4.4 8.1 - - + -
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Residues in contact with THR 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B PHE* 4.3 8.7 - - + -
439B GLN* 2.7 28.2 + - - +
440B TYR* 3.6 3.1 - - - -
442B VAL* 1.3 76.1 - - - +
444B LYS* 1.3 63.1 + - - +
445B LYS 3.3 0.2 + - - -
446B ARG 3.4 1.6 + - - -
447B CYS* 2.9 30.2 + - - -
454B PHE* 3.8 11.9 - - + -
467B HIS* 4.7 2.1 + - - -
469B VAL* 3.5 40.8 - - + +
491B LEU* 3.3 30.1 - - + +
495B CYS* 4.7 2.4 - - - -
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Residues in contact with LYS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 4.1 12.1 + - - -
336B ASP* 4.6 14.6 + - - -
350B ARG* 6.1 0.2 - - - +
440B TYR* 2.5 61.5 + - + +
441B ALA* 4.3 7.1 - - - +
443B THR* 1.3 71.1 - - - +
445B LYS* 1.3 61.0 + - - +
447B CYS* 3.5 4.5 - - - +
448B GLN* 3.2 42.3 + - - +
454B PHE* 4.3 17.6 - - + -
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Residues in contact with LYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ALA 3.2 19.0 + - - +
442B VAL* 3.8 7.0 - - - +
443B THR 3.2 0.2 - - - -
444B LYS* 1.3 79.1 - - - +
446B ARG* 1.3 68.9 + - + +
448B GLN* 3.2 7.1 + - - +
449B GLU* 3.2 45.2 + - + +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B VAL 3.7 15.0 + - - +
443B THR 3.4 5.5 + - - +
445B LYS* 1.3 79.5 - - - +
447B CYS* 1.3 60.3 + - - +
449B GLU* 3.2 35.2 + - - +
450B ALA* 2.9 25.5 + - - +
486B TRP* 4.1 15.3 - - + -
487B LEU* 3.6 21.7 - - + +
490B THR* 3.6 27.5 - - + +
491B LEU* 4.3 13.7 - - + +
494B ASP* 2.7 38.9 + - - +
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Residues in contact with CYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B THR* 2.9 34.2 + - - -
444B LYS* 3.5 9.6 - - - +
446B ARG* 1.3 77.9 - - - +
448B GLN* 1.3 60.6 + - - +
450B ALA* 3.3 2.8 + - - +
451B GLY 2.9 7.4 + - - -
452B LEU* 2.8 41.8 + - + +
453B ASP 4.6 6.3 - - - +
454B PHE* 4.0 25.6 - - + -
469B VAL* 4.8 7.9 - - - -
471B ILE* 5.8 1.3 - - - -
487B LEU* 3.7 20.6 - - - +
491B LEU* 4.9 0.4 - - - -
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Residues in contact with GLN 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B GLU* 5.1 2.6 - - - +
333B PRO* 3.3 28.0 - - + +
334B LEU 5.0 7.4 + - - +
444B LYS* 3.2 41.4 + - - +
445B LYS* 3.2 5.6 + - - +
447B CYS* 1.3 79.1 - - - +
449B GLU* 1.3 58.8 + - - +
451B GLY* 3.0 18.7 + - - +
452B LEU 2.9 24.6 - - - +
453B ASP* 3.9 5.9 - - - -
454B PHE* 4.1 6.0 + - - +
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LYS* 3.2 39.9 + - + +
446B ARG* 3.2 39.1 + - - +
448B GLN* 1.3 74.4 - - - +
450B ALA* 1.3 59.3 + - - +
451B GLY* 3.0 5.1 + - - -
483B LYS* 5.1 5.4 + - - +
486B TRP* 3.5 19.0 - - + -
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ARG 2.9 18.1 + - - +
447B CYS* 3.3 3.8 + - - +
449B GLU* 1.3 72.5 - - - +
451B GLY* 1.3 59.4 + - - +
452B LEU* 3.6 9.5 + - + +
480B GLN* 5.5 4.2 + - - +
483B LYS* 3.8 53.5 + - - +
486B TRP* 4.1 9.1 - - + -
487B LEU* 3.9 19.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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