Contacts of the helix formed by residues 431 - 447 (chain B) in PDB entry 1XJP
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 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288B LYS* 3.0 47.0 + - - +
429B GLN* 3.1 36.0 - - - +
430B GLU* 1.3 77.4 - - - +
432B ASN* 1.3 65.0 + - - +
433B GLU* 2.9 7.0 - - + +
434B THR* 2.7 27.7 + - - +
435B GLU* 3.3 16.8 + - - +
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Residues in contact with ASN 432 (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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431B ASP* 1.3 76.6 - - - +
433B GLU* 1.3 77.5 + - - +
435B GLU* 3.5 9.0 - - - +
436B ILE* 3.3 28.9 + - - +
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Residues in contact with GLU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 3.3 59.7 - - + +
287B GLN* 4.7 2.1 + - - -
288B LYS* 3.0 33.8 + - + +
431B ASP 2.9 0.4 - - - -
432B ASN* 1.3 91.4 + - - +
434B THR* 1.3 56.4 + - - +
435B GLU 3.0 4.7 - - - -
436B ILE 3.9 0.2 - - - -
437B ASN* 3.0 34.5 + - - +
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 3.9 21.8 - - + -
289B PRO* 4.5 13.7 - - + +
291B ILE* 6.0 4.5 - - - -
428B PHE* 4.8 11.2 - - + -
429B GLN 4.7 5.6 - - - +
430B GLU* 3.6 8.1 - - - +
431B ASP* 2.7 50.2 + - - +
433B GLU* 1.3 76.3 - - - +
435B GLU* 1.3 62.5 + - - +
437B ASN* 3.7 10.1 - - - +
438B PHE* 3.2 21.8 + - - +
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Residues in contact with GLU 435 (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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415B PRO* 5.4 6.4 - - - +
430B GLU* 4.5 11.8 - - - +
431B ASP 3.3 14.8 + - - +
432B ASN* 3.5 14.2 - - - +
434B THR* 1.3 83.2 + - - +
436B ILE* 1.3 70.9 + - + +
437B ASN 3.1 1.1 - - - -
438B PHE* 3.0 8.4 + - - +
439B LEU* 2.9 26.6 + - + +
540B HIS* 3.1 37.4 + - + +
541B LYS* 3.4 30.3 + - - +
590B PRO* 6.1 1.6 - - + -
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 3.6 29.6 - - + -
285B PHE* 3.9 12.3 - - + -
432B ASN* 3.3 18.3 + - + +
433B GLU 3.4 2.6 + - - +
435B GLU* 1.3 84.2 - - + +
437B ASN* 1.3 58.0 + - - +
439B LEU* 3.9 4.4 - - + +
440B LEU* 2.9 30.0 + - - +
590B PRO* 3.9 31.9 - - + +
591B LEU* 4.2 8.0 - - + +
594B TRP* 3.8 39.3 - - + -
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Residues in contact with ASN 437 (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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279B TYR* 3.1 28.9 + - - +
283B VAL* 3.9 5.7 - - - +
284B PRO* 3.3 17.2 - - - +
285B PHE* 3.0 49.6 + - - +
288B LYS* 3.9 21.2 + - - +
289B PRO 6.0 0.8 - - - -
290B ASN* 5.6 3.1 - - - +
433B GLU 3.0 16.4 + - - +
434B THR* 3.7 8.2 - - - +
435B GLU 3.1 0.2 - - - -
436B ILE* 1.3 78.8 - - - +
438B PHE* 1.3 56.1 + - - +
440B LEU* 4.1 0.3 - - - +
441B LYS* 3.2 20.1 + - - +
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Residues in contact with PHE 438 (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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290B ASN* 5.8 4.7 - - - -
410B LEU* 5.9 2.5 - - + -
413B ALA* 5.5 14.1 - - + -
414B THR* 6.5 0.9 - - - -
434B THR 3.2 11.8 + - - +
435B GLU* 3.0 10.2 + - - +
437B ASN* 1.3 79.9 - - - +
439B LEU* 1.3 63.5 + - + +
441B LYS* 3.3 14.1 + - + +
442B GLN* 2.9 61.5 + - + +
540B HIS* 3.9 33.4 - + + -
587B TYR* 3.7 17.7 - - - -
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Residues in contact with LEU 439 (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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435B GLU* 2.9 17.6 + - + +
436B ILE* 3.9 4.5 - - + +
438B PHE* 1.3 79.1 - - + +
440B LEU* 1.3 60.6 + - - +
442B GLN* 3.3 2.2 + - + -
443B ALA* 2.8 29.8 + - - +
540B HIS* 3.6 50.7 - - + +
587B TYR* 4.1 17.7 - - + +
588B PHE* 3.4 13.5 - - + -
590B PRO* 3.5 35.7 - - + -
591B LEU* 3.8 24.5 - - + +
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Residues in contact with LEU 440 (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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240B LEU* 4.0 24.0 - - + -
243B TYR* 3.9 22.0 - - + -
279B TYR* 3.8 16.4 - - + -
282B THR* 3.8 9.9 - - - +
284B PRO* 3.7 27.6 - - + -
436B ILE 2.9 18.8 + - - +
437B ASN 4.1 1.6 - - - +
439B LEU* 1.3 73.3 - - - +
441B LYS* 1.3 69.1 + - - +
443B ALA* 3.1 1.9 + - - +
444B LEU* 3.0 48.6 + - + +
591B LEU* 3.8 17.9 - - + +
595B LEU* 5.2 1.1 - - + -
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Residues in contact with LYS 441 (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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276B THR* 4.5 20.9 + - + +
279B TYR* 3.5 38.5 - - + +
290B ASN* 4.5 23.8 - - - +
437B ASN 3.2 17.1 + - - +
438B PHE* 3.5 15.0 - - + +
439B LEU 3.3 0.2 - - - -
440B LEU* 1.3 82.2 - - - +
442B GLN* 1.3 65.9 + - + +
444B LEU* 3.5 15.2 + - + +
445B THR* 3.7 10.6 + - - -
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Residues in contact with GLN 442 (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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410B LEU* 3.9 12.5 - - - +
438B PHE* 2.9 52.4 + - + +
439B LEU* 3.5 7.4 - - - +
441B LYS* 1.3 81.3 - - - +
443B ALA* 1.3 58.1 + - - +
445B THR* 3.3 5.9 + - - -
446B ILE* 2.8 50.7 + - + +
587B TYR* 3.0 20.2 + - + +
588B PHE* 3.7 16.6 - - + -
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Residues in contact with ALA 443 (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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236B LEU* 6.2 0.9 - - + -
240B LEU* 4.6 12.9 - - + +
439B LEU 2.8 18.4 + - - +
440B LEU* 3.7 3.4 - - - +
442B GLN* 1.3 75.2 - - - +
444B LEU* 1.3 60.8 + - - +
447B VAL* 2.8 35.7 + - + +
448B GLY* 2.9 12.5 + - - -
588B PHE* 3.5 19.0 - - + -
591B LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 444 (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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240B LEU* 4.3 6.7 - - + -
244B VAL* 4.1 25.4 - - + -
275B TRP* 2.9 65.4 + - + +
276B THR* 4.0 4.7 - - - +
278B LEU* 4.6 2.5 - - + -
279B TYR* 3.9 20.0 - - + +
282B THR* 3.6 14.6 - - - +
440B LEU* 3.0 46.7 + - + +
441B LYS* 3.6 8.1 - - + +
442B GLN 3.3 0.2 - - - -
443B ALA* 1.3 76.9 - - - +
445B THR* 1.3 60.7 + - - +
448B GLY* 3.9 7.6 - - - +
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Residues in contact with THR 445 (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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274B PHE* 3.6 21.6 - - + -
276B THR* 2.9 36.4 + - + +
441B LYS* 3.7 8.9 + - - -
442B GLN* 3.3 9.2 + - - -
443B ALA 3.1 0.2 - - - -
444B LEU* 1.3 78.4 - - - +
446B ILE* 1.3 71.5 + - + +
448B GLY 4.4 0.2 - - - -
449B THR* 3.3 27.5 + - - +
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Residues in contact with ILE 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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410B LEU* 5.8 1.6 - - + -
442B GLN* 2.8 54.1 + - + +
445B THR* 1.3 81.2 - - + +
447B VAL* 1.3 64.1 + - - +
449B THR* 3.3 18.5 - - - +
450B LEU* 3.5 10.2 - - - +
518B ARG* 5.5 7.0 - - - +
519B THR* 3.9 16.2 - - + +
522B GLN* 4.9 8.3 - - - +
523B PHE* 3.8 38.4 - - + -
584B LEU* 4.5 4.0 - - + -
588B PHE* 3.9 15.3 - - + -
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 3.9 23.3 - - + -
236B LEU* 3.7 24.5 - - + -
237B TYR* 4.2 22.9 - - + -
240B LEU* 4.9 7.6 - - + -
443B ALA* 2.8 25.1 + - + +
446B ILE* 1.3 70.8 - - + +
448B GLY* 1.3 65.2 + - - +
449B THR 3.1 2.9 + - - -
450B LEU* 3.1 16.1 + - - +
451B PRO* 3.1 12.5 - - + +
584B LEU* 4.8 3.6 - - + -
588B PHE* 3.7 30.5 - - + -
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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