Contacts of the helix formed by residues 431 - 454 (chain B) in PDB entry 1XR2
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 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425B TYR* 4.2 0.9 - - - -
430B ILE* 1.3 76.4 - - - +
432B LYS* 1.3 64.0 + - - +
433B GLU* 3.5 8.4 + - - +
434B GLU* 3.0 41.5 + - - +
435B TYR* 3.0 21.3 + - - +
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B TYR* 3.5 37.0 - - + +
430B ILE 3.9 0.2 + - - -
431B SER* 1.3 74.1 - - - +
433B GLU* 1.3 61.1 + - - +
435B TYR* 3.4 1.5 + - + +
436B GLU* 2.9 60.9 + - + +
513B LYS* 4.9 6.8 - - - +
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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
----------------------------------------------------------
431B SER* 3.2 8.3 + - - +
432B LYS* 1.3 81.2 - - - +
434B GLU* 1.3 58.4 + - + +
436B GLU* 3.5 11.6 + - - +
437B ALA* 3.0 28.3 + - - +
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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
----------------------------------------------------------
429B GLU 4.8 0.7 - - - +
430B ILE* 3.5 14.4 - - + +
431B SER* 3.0 42.9 + - - +
433B GLU* 1.3 74.4 - - + +
435B TYR* 1.3 60.6 + - - +
437B ALA* 3.0 8.5 + - - +
438B PHE* 2.9 28.8 + - - +
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Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL* 5.2 1.6 + - + +
421B MET* 3.7 27.4 - - + -
422B ARG* 3.7 38.3 - - - +
425B TYR* 3.6 43.1 - + + -
430B ILE* 5.4 4.1 - - + +
431B SER 3.0 14.6 + - - +
432B LYS 3.7 4.9 - - - +
434B GLU* 1.3 76.9 - - - +
436B GLU* 1.3 67.7 + - + +
438B PHE* 3.0 10.4 + + - +
439B ILE* 2.9 48.9 + - + +
463B PHE 4.2 2.6 + - - -
464B GLU* 3.7 31.7 + - + -
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LYS* 2.9 50.0 + - + +
433B GLU* 3.9 10.0 - - - +
435B TYR* 1.3 82.0 - - + +
437B ALA* 1.3 57.9 + - - +
439B ILE* 3.3 10.6 + - - +
440B LYS* 2.8 30.2 + - - +
513B LYS* 3.0 43.4 + - - +
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU 3.0 15.4 + - - +
434B GLU* 3.0 11.6 + - - +
436B GLU* 1.3 73.8 - - - +
438B PHE* 1.3 67.9 + - - +
440B LYS* 3.2 10.2 + - - +
441B GLU* 3.1 18.5 + - - +
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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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417B GLU* 4.1 7.4 - - + -
418B VAL* 3.7 40.6 - - + -
421B MET* 3.5 53.6 - - + -
434B GLU 2.9 12.4 + - - +
435B TYR* 3.2 13.7 - + - +
437B ALA* 1.3 76.5 - - - +
439B ILE* 1.3 76.9 + - + +
441B GLU* 2.8 25.1 + - + +
442B GLN* 3.1 39.2 + - + +
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL* 5.6 0.4 - - + -
435B TYR* 2.9 42.2 + - + +
436B GLU* 3.4 12.3 - - - +
438B PHE* 1.3 87.6 - - + +
440B LYS* 1.3 65.5 + - - +
442B GLN* 3.0 15.7 + - + +
443B ILE* 3.0 32.5 + - + +
463B PHE* 3.9 13.2 - - + +
464B GLU* 3.7 48.7 - - + +
513B LYS* 6.3 0.2 - - - +
514B GLU* 4.9 8.5 - - + +
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Residues in contact with LYS 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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436B GLU 2.8 17.1 + - - +
437B ALA* 3.4 12.8 - - - +
439B ILE* 1.3 75.5 - - - +
441B GLU* 1.3 62.6 + - - +
443B ILE* 3.4 2.4 + - - -
444B LYS* 3.1 20.6 + - - +
517B TYR* 3.3 41.8 + - + +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ALA 3.1 10.9 + - - +
438B PHE* 2.8 17.6 + - + +
440B LYS* 1.3 73.4 - - - +
442B GLN* 1.3 73.1 + - - +
444B LYS* 3.4 10.0 + - - +
445B LYS* 3.1 24.0 + - + +
517B TYR* 5.5 0.2 - - - -
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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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415B THR* 5.6 1.0 + - - -
418B VAL* 4.3 15.3 - - + +
438B PHE* 3.1 58.5 + - + +
439B ILE* 3.0 7.3 + - - +
441B GLU* 1.3 81.7 - - - +
443B ILE* 1.3 60.3 + - - +
445B LYS* 3.1 9.9 + - - +
446B ALA* 2.8 31.0 + - - +
463B PHE* 3.4 31.3 - - + -
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Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ILE* 3.0 33.9 + - + +
440B LYS* 3.6 7.9 - - - +
442B GLN* 1.3 77.9 - - - +
444B LYS* 1.3 52.7 + - - +
446B ALA* 3.3 1.8 + - - +
447B ILE* 2.8 44.5 + - + +
460B HIS* 3.4 33.2 - - + +
463B PHE* 4.6 4.5 - - + -
464B GLU* 5.6 0.4 - - - +
514B GLU* 3.9 29.8 - - + +
517B TYR* 3.9 18.2 - - + -
518B ALA* 3.6 29.8 - - + -
521B LEU* 4.6 0.4 - - + -
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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
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440B LYS 3.1 13.1 + - - +
441B GLU* 3.6 16.4 - - - +
442B GLN 3.2 0.2 - - - -
443B ILE* 1.3 76.6 - - - +
445B LYS* 1.3 54.4 + - - +
447B ILE* 3.1 2.3 + - - +
448B GLU* 2.8 52.4 + - - +
517B TYR* 4.2 6.7 - - - +
521B LEU* 3.5 26.2 - - + +
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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
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441B GLU* 3.1 15.2 + - + +
442B GLN* 3.1 15.0 + - - +
444B LYS* 1.3 79.6 - - - +
446B ALA* 1.3 63.5 + - - +
448B GLU* 3.2 10.7 + - - +
449B LEU* 2.8 26.5 + - - +
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B PHE* 4.1 11.0 - - + -
442B GLN 2.8 20.2 + - - +
443B ILE* 3.4 5.2 - - - +
445B LYS* 1.3 74.1 - - - +
447B ILE* 1.3 63.2 + - - +
449B LEU* 3.2 10.1 + - - +
450B GLN* 2.9 40.5 + - - +
460B HIS 4.4 4.9 - - - +
463B PHE* 3.8 25.4 - - + -
711B TRP* 5.1 3.8 - - + -
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Residues in contact with ILE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ILE* 2.8 40.9 + - + +
444B LYS* 3.4 6.3 - - - +
446B ALA* 1.3 72.1 - - - +
448B GLU* 1.3 67.0 + - + +
450B GLN* 3.0 9.2 + - - +
451B GLU* 2.9 29.1 + - + +
458B LEU* 4.2 16.4 - - + -
459B VAL 3.7 23.6 - - - +
518B ALA* 4.1 25.6 - - + +
521B LEU* 4.1 20.2 - - + +
522B THR* 4.1 25.4 - - + -
526B VAL* 4.5 4.5 - - + -
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Residues in contact with GLU 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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444B LYS* 2.8 37.6 + - - +
445B LYS* 3.6 8.1 + - - +
447B ILE* 1.3 73.0 - - + +
449B LEU* 1.3 63.7 + - - +
451B GLU* 3.1 11.1 + - - +
452B GLU* 2.9 23.1 + - - +
521B LEU* 6.5 0.2 - - + -
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Residues in contact with LEU 449 (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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412B PHE* 6.2 0.7 - - + -
445B LYS 2.8 14.1 + - - +
446B ALA* 3.3 10.1 - - - +
448B GLU* 1.3 76.9 - - - +
450B GLN* 1.3 60.4 + - + +
452B GLU* 3.1 11.0 + - + +
453B ILE* 2.8 54.3 + - + +
711B TRP* 3.5 39.5 - - + -
715B ILE* 4.0 24.7 - - + -
718B LEU* 6.3 2.5 - - + -
719B ARG* 5.2 4.3 - - - +
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Residues in contact with GLN 450 (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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408B THR* 4.4 1.7 + - - -
412B PHE* 3.3 32.1 - - + -
446B ALA* 2.9 28.0 + - - +
447B ILE* 3.6 10.3 - - - +
449B LEU* 1.3 78.1 - - + +
451B GLU* 1.3 57.4 + - - +
453B ILE* 3.3 4.0 + - - +
454B GLY 2.9 24.6 + - - -
455B LEU* 3.2 36.7 + - + +
457B VAL 4.8 0.2 - - - +
458B LEU* 3.3 23.6 - - + +
459B VAL* 2.8 47.9 + - - +
718B LEU* 6.2 0.7 - - + -
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Residues in contact with GLU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ILE* 2.9 25.6 + - + +
448B GLU* 3.4 8.7 - - - +
450B GLN* 1.3 75.8 - - - +
452B GLU* 1.3 65.2 + - - +
454B GLY* 3.1 13.5 + - - -
458B LEU* 4.2 8.0 - - + +
521B LEU 3.8 7.3 - - - +
522B THR* 2.9 36.4 + - - +
523B GLU 4.8 0.3 + - - -
524B LYS* 3.6 28.0 + - - +
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Residues in contact with GLU 452 (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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448B GLU 2.9 12.4 + - - +
449B LEU* 3.3 14.8 - - + +
451B GLU* 1.3 76.2 - - - +
453B ILE* 1.3 67.3 + - - +
454B GLY* 3.2 1.0 + - - -
719B ARG* 2.8 41.0 + - - -
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Residues in contact with ILE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 2.8 51.2 + - + +
450B GLN* 3.6 8.5 - - - +
452B GLU* 1.3 73.8 - - - +
454B GLY* 1.3 59.7 + - - +
455B LEU* 4.4 10.1 - - + -
715B ILE* 4.3 13.9 - - + +
718B LEU* 3.9 30.5 - - + -
719B ARG* 3.7 40.2 + - + +
722B VAL* 3.7 32.1 - - + +
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Residues in contact with GLY 454 (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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406B THR* 3.9 5.2 + - - -
450B GLN 2.9 4.4 + - - -
451B GLU 3.1 11.2 + - - -
452B GLU 3.1 3.5 - - - -
453B ILE* 1.3 80.9 - - - +
455B LEU* 1.3 67.9 + - - +
456B ASP* 3.9 6.1 + - - +
524B LYS* 4.7 4.0 - - - -
722B VAL* 3.9 16.0 - - - +
729B ARG* 5.6 2.6 + - - -
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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