Contacts of the helix formed by residues 515 - 535 (chain B) in PDB entry 5XOU
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 PRO 515 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B GLU* 6.3 0.2 - - + -
508B ALA 5.8 0.7 - - - +
509B GLN* 3.7 19.5 - - + +
513B ARG* 3.6 12.1 - - + +
514B ILE* 1.3 94.2 - - + +
516B GLN* 1.3 66.2 + - - +
517B GLU* 3.2 22.0 - - - +
518B VAL* 3.0 20.7 + - + +
519B VAL* 3.0 19.9 + - - +
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Residues in contact with GLN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ARG* 6.0 2.8 - - - +
514B ILE 3.6 1.4 + - - -
515B PRO* 1.3 71.1 - - - +
517B GLU* 1.3 66.0 + - - +
519B VAL* 3.3 4.4 + - - +
520B TRP* 3.0 28.1 + - - +
552B ASP* 3.3 32.8 + - - +
553B GLU* 3.6 16.7 - - - +
555B ALA* 3.4 7.2 - - - +
556B LEU* 3.2 48.2 + - + +
557B ALA 4.8 0.9 + - - -
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Residues in contact with GLU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ARG* 4.3 11.7 + - - +
515B PRO* 3.7 18.3 - - - +
516B GLN* 1.3 89.0 + - + +
518B VAL* 1.3 63.7 + - - +
520B TRP* 3.5 5.9 + - - +
521B ASP* 2.9 37.6 + - - +
556B LEU* 4.7 14.1 - - + -
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Residues in contact with VAL 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ARG* 3.4 36.1 - - - +
488B GLY 5.1 1.3 - - - +
507B GLU* 3.9 26.5 - - + -
509B GLN* 5.0 1.8 - - - +
514B ILE* 3.7 18.4 - - + -
515B PRO* 3.0 32.6 + - + +
517B GLU* 1.3 77.1 - - - +
519B VAL* 1.3 66.9 + - - +
521B ASP* 3.1 1.7 + - - +
522B LEU* 2.9 43.8 + - + +
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PHE* 3.9 15.6 - - + -
514B ILE* 3.5 34.5 - - + +
515B PRO 3.0 12.0 + - - +
516B GLN 3.5 7.0 - - - +
518B VAL* 1.3 74.4 - - - +
520B TRP* 1.3 64.8 + - - +
522B LEU* 3.4 3.4 + - - +
523B LEU* 3.0 24.5 + - + +
553B GLU* 3.8 22.7 - - + +
554B PHE* 3.7 38.1 - - + -
557B ALA* 3.9 12.6 - - + -
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Residues in contact with TRP 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 4.7 9.6 - - + -
427A ARG* 5.2 0.8 - - - +
516B GLN 3.0 16.7 + - - +
517B GLU* 3.8 3.8 - - - +
519B VAL* 1.3 78.8 - - - +
521B ASP* 1.3 69.3 + - - +
523B LEU* 3.3 26.6 + - + -
524B GLU* 2.8 54.9 + - + +
527B LEU* 3.8 23.3 - - + -
556B LEU* 4.1 23.6 - - + -
557B ALA* 3.7 28.3 - - - -
560B ALA* 3.6 33.5 - - + +
561B LEU* 4.3 6.1 - - + -
564B GLU* 5.7 3.4 - - + -
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Residues in contact with ASP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA* 5.4 0.2 - - - +
427A ARG* 3.3 33.2 + - - +
672A ARG* 2.9 45.5 + - - +
673A HIS* 3.1 8.9 - - + -
517B GLU* 2.9 22.9 + - - +
518B VAL 3.1 2.0 + - - +
520B TRP* 1.3 80.6 - - - +
522B LEU* 1.3 66.4 + - - +
524B GLU* 3.2 6.7 + - - +
525B GLU* 2.9 27.3 + - - +
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ARG* 4.9 9.2 - - + -
477B PHE* 4.2 12.3 - - + -
488B GLY 4.3 6.1 - - - +
489B GLY* 4.3 25.4 - - - +
490B ALA* 4.0 17.5 - - + +
504B THR* 4.2 14.2 + - - +
505B LEU 3.5 25.8 - - - +
506B PRO* 5.0 0.9 - - + -
514B ILE* 4.8 3.4 - - + -
518B VAL* 2.9 41.8 + - + +
519B VAL* 3.7 3.6 - - - +
521B ASP* 1.3 75.8 - - + +
523B LEU* 1.3 64.6 + - - +
525B GLU* 3.1 11.6 + - + +
526B THR* 3.0 26.2 + - - +
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LEU* 5.3 0.9 - - + -
475B VAL* 4.3 7.0 - - + -
477B PHE* 4.3 12.0 - - + -
519B VAL 3.0 17.4 + - - +
520B TRP* 3.4 28.7 - - + +
522B LEU* 1.3 77.3 - - - +
524B GLU* 1.3 62.3 + - - +
526B THR* 2.8 32.7 + - - +
527B LEU* 2.9 20.7 + - + +
541B VAL* 5.2 2.9 - - + -
543B LEU* 3.8 31.4 - - + -
557B ALA* 3.9 14.8 - - + -
561B LEU* 3.9 23.8 - - + -
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 3.9 20.9 - - + +
392A ARG* 2.8 38.3 + - - +
424A LEU* 3.9 6.8 - - - +
427A ARG* 2.8 26.8 + - - +
520B TRP* 2.8 48.6 + - + +
521B ASP* 3.2 6.3 + - - +
523B LEU* 1.3 74.7 - - - +
525B GLU* 1.3 56.4 + - - +
527B LEU* 3.3 12.0 + - - +
528B TRP* 2.9 28.3 + - + +
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Residues in contact with GLU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG* 2.8 36.4 + - - +
427A ARG* 4.0 21.2 - - - +
672A ARG 6.0 1.1 - - - +
504B THR* 3.4 20.4 - - + +
521B ASP 2.9 15.2 + - - +
522B LEU* 3.1 11.0 + - + +
524B GLU* 1.3 75.9 - - - +
526B THR* 1.3 58.1 + - - +
528B TRP* 3.2 4.5 + - - +
529B ALA* 2.9 27.2 + - - +
532B ARG* 4.5 9.9 + - - -
679B ARG* 3.4 39.6 + - - +
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Residues in contact with THR 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LEU* 3.9 9.4 - - - +
475B VAL* 3.4 30.0 - - + +
490B ALA* 4.9 3.1 - - + -
491B ALA* 5.3 0.7 - - - -
492B CYS* 3.7 35.3 - - + +
503B TRP 6.4 0.2 - - - -
504B THR* 4.5 16.2 - - + +
522B LEU 3.0 14.2 + - - +
523B LEU* 2.8 20.3 + - - +
525B GLU* 1.3 74.3 - - - +
527B LEU* 1.3 57.2 + - - +
529B ALA* 3.1 10.2 + - - +
530B PHE* 2.9 27.5 + - - +
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 4.2 18.6 - - + -
473B LEU* 3.9 14.4 - - + -
520B TRP* 3.8 30.5 - - + -
523B LEU* 2.9 21.7 + - + +
524B GLU* 3.5 8.1 - - + +
526B THR* 1.3 77.1 + - - +
528B TRP* 1.3 59.5 + - + +
530B PHE* 3.3 6.0 + - - +
531B ARG* 2.9 27.4 + - - +
537B LEU* 4.8 4.7 - - + +
538B PRO* 3.8 21.8 - - + +
541B VAL* 4.1 8.3 - - + -
561B LEU* 4.1 13.5 - - + -
564B GLU* 5.6 0.4 - - + -
566B ILE* 3.7 28.7 - - + -
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Residues in contact with TRP 528 (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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389A LEU* 4.1 33.2 - - + -
392A ARG* 3.6 40.8 - - + +
393A GLU* 3.0 52.3 - - + -
396A ARG* 4.0 21.4 - - + +
428A GLU* 3.3 15.2 + - - -
524B GLU* 2.9 17.9 + - + +
525B GLU* 3.5 8.5 - - - +
527B LEU* 1.3 76.8 - - - +
529B ALA* 1.3 59.8 + - - +
531B ARG* 3.3 21.7 + - + +
532B ARG* 2.8 62.4 + - + +
537B LEU* 5.5 2.9 - - + -
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Residues in contact with ALA 529 (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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492B CYS* 4.8 0.4 - - - -
494B VAL* 4.7 3.6 - - + -
502B LEU* 3.4 32.4 - - + +
525B GLU 2.9 13.1 + - - +
526B THR* 3.1 13.4 + - - +
528B TRP* 1.3 74.3 - - - +
530B PHE* 1.3 65.3 + - - +
532B ARG* 3.2 24.0 + - - +
533B LYS* 2.9 28.6 + - - +
679B ARG* 6.5 1.1 - - - -
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Residues in contact with PHE 530 (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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472B GLU* 3.4 34.3 - - + -
473B LEU* 4.2 9.9 - - + -
494B VAL* 3.5 27.3 - - + +
495B GLY* 4.0 9.6 - - - -
526B THR 2.9 11.6 + - - +
527B LEU* 3.4 11.4 - - - +
529B ALA* 1.3 75.8 - - - +
531B ARG* 1.3 59.2 + - - +
533B LYS 3.1 0.7 + - - -
534B ALA* 3.0 40.0 + - + +
536B ARG* 3.1 52.0 - - - -
537B LEU 3.5 4.0 - - - -
538B PRO* 3.2 45.1 - - + -
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Residues in contact with ARG 531 (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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393A GLU* 2.8 40.0 + - - -
396A ARG* 3.4 22.7 - - - +
527B LEU 2.9 17.0 + - - +
528B TRP* 3.6 34.8 - - + +
529B ALA 3.2 0.2 - - - -
530B PHE* 1.3 77.4 - - - +
532B ARG* 1.3 69.0 + - + +
535B GLY* 2.9 36.3 + - - -
536B ARG* 3.4 18.6 - - - +
537B LEU* 4.4 11.7 - - + -
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Residues in contact with ARG 532 (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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396A ARG* 5.4 7.9 - - - +
502B LEU* 5.2 6.1 - - - +
525B GLU* 4.5 10.9 + - - -
528B TRP* 2.8 53.9 + - + +
529B ALA* 3.2 28.3 + - - +
531B ARG* 1.3 92.4 + - + +
533B LYS* 1.3 71.9 + - + +
534B ALA 3.5 0.4 + - - -
535B GLY 4.8 0.9 + - - -
679B ARG* 5.0 16.6 - - - +
680B GLU* 4.6 13.3 + - - -
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Residues in contact with LYS 533 (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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494B VAL* 4.4 9.9 - - + -
500B HIS* 3.0 50.1 - - + +
502B LEU* 6.0 5.6 - - + -
529B ALA* 2.9 17.3 + - + +
530B PHE 3.1 2.9 + - - +
532B ARG* 1.3 89.8 - - + +
534B ALA* 1.3 58.3 + - - +
680B GLU* 4.5 21.1 + - - +
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Residues in contact with ALA 534 (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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494B VAL* 5.8 1.6 - - + -
530B PHE* 3.0 39.7 + - + +
532B ARG 3.5 0.4 + - - -
533B LYS* 1.3 79.8 - - + +
535B GLY* 1.3 65.6 + - - +
536B ARG* 3.2 18.6 + - + +
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Residues in contact with GLY 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B ARG* 2.9 30.2 + - - -
532B ARG 4.6 0.8 + - - -
534B ALA* 1.3 79.0 - - - +
536B ARG* 1.3 62.6 + - - +
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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
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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