Contacts of the helix formed by residues 507 - 525 (chain B) in PDB entry 5ULM
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 507 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASP* 5.8 5.4 - - - +
475B TYR* 3.4 51.8 - - + +
505B LYS 3.5 5.8 - - - +
506B THR* 1.3 84.5 - - + +
508B ALA* 1.3 60.0 + - - +
509B TRP* 3.3 26.7 - - + +
510B TYR* 3.0 7.8 + - + +
511B LEU* 3.0 24.7 + - - +
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASP 5.7 5.5 + - - +
325B GLN* 3.7 28.0 - - + +
506B THR 3.6 3.3 + - - -
507B PRO* 1.3 68.2 - - - +
509B TRP* 1.4 68.1 + - - +
511B LEU* 3.3 7.6 + - - +
512B LYS* 2.9 26.3 + - - +
549B ALA 5.5 7.4 - - - +
550B THR* 5.3 3.6 - - - +
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Residues in contact with TRP 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ARG* 3.4 67.4 + - + +
323B ASP* 5.2 7.1 + - - -
325B GLN* 3.6 11.9 + - - +
327B TYR* 3.3 23.8 - - - +
357B PHE* 3.7 24.9 - + + -
395B ARG* 4.5 6.8 + - - -
475B TYR* 3.6 20.1 + - - -
507B PRO* 3.7 25.8 - - + +
508B ALA* 1.4 78.3 - - - +
510B TYR* 1.4 90.8 + + + +
512B LYS* 3.4 14.1 - - - +
513B SER* 3.8 9.1 + - - -
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Residues in contact with TYR 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B TYR* 3.6 37.2 - + + -
476B TRP* 2.9 38.3 + - + -
479B GLY* 3.2 17.9 - - - -
480B PHE* 3.4 27.5 + + - -
501B LEU* 4.8 1.6 - - + -
506B THR* 3.7 17.5 - - + -
507B PRO* 3.0 9.3 + - + +
509B TRP* 1.4 108.2 - + + +
511B LEU* 1.3 67.6 + - - +
512B LYS 3.1 1.3 - - - -
513B SER* 2.9 24.8 + - - -
514B ILE* 3.4 30.6 + - + +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 3.8 31.2 - - + -
506B THR* 4.2 12.8 - - + +
507B PRO 3.0 15.0 + - - +
508B ALA* 4.0 7.0 - - - +
510B TYR* 1.3 80.4 - - - +
512B LYS* 1.3 63.8 + - - +
513B SER 3.3 0.2 + - - -
514B ILE* 3.3 8.7 + - + +
515B VAL* 2.9 32.4 + - + +
546B LEU* 3.9 23.8 - - + +
549B ALA* 3.7 33.0 - - + +
550B THR* 4.2 11.0 - - + -
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Residues in contact with LYS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN* 4.6 10.5 + - - +
361B ARG* 3.1 32.1 - - - +
395B ARG* 3.9 14.8 - - - +
508B ALA 2.9 17.9 + - - +
509B TRP* 3.4 11.0 - - - +
511B LEU* 1.3 75.6 - - - +
513B SER* 1.3 57.4 + - - +
515B VAL* 3.2 4.8 + - + +
516B GLU* 3.0 42.5 + - + +
550B THR* 3.9 32.6 + - + +
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Residues in contact with SER 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ARG* 3.6 31.3 + - - +
398B LYS* 3.3 8.8 + - - -
480B PHE* 5.7 2.1 - - - -
509B TRP* 3.8 5.9 + - - -
510B TYR* 2.9 23.9 + - - -
512B LYS* 1.3 74.6 - - - +
514B ILE* 1.3 68.7 + - - +
516B GLU* 3.3 11.8 + - - -
517B THR* 3.2 25.2 + - - -
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ILE* 5.3 5.2 - - + -
479B GLY* 3.9 15.0 - - - +
480B PHE* 3.6 26.9 - - + -
482B LEU* 4.2 17.9 - - + -
483B GLY* 5.2 4.3 - - - +
501B LEU* 5.0 3.1 - - + -
510B TYR* 3.5 46.4 - - + +
511B LEU* 3.3 13.0 + - + +
513B SER* 1.3 79.3 + - - +
515B VAL* 1.3 63.3 + - + +
517B THR* 3.2 9.3 + - - +
518B ILE* 3.1 38.4 + - + +
546B LEU* 6.0 0.2 - - + -
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Residues in contact with VAL 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LEU* 2.9 33.5 + - + +
512B LYS* 3.6 6.5 - - + +
514B ILE* 1.3 72.0 - - - +
516B GLU* 1.3 59.7 + - + +
518B ILE* 3.0 14.2 + - + +
519B LEU* 2.8 46.5 + - + +
546B LEU* 3.6 33.9 - - + +
547B VAL* 4.1 17.7 - - + +
550B THR* 3.8 23.6 - - + +
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ARG* 3.1 26.3 + - - -
395B ARG* 3.1 21.5 + - - -
398B LYS* 2.8 35.2 + - - -
399B ASP* 2.9 23.0 - - - +
402B LEU* 3.9 23.0 - - + +
512B LYS* 3.0 27.3 + - + +
513B SER* 3.5 5.0 - - - +
514B ILE 3.3 0.2 - - - -
515B VAL* 1.3 78.6 - - + +
517B THR* 1.3 62.6 + - - +
519B LEU* 3.5 6.9 + - + +
520B ILE* 3.3 27.7 + - - +
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Residues in contact with THR 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 3.5 7.0 + - - +
433B ILE* 4.5 20.4 - - + -
434B ASN* 2.8 35.5 + - - +
437B VAL* 3.8 25.7 - - + +
483B GLY* 6.0 1.6 - - - -
487B LEU* 5.1 3.6 - - + -
513B SER 3.2 10.8 + - - -
514B ILE* 3.2 13.6 + - - +
516B GLU* 1.3 79.4 - - - +
518B ILE* 1.3 63.1 + - + +
520B ILE* 3.4 6.2 + - - +
521B TYR* 3.2 21.4 + - - +
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Residues in contact with ILE 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 4.4 14.8 - - + -
483B GLY* 5.5 4.0 - - - -
486B VAL* 4.4 23.6 - - + -
514B ILE* 3.1 36.2 + - + +
515B VAL* 3.0 14.9 + - + +
517B THR* 1.3 76.6 - - + +
519B LEU* 1.3 60.9 + - + +
521B TYR* 3.5 6.7 - - - +
522B LYS* 2.9 39.2 + - + +
543B MET* 3.7 36.3 - - + -
546B LEU* 5.2 3.8 - - + -
547B VAL* 5.7 8.5 - - + -
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 4.9 19.7 - - + -
406B PHE* 4.7 3.5 - - + -
515B VAL* 2.8 41.1 + - + +
516B GLU* 3.9 9.4 - - + +
517B THR 3.4 0.4 - - - -
518B ILE* 1.3 74.0 - - + +
520B ILE* 1.3 58.8 + - - +
522B LYS* 3.9 6.3 - - + +
523B HIS* 3.0 28.2 + - - +
547B VAL* 4.1 28.5 - - + -
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Residues in contact with ILE 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LYS* 3.7 31.6 - - + -
401B PHE* 4.1 26.9 - - + -
402B LEU* 4.3 16.4 - - + -
406B PHE* 3.8 20.4 - - + -
437B VAL* 3.5 25.3 - - + +
438B LEU* 4.6 2.9 - - + -
441B ALA* 4.1 5.4 - - + -
516B GLU 3.3 16.9 + - - +
517B THR* 3.8 1.6 - - - +
518B ILE 3.2 0.4 - - - -
519B LEU* 1.3 71.9 - - - +
521B TYR* 1.3 66.1 + - - +
523B HIS* 3.3 1.4 + - - +
524B PHE* 3.2 42.2 + - + +
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Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B VAL* 4.0 14.0 - - + +
440B LEU* 3.6 27.1 - - + +
486B VAL* 3.5 39.6 + - + -
487B LEU* 4.2 29.7 + - + -
489B ASN* 4.2 15.9 + - - +
517B THR 3.2 11.7 + - - +
518B ILE* 3.5 10.3 - - - +
520B ILE* 1.3 77.1 - - - +
522B LYS* 1.3 75.7 + - + +
524B PHE* 3.2 1.5 + - - -
525B VAL* 2.8 72.0 + - + +
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B VAL* 5.9 2.1 - - - +
518B ILE* 2.9 32.4 + - + +
519B LEU* 3.9 8.1 - - + +
521B TYR* 1.3 91.7 - - + +
523B HIS* 1.3 62.7 + - - +
524B PHE 3.4 0.2 + - - -
525B VAL* 4.1 15.4 + - + +
536B GLN* 4.6 9.9 - - - +
539B VAL* 4.2 15.6 - - - +
540B ASP* 4.9 4.1 + - - -
543B MET* 3.8 34.5 - - + +
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Residues in contact with HIS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PHE* 3.4 43.6 - + + +
519B LEU 3.0 17.8 + - - +
520B ILE 3.6 5.4 - - - +
521B TYR 3.2 0.2 - - - -
522B LYS* 1.3 78.8 - - - +
524B PHE* 1.3 83.0 + + - +
525B VAL 4.9 1.1 - - - +
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Residues in contact with PHE 524 (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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401B PHE* 3.9 20.6 - + - -
406B PHE* 4.0 17.7 - + + -
440B LEU* 4.0 22.0 - - + +
441B ALA* 3.4 47.1 - - + +
445B GLN* 3.9 7.7 - - - +
520B ILE* 3.2 26.5 + - + +
521B TYR 4.3 0.2 - - - +
523B HIS* 1.3 104.5 - + - +
525B VAL* 1.3 67.7 + - - +
526B LYS* 3.4 2.1 + - - -
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Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B LEU* 5.1 9.7 - - + +
445B GLN* 4.1 11.2 - - - +
521B TYR* 2.8 66.6 + - + +
522B LYS* 4.1 16.8 - - + +
523B HIS 4.9 1.0 - - - +
524B PHE* 1.3 75.3 - - - +
526B LYS* 1.3 72.9 + - - +
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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