Contacts of the helix formed by residues 512 - 530 (chain B) in PDB entry 4OL0
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 GLU 512 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLU* 3.7 18.5 - - - +
475B THR* 5.8 1.0 - - - +
478B ARG* 2.8 39.5 + - - -
508B LYS* 3.6 12.7 + - - +
509B GLY* 3.3 11.1 + - - +
510B LEU 3.4 0.9 - - - -
511B CYS* 1.3 79.5 - - + +
513B LYS* 1.3 69.6 + - - +
514B PRO* 4.4 6.6 - - + +
515B LEU* 3.2 20.4 + - + +
516B ALA* 3.1 18.5 + - - +
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Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B CYS 3.6 4.6 + - - +
512B GLU* 1.3 69.2 - - - +
514B PRO* 1.3 67.9 - - + +
515B LEU 2.8 7.1 + - - -
516B ALA* 2.8 23.9 + - - +
517B SER 4.5 0.7 + - - -
552B LEU* 4.7 34.7 - - + +
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Residues in contact with PRO 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLY* 6.4 0.2 - - - -
389B VAL* 3.5 38.4 - - + +
475B THR* 5.4 9.6 - - + -
479B TYR* 3.7 9.9 - - - -
512B GLU* 3.6 8.3 - - + +
513B LYS* 1.3 93.8 - - + +
515B LEU* 1.3 68.1 + - + +
517B SER* 4.6 3.3 + - - -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B VAL* 3.7 17.3 - - + -
475B THR* 3.7 27.1 - - + +
478B ARG* 4.0 22.4 - - - +
479B TYR* 3.8 18.4 - - + +
482B ILE* 3.9 21.1 - - + -
509B GLY* 3.5 17.7 - - - +
512B GLU* 3.2 32.5 + - + +
513B LYS 3.0 0.8 - - - -
514B PRO* 1.3 80.4 - - + +
516B ALA* 1.3 57.4 + - - +
517B SER 3.2 2.9 - - - -
518B ALA* 2.7 28.8 + - - +
519B ALA* 3.1 9.5 + - - +
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Residues in contact with ALA 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLY 3.9 7.2 - - - -
510B LEU* 3.7 20.1 - - + +
512B GLU 3.1 11.4 + - - +
513B LYS* 2.8 18.7 + - - +
515B LEU* 1.3 76.9 - - - +
517B SER* 1.3 61.9 + - - +
519B ALA 3.5 0.3 + - - -
520B ALA* 3.0 19.1 + - - +
551B PHE* 4.5 7.2 - - + -
552B LEU 4.4 12.3 - - - +
553B LEU* 3.2 23.0 - - + +
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Residues in contact with SER 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B TYR* 4.0 19.9 + - - -
513B LYS 4.5 1.2 + - - -
514B PRO 4.6 3.5 + - - -
515B LEU 4.3 1.2 + - - -
516B ALA* 1.3 79.8 - - - +
518B ALA* 1.3 65.1 + - - +
520B ALA* 3.5 1.6 - - - +
521B LYS* 3.1 38.4 + - - +
552B LEU 5.4 0.8 + - - -
553B LEU* 3.6 13.4 - - - +
554B SER* 5.5 7.6 - - - -
557B ALA* 4.8 2.2 - - - -
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Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B TYR* 3.6 33.9 - - + +
482B ILE* 3.7 24.7 - - + +
483B GLU* 4.5 11.3 + - + +
515B LEU 2.7 16.1 + - - +
517B SER* 1.3 72.1 + - - +
519B ALA* 1.3 56.4 + - - +
520B ALA 3.0 1.3 - - - -
521B LYS* 2.8 30.5 + - - +
522B ALA 3.1 9.2 + - - -
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ILE* 3.5 16.2 - - + +
506B LEU* 3.3 29.4 - - - +
509B GLY* 4.0 6.1 - - - -
510B LEU* 3.9 19.5 - - + +
515B LEU 3.1 4.2 + - - +
516B ALA 3.9 6.3 - - - +
518B ALA* 1.3 78.3 - - - +
520B ALA* 1.3 57.1 + - - +
522B ALA* 3.7 3.1 - - - +
523B ILE* 3.0 37.9 + - + +
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B LEU* 4.3 2.6 - - + +
516B ALA 3.0 18.8 + - - +
517B SER 3.5 7.9 - - - +
518B ALA 3.0 0.4 - - - -
519B ALA* 1.3 77.4 - - - +
521B LYS* 1.3 60.9 + - - +
524B HIS* 3.3 22.3 + - - +
553B LEU* 3.7 16.6 - - + -
557B ALA* 3.8 19.9 - - + +
560B GLY* 5.6 0.2 - - - -
561B LEU* 4.1 31.4 - - + +
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Residues in contact with LYS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B GLU* 6.4 2.0 - - + -
517B SER* 3.1 29.1 + - - +
518B ALA* 2.8 12.9 + - - +
520B ALA* 1.3 73.7 - - - +
522B ALA* 1.3 65.4 + - - +
524B HIS* 3.4 8.4 + - + +
525B ASN* 3.0 23.7 + - - +
554B SER* 4.5 4.2 + - - -
556B GLU* 5.2 4.3 - - - -
557B ALA* 3.4 32.7 - - - +
560B GLY* 6.3 1.8 - - - -
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ILE* 3.9 7.4 - - + +
483B GLU* 5.6 0.9 - - - -
486B GLY* 3.5 31.7 - - - +
506B LEU* 3.6 32.8 - - + -
518B ALA 3.1 9.8 + - - +
519B ALA 3.7 4.5 - - - +
521B LYS* 1.3 77.9 - - - +
523B ILE* 1.3 62.4 + - - +
525B ASN* 3.3 3.1 + - - +
526B ILE* 3.0 27.0 + - - +
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Residues in contact with ILE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 4.8 11.9 - - + -
506B LEU* 3.7 38.4 - - + -
507B MET* 4.5 5.8 - - + +
510B LEU* 4.4 11.7 - - + -
519B ALA 3.0 24.9 + - - +
522B ALA* 1.3 72.7 - - - +
524B HIS* 1.3 66.0 + - - +
526B ILE* 3.7 4.1 - - - +
527B CYS* 2.9 39.8 + - - -
541B LEU* 4.5 11.2 - - + -
544B ILE* 4.3 16.4 - - + -
561B LEU* 3.5 29.6 - - + -
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Residues in contact with HIS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ALA 3.3 18.4 + - - +
521B LYS* 3.5 11.2 + - + +
522B ALA 3.3 0.2 - - - -
523B ILE* 1.3 79.7 - - - +
525B ASN* 1.3 68.1 + - - +
527B CYS* 3.4 7.2 + - - +
528B SER* 3.0 27.4 + - - -
560B GLY* 3.0 44.2 - - - +
561B LEU* 4.8 2.2 - - - +
563B LYS* 3.3 40.3 + - + +
564B GLY* 4.3 7.2 - - - -
567B LEU* 5.5 0.2 - - + -
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Residues in contact with ASN 525 (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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449B LYS* 3.4 29.9 + - - +
486B GLY 2.6 27.5 + - - +
487B GLU* 4.2 4.9 + - - +
489B SER* 3.1 9.8 + - - +
521B LYS 3.0 13.1 + - - +
522B ALA 3.6 2.9 - - - +
524B HIS* 1.3 86.3 + - - +
526B ILE* 1.3 55.8 + - - +
528B SER* 2.7 29.1 + - - -
529B VAL* 2.9 21.7 + - - +
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Residues in contact with ILE 526 (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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485B VAL* 4.9 8.3 - - + +
489B SER* 3.2 28.2 + - - +
492B VAL* 4.9 6.7 - - + -
499B LEU* 4.0 25.8 - - + -
502B VAL* 3.5 21.5 - - + -
503B LEU* 4.7 7.6 - - + -
506B LEU* 3.4 33.0 - - + -
522B ALA* 3.0 11.3 + - + +
523B ILE* 3.7 5.4 - - - +
525B ASN* 1.3 77.9 - - - +
527B CYS* 1.3 55.3 + - - +
529B VAL 2.8 5.7 + - - -
530B CYS* 2.6 42.3 + - + -
534B MET* 4.3 9.0 - - + -
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Residues in contact with CYS 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 5.8 0.2 - - - -
523B ILE* 2.9 44.3 + - - +
524B HIS* 3.5 5.8 - - - +
526B ILE* 1.3 74.4 - - - +
528B SER* 1.3 58.0 + - - +
531B ARG* 3.4 23.4 + - - +
534B MET* 3.9 18.4 - - - -
541B LEU* 3.8 22.0 - - - -
561B LEU 5.7 0.9 - - - -
564B GLY* 3.8 22.1 - - - +
565B THR 4.7 0.7 - - - -
567B LEU* 4.7 0.4 - - - +
568B VAL* 3.5 26.0 + - + +
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Residues in contact with SER 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B HIS* 3.0 20.1 + - - -
525B ASN* 2.7 19.5 + - - -
527B CYS* 1.3 74.5 - - - +
529B VAL* 1.3 63.3 + - - +
531B ARG* 2.9 43.7 + - - +
563B LYS* 4.7 2.9 + - - -
567B LEU* 3.6 16.6 - - - +
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Residues in contact with VAL 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 4.6 1.1 - - - +
489B SER* 3.7 34.5 - - - +
490B GLU* 3.3 39.9 - - - +
493B ASP* 3.7 19.7 - - + +
525B ASN* 2.9 26.3 + - - +
526B ILE 2.8 3.9 + - - +
528B SER* 1.3 81.9 - - - +
530B CYS* 1.3 57.4 + - - +
531B ARG* 3.0 11.2 + - - +
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Residues in contact with CYS 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B SER 3.7 8.7 - - - -
492B VAL* 4.0 15.0 - - - -
493B ASP* 3.5 44.4 - - - +
499B LEU* 4.6 4.9 - - + -
526B ILE* 2.6 33.9 + - + +
529B VAL* 1.3 71.6 - - - +
531B ARG* 1.3 61.6 + - - +
532B ASP 3.2 3.1 - - - -
533B HIS* 3.1 27.7 + - + -
534B MET* 3.1 16.5 + - + +
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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
------------------------------------------------------------
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