Contacts of the helix formed by residues 554 - 570 (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 SER 554 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517B SER* 5.5 6.5 - - - -
521B LYS* 4.5 4.9 + - - -
553B LEU* 1.3 80.0 - - - +
555B PRO* 1.3 74.3 - - - +
556B GLU* 3.8 12.0 + - - +
557B ALA* 3.2 27.5 + - - +
558B ALA* 3.3 11.1 + - - +
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Residues in contact with PRO 555 (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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553B LEU 4.0 2.0 - - - +
554B SER* 1.3 84.5 - - - +
556B GLU* 1.3 74.4 + - - +
558B ALA* 3.4 5.6 + - + +
559B VAL* 2.9 35.8 + - + +
610B VAL* 5.0 19.7 - - + -
614B ARG* 5.6 5.7 + - - +
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Residues in contact with GLU 556 (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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521B LYS* 5.2 5.5 - - - -
554B SER* 3.2 11.4 - - - +
555B PRO* 1.3 97.0 - - - +
557B ALA* 1.3 51.6 + - - +
559B VAL* 3.4 11.1 + - - +
560B GLY* 2.7 31.4 + - - -
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Residues in contact with ALA 557 (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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517B SER* 4.6 2.2 - - - +
520B ALA* 3.8 22.8 - - + +
521B LYS* 3.4 33.3 - - - +
553B LEU* 4.0 12.1 - - + -
554B SER* 3.2 18.0 + - - +
556B GLU* 1.3 76.2 - - - +
558B ALA* 1.3 60.3 + - - +
560B GLY* 3.0 4.0 + - - -
561B LEU* 2.8 29.8 + - - +
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Residues in contact with ALA 558 (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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548B LEU* 3.6 37.8 - - + +
553B LEU* 3.9 9.5 - - + +
554B SER 3.3 9.1 + - - +
555B PRO* 3.7 7.0 - - + +
557B ALA* 1.3 73.7 - - - +
559B VAL* 1.3 67.1 - - - +
561B LEU* 3.0 4.9 + - - +
562B LEU* 2.9 26.7 + - - +
614B ARG* 4.0 21.5 - - - +
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Residues in contact with VAL 559 (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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555B PRO* 2.9 22.4 + - + +
556B GLU* 3.4 9.6 - - - +
558B ALA* 1.3 75.2 - - - +
560B GLY* 1.3 60.3 + - - +
562B LEU* 3.4 8.0 + - - +
563B LYS* 2.8 29.4 + - + +
613B ASP* 4.6 14.6 - - + -
614B ARG* 4.6 16.8 - - + +
617B VAL* 3.7 32.1 - - + +
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Residues in contact with GLY 560 (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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520B ALA 5.6 0.4 - - - -
521B LYS* 6.3 1.6 - - - -
524B HIS* 3.0 32.4 - - - -
556B GLU 2.7 18.7 + - - -
557B ALA* 3.0 5.3 + - - -
559B VAL* 1.3 72.8 - - - +
561B LEU* 1.3 66.3 + - - +
563B LYS* 3.1 4.9 + - - +
564B GLY* 2.9 21.0 + - - -
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Residues in contact with LEU 561 (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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510B LEU* 4.2 11.2 - - + -
520B ALA* 4.1 22.3 + - + +
523B ILE* 3.5 41.1 - - + -
524B HIS* 4.8 3.1 - - - +
527B CYS* 5.7 1.0 - - - -
541B LEU* 5.9 1.6 - - + -
544B ILE* 3.8 28.0 - - + -
548B LEU* 3.7 26.7 - - + -
551B PHE* 5.2 0.2 - - + -
553B LEU* 4.1 14.4 - - + -
557B ALA 2.8 11.8 + - - +
558B ALA 3.4 7.4 - - - +
560B GLY* 1.3 71.6 - - - +
562B LEU* 1.3 59.0 + - - +
564B GLY* 3.3 1.4 + - - -
565B THR* 2.9 34.7 + - - +
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Residues in contact with LEU 562 (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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545B ALA* 4.0 27.6 - - + -
548B LEU* 3.6 23.6 - - + -
558B ALA 2.9 9.7 + - - +
559B VAL* 3.7 7.0 - - - +
561B LEU* 1.3 72.9 - - - +
563B LYS* 1.3 61.0 + - - +
565B THR* 3.2 6.8 + - - +
566B ALA* 2.8 30.7 + - - +
584B LEU* 4.4 7.6 - - + -
588B GLN* 4.1 11.0 - - - +
614B ARG* 3.4 49.6 - - + +
617B VAL* 4.6 4.5 - - + -
618B ILE* 4.2 26.4 - - + +
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Residues in contact with LYS 563 (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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524B HIS* 3.3 31.4 + - + +
528B SER* 4.7 2.4 + - - -
559B VAL* 2.8 17.3 + - + +
560B GLY* 3.1 10.5 + - - +
562B LEU* 1.3 75.9 - - - +
564B GLY* 1.3 62.3 + - - +
566B ALA* 3.0 7.1 + - - +
567B LEU* 2.9 42.2 + - + +
617B VAL* 3.5 16.5 - - + +
621B HIS* 3.4 42.6 - - + +
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Residues in contact with GLY 564 (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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524B HIS* 4.3 11.4 - - - -
527B CYS* 3.8 23.6 - - - -
560B GLY 2.9 13.1 + - - -
561B LEU 3.7 2.9 - - - -
563B LYS* 1.3 76.3 - - - +
565B THR* 1.3 63.5 + - - +
567B LEU* 3.0 11.8 + - - +
568B VAL* 2.8 26.7 + - - +
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Residues in contact with THR 565 (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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527B CYS* 4.7 2.4 - - - +
538B PHE* 4.0 17.5 - - + -
541B LEU* 4.1 36.5 + - + +
544B ILE* 5.9 1.4 - - - +
545B ALA* 5.4 0.3 - - - +
561B LEU* 2.9 18.6 + - - +
562B LEU* 3.2 14.8 + - + +
564B GLY* 1.3 74.0 - - - +
566B ALA* 1.3 57.5 + - - +
568B VAL* 3.4 6.1 + - - +
569B LEU* 2.8 27.6 + - - +
584B LEU* 3.8 31.9 - - + -
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Residues in contact with ALA 566 (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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562B LEU 2.8 16.5 + - - +
563B LYS* 3.3 9.2 - - - +
565B THR* 1.3 71.7 - - - +
567B LEU* 1.3 60.5 + - - +
569B LEU* 3.0 9.7 + - - +
570B ALA* 2.8 31.7 + - - +
584B LEU* 5.0 1.7 - - - +
618B ILE* 3.8 20.0 - - + +
621B HIS* 3.6 14.7 - - + +
622B THR* 3.4 23.3 + - - +
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Residues in contact with LEU 567 (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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527B CYS 4.7 2.5 - - - +
528B SER* 3.6 26.5 - - - +
531B ARG* 3.3 47.9 - - + +
563B LYS* 2.9 43.2 + - + +
564B GLY* 3.4 9.9 - - - +
566B ALA* 1.3 77.2 - - - +
568B VAL* 1.3 62.6 + - - +
570B ALA* 3.6 9.9 + - + +
571B ARG* 3.8 5.7 - - - +
621B HIS* 3.6 33.8 + - + +
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Residues in contact with VAL 568 (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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527B CYS* 3.5 36.3 - - + +
531B ARG* 3.9 13.6 - - - +
534B MET* 3.6 42.0 - - + +
535B ALA* 4.4 4.5 - - - +
538B PHE* 4.3 9.2 - - + -
541B LEU* 4.1 12.8 - - + -
564B GLY 2.8 17.8 + - - +
565B THR 3.7 6.3 - - - +
567B LEU* 1.3 73.7 - - - +
569B LEU* 1.3 67.3 + - - +
571B ARG* 3.1 18.0 + - - +
572B LEU* 3.8 6.3 + - + +
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Residues in contact with LEU 569 (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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538B PHE* 3.8 13.2 - - + -
565B THR 2.8 21.5 + - - +
566B ALA* 3.0 4.5 + - - +
568B VAL* 1.3 73.7 - - - +
570B ALA* 1.3 57.8 + - - +
571B ARG 2.9 6.6 + - - -
572B LEU* 3.1 25.8 + - + +
577B ILE* 3.8 21.7 - - + +
580B CYS* 3.5 30.7 - - + -
581B LEU* 3.8 39.0 - - + +
584B LEU* 4.0 15.0 - - + -
622B THR* 4.0 18.2 - - + +
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Residues in contact with ALA 570 (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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566B ALA 2.8 15.6 + - - +
567B LEU* 3.8 8.7 - - + +
568B VAL 3.2 0.8 - - - -
569B LEU* 1.3 76.1 - - - +
571B ARG* 1.3 61.4 + - + +
572B LEU 4.8 0.2 - - - +
577B ILE* 4.4 3.8 - - - +
621B HIS 4.3 2.7 - - - +
622B THR* 4.2 5.8 - - - -
623B ASN 3.7 34.8 - - - +
624B PRO* 3.5 28.0 - - - +
625B ILE* 4.5 7.3 + - - +
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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