Contacts of the helix formed by residues 514 - 526 (chain A) in PDB entry 2O1S
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 LEU 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A ASN* 3.6 4.3 - - - +
511A PHE 5.5 1.1 - - - +
512A GLY 3.0 2.7 + - - -
513A THR* 1.3 80.3 + - - +
515A MSE 1.3 64.8 + - - +
516A PRO* 3.4 3.1 - - - -
517A GLU* 3.2 14.5 + - + +
518A ALA* 3.1 17.2 + - - +
556A VAL* 3.8 22.7 - - + -
557A GLU 3.9 26.7 - - - +
558A GLU* 3.5 34.5 - - + +
601A ARG* 4.5 15.0 - - - +
606A LEU* 4.1 25.4 - - + +
611A MSE 3.9 19.6 - - + +
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Residues in contact with MSE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A SER* 3.8 16.4 - - - +
500A LYS* 4.3 13.2 - - + +
510A ASN* 3.2 27.2 - - + +
512A GLY 3.7 12.3 - - - +
514A LEU* 1.3 77.0 - - - +
516A PRO* 1.3 63.0 - - + +
518A ALA* 2.9 2.3 + - - -
519A ALA* 2.6 37.2 + - + +
529A LEU* 3.6 39.7 - - + -
531A ASP* 3.5 48.7 - - + +
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Residues in contact with PRO 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A SER 4.8 4.3 - - - +
482A VAL* 4.2 27.1 - - + -
513A THR 3.5 13.7 - - - +
514A LEU 3.4 4.7 - - - -
515A MSE 1.3 95.8 - - + +
517A GLU* 1.3 69.1 + - + +
519A ALA* 3.5 7.5 + - + +
520A LYS* 3.3 27.2 + - - +
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Residues in contact with GLU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LEU* 3.2 14.0 + - + +
515A MSE 3.1 0.6 - - - -
516A PRO* 1.3 81.7 - - + +
518A ALA* 1.3 67.0 + - - +
520A LYS* 3.1 36.8 + - - +
521A VAL* 3.1 18.6 + - - +
606A LEU 4.0 5.6 - - - +
607A ASP* 3.4 18.7 - - + +
608A ALA* 2.7 38.0 + - - +
611A MSE 3.9 13.0 - - + -
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A ILE* 4.2 17.1 - - + +
510A ASN* 4.1 16.8 - - + +
514A LEU 3.1 9.8 + - - +
515A MSE 2.9 7.7 + - - +
517A GLU* 1.3 78.6 - - - +
519A ALA* 1.3 56.9 + - - +
521A VAL* 3.2 6.9 + - - +
522A ALA* 3.0 28.6 + - - +
529A LEU* 4.2 15.8 - - + +
556A VAL* 4.6 11.2 - - + -
611A MSE 4.2 8.6 - - - -
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ARG* 5.5 0.9 - - - -
515A MSE 2.6 24.9 + - + +
516A PRO* 3.5 10.1 - - + +
518A ALA* 1.3 73.2 - - - +
520A LYS* 1.3 61.8 + - + +
522A ALA* 3.4 2.1 + - - +
523A GLU* 3.1 24.6 + - - +
529A LEU* 4.0 24.2 - - + +
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Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A PRO* 3.3 14.8 + - - +
517A GLU* 3.1 30.0 + - - +
519A ALA* 1.3 77.7 - - + +
521A VAL* 1.3 57.5 + - - +
523A GLU* 3.4 5.9 + - - +
524A SER* 2.9 32.0 + - - -
608A ALA* 3.7 25.2 - - + +
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A ILE* 3.7 18.4 - - + -
517A GLU 3.1 15.2 + - - +
518A ALA* 3.2 8.0 + - - +
520A LYS* 1.3 74.4 - - - +
522A ALA* 1.3 60.0 + - - +
524A SER* 3.2 5.8 + - - -
525A LEU* 2.8 49.9 + - + +
608A ALA* 3.6 28.0 - - + +
611A MSE 3.8 19.3 - - + -
612A GLU* 4.6 8.7 - - + +
615A ILE* 3.9 13.9 - - + -
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ARG* 4.0 6.6 + - - -
508A ILE* 3.8 15.9 - - + +
518A ALA 3.0 16.3 + - - +
519A ALA* 3.8 4.7 - - - +
521A VAL* 1.3 75.7 - - - +
523A GLU* 1.3 55.1 + - - +
526A ASN* 2.6 32.2 + - - -
527A ALA* 2.8 29.3 + - - +
528A THR 4.8 0.2 - - - +
529A LEU* 4.0 23.3 - - + -
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ARG* 2.8 44.4 + - - +
519A ALA 3.1 17.5 + - - +
520A LYS* 3.8 6.1 - - - +
522A ALA* 1.3 77.5 - - - +
524A SER* 1.3 61.8 + - - +
525A LEU 3.5 0.5 + - - -
526A ASN* 3.5 7.8 + - - +
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Residues in contact with SER 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A LYS 2.9 19.8 + - - -
521A VAL 3.6 4.9 - - - -
523A GLU* 1.3 77.8 - - - +
525A LEU* 1.3 60.8 + - - +
526A ASN 3.5 0.2 - - - -
612A GLU* 2.8 27.3 + - - -
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A GLU* 4.7 5.5 - - - +
506A LEU* 4.1 24.4 - - + +
508A ILE* 5.5 0.7 - - + -
521A VAL* 2.8 36.0 + - + +
522A ALA 4.4 0.4 - - - +
524A SER* 1.3 82.7 - - - +
526A ASN* 1.3 71.0 + - - +
527A ALA* 3.0 11.1 + - + +
612A GLU* 4.0 27.8 - - + +
615A ILE* 4.2 13.7 - - + -
616A LYS* 4.1 18.8 - - - +
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Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ARG* 3.1 32.0 + - - +
502A ARG 4.5 1.9 - - - +
503A GLY* 3.1 5.2 - - - -
504A GLU* 2.9 53.2 + - - +
522A ALA 2.6 14.3 + - - -
523A GLU 3.5 4.6 + - - +
524A SER 3.5 2.4 - - - -
525A LEU* 1.3 75.3 - - - +
527A ALA* 1.3 58.8 + - - +
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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