Contacts of the helix formed by residues 514 - 526 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510D ASN* 3.7 3.8 - - - +
511D PHE 5.9 1.1 - - - +
512D GLY 3.1 3.0 + - - -
513D THR* 1.3 79.4 - - - +
515D MSE 1.3 65.1 + - - +
516D PRO* 3.2 4.5 - - - -
517D GLU* 3.1 14.0 + - + +
518D ALA* 3.1 17.7 + - - +
556D VAL* 4.2 16.8 - - + -
557D GLU* 4.0 8.7 - - - +
558D GLU* 3.7 52.3 - - + +
601D ARG* 4.4 22.0 - - + +
606D LEU* 4.1 34.5 - - + +
611D MSE 4.2 9.1 - - + +
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Residues in contact with MSE 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D SER* 4.1 14.6 - - - +
500D LYS* 4.0 16.4 - - + -
510D ASN* 3.1 33.3 - - + +
512D GLY 3.6 13.7 - - - +
514D LEU* 1.3 77.8 - - - +
516D PRO* 1.3 59.9 - - + +
518D ALA* 3.9 1.3 - - - -
519D ALA* 2.6 37.1 + - + +
529D LEU* 3.8 26.5 - - + -
530D VAL 4.1 1.8 - - - +
531D ASP* 3.3 51.6 - - + +
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Residues in contact with PRO 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D SER 4.9 2.9 - - - +
482D VAL* 4.5 24.9 - - + -
513D THR* 3.5 14.1 - - - +
514D LEU 3.3 5.8 - - - -
515D MSE 1.3 95.0 - - + +
517D GLU* 1.3 69.2 + - + +
519D ALA* 3.3 6.7 + - + +
520D LYS* 3.1 33.2 + - - +
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Residues in contact with GLU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D LEU* 3.1 14.2 + - + +
516D PRO* 1.3 78.7 - - + +
518D ALA* 1.3 66.2 + - - +
520D LYS* 2.8 33.9 + - - +
521D VAL* 3.1 26.5 + - - +
606D LEU 4.0 4.9 - - - +
607D ASP* 3.6 19.1 - - - +
608D ALA* 2.7 40.2 + - - +
611D MSE 3.9 13.0 - - + -
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Residues in contact with ALA 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D ILE* 4.1 23.3 - - + +
510D ASN* 4.0 11.0 - - + +
514D LEU 3.1 12.4 + - - +
515D MSE 3.5 18.4 - - - +
517D GLU* 1.3 77.7 - - - +
519D ALA* 1.3 61.1 + - - +
521D VAL* 3.2 8.1 + - - +
522D ALA* 3.0 20.8 + - - +
529D LEU* 4.2 3.4 - - + +
556D VAL* 4.6 4.7 - - + -
611D MSE 4.2 16.3 - - - -
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Residues in contact with ALA 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ARG* 5.5 0.2 - - - -
515D MSE 2.6 25.8 + - + +
516D PRO* 3.6 7.0 - - + +
518D ALA* 1.3 71.8 - - - +
520D LYS* 1.3 65.2 + - + +
522D ALA* 3.1 12.2 + - - +
523D GLU* 3.1 18.0 + - + +
529D LEU* 3.6 27.9 - - + +
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Residues in contact with LYS 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D PRO* 3.1 19.5 + - - +
517D GLU* 2.8 36.8 + - - +
519D ALA* 1.3 76.7 - - + +
521D VAL* 1.3 58.5 + - - +
523D GLU* 3.4 7.9 + - - +
524D SER* 3.0 28.3 + - - -
608D ALA* 3.9 22.4 - - + -
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Residues in contact with VAL 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D ILE* 3.9 14.4 - - + -
517D GLU 3.1 16.1 + - - +
518D ALA* 3.4 9.6 - - - +
519D ALA 3.1 0.2 - - - -
520D LYS* 1.3 75.1 - - - +
522D ALA* 1.3 59.2 + - - +
524D SER* 3.3 5.9 + - - -
525D LEU* 2.9 54.7 + - + +
608D ALA* 3.6 30.7 - - + +
611D MSE 3.9 14.4 - - + -
612D GLU* 4.6 8.7 - - + +
615D ILE* 3.9 13.2 - - + -
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ARG* 3.6 11.1 - - - -
508D ILE* 4.0 13.7 - - + +
518D ALA 3.0 11.9 + - - +
519D ALA* 3.4 10.8 - - - +
521D VAL* 1.3 77.9 - - - +
523D GLU* 1.3 51.9 + - - +
526D ASN* 2.7 29.5 + - - -
527D ALA* 2.8 27.9 + - - +
529D LEU* 3.9 22.9 - - + -
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Residues in contact with GLU 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ARG* 2.7 37.9 + - - +
519D ALA 3.1 15.4 + - - +
520D LYS* 3.7 9.9 - - - +
521D VAL 3.2 0.2 - - - -
522D ALA* 1.3 75.7 - - - +
524D SER* 1.3 64.4 + - - +
525D LEU 3.3 0.5 + - - -
526D ASN* 3.3 10.6 + - - +
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Residues in contact with SER 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D LYS 3.0 16.5 + - - -
521D VAL* 3.7 4.0 - - - -
523D GLU* 1.3 77.8 - - - +
525D LEU* 1.3 60.1 + - - +
526D ASN 4.0 0.2 + - - -
612D GLU* 2.6 35.4 + - - -
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Residues in contact with LEU 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D GLU* 4.9 4.0 - - - +
506D LEU* 4.4 14.0 - - + +
508D ILE* 5.4 1.3 - - + -
521D VAL* 2.9 32.9 + - + +
524D SER* 1.3 82.1 - - - +
526D ASN* 1.3 72.5 + - - +
527D ALA* 3.4 10.1 + - + +
612D GLU* 3.2 43.5 - - + +
615D ILE* 3.9 24.0 - - + -
616D LYS* 4.5 10.8 - - - +
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Residues in contact with ASN 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ARG* 2.9 28.7 + - - +
502D ARG 4.7 1.4 - - - +
503D GLY* 3.3 5.3 - - - -
504D GLU* 3.1 48.9 + - - +
522D ALA 2.7 11.5 + - - -
523D GLU 3.3 6.7 + - - +
524D SER 3.5 0.2 - - - -
525D LEU* 1.3 82.0 - - - +
527D ALA* 1.3 56.8 + - - +
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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