Contacts of the helix formed by residues 435 - 440 (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 PHE 435 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C LEU* 3.6 37.0 - - + -
442C CYS* 3.6 35.9 - - - -
443C ILE* 5.1 0.2 - - - -
444C PRO* 3.9 24.5 - - + -
393D SER* 4.5 0.6 + - - -
397D GLN* 3.6 13.1 + - - -
429D GLN 6.1 0.9 - - - -
432D GLN* 4.8 6.5 - - + -
433D GLY 3.6 1.2 - - - -
434D ALA* 1.3 104.2 - - + +
436D ASP* 1.3 60.6 + - - +
437D LEU 3.2 3.4 - - - -
438D SER* 2.8 20.4 + - - -
439D TYR* 3.1 29.5 + - + -
559D ASN* 3.3 3.6 - - - +
560D ALA* 3.8 14.4 - - + -
590D PHE 6.0 0.2 - - - -
591D PHE* 4.1 13.7 - + - -
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Residues in contact with ASP 436 (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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393D SER* 2.6 33.1 + - - +
418D ILE* 4.4 9.6 - - + +
433D GLY 3.7 1.6 - - - +
435D PHE* 1.3 72.0 - - - +
437D LEU* 1.3 66.4 + - - +
438D SER 3.0 1.1 + - - -
439D TYR* 3.4 26.3 - - + +
440D LEU* 3.1 42.0 + - + +
448D ILE* 5.7 0.2 - - - +
475D ARG* 2.7 54.8 + - - +
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Residues in contact with LEU 437 (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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436D ASP* 1.3 88.2 - - - +
438D SER* 1.3 58.0 + - - +
441D ARG* 3.1 33.5 - - - +
448D ILE* 3.8 20.6 - - + -
450D THR* 3.7 31.6 - - + -
475D ARG* 3.7 22.4 - - + +
511D PHE 5.3 2.0 - - - +
535D VAL* 4.0 12.3 - - + -
557D GLU* 3.8 22.2 - - + +
558D GLU 5.1 0.2 - - - +
559D ASN* 3.0 38.7 + - + +
563D GLY 3.7 1.2 - - - +
564D GLY* 3.9 0.9 - - - -
565D ALA 4.4 3.4 - - - +
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Residues in contact with SER 438 (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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438C SER* 5.3 5.3 - - - +
442C CYS* 3.8 19.5 - - - +
563C GLY* 5.8 2.1 - - - -
435D PHE* 2.8 12.1 + - - -
437D LEU* 1.3 78.2 - - - +
439D TYR* 1.3 64.1 + - - -
440D LEU 3.2 1.3 - - - -
441D ARG* 3.3 15.2 + - - +
442D CYS* 3.8 8.1 + - - +
559D ASN* 3.2 12.3 + - - +
560D ALA* 4.1 1.4 + - - +
562D MSE 2.8 26.2 + - - -
563D GLY* 3.1 20.0 - - - +
564D GLY 3.2 2.6 + - - -
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Residues in contact with TYR 439 (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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400C TYR* 3.5 32.5 - + + +
439C TYR* 4.5 7.9 - - + +
442C CYS* 4.8 0.2 - - - -
393D SER* 2.9 25.2 + - - -
396D LEU* 3.6 21.4 - - + +
397D GLN* 3.7 25.6 - - + +
400D TYR* 2.6 56.8 + + + -
435D PHE* 3.1 28.0 + - + -
436D ASP* 3.4 27.6 - - - +
438D SER* 1.3 78.9 - - - +
440D LEU* 1.3 85.0 + - + +
442D CYS* 3.4 8.8 - - - -
443D ILE* 3.5 2.1 - - - +
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Residues in contact with LEU 440 (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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396D LEU* 4.4 8.5 - - + -
400D TYR* 5.0 1.6 - - + -
403D VAL* 4.4 16.8 - - + -
416D PHE* 6.6 0.4 - - + -
418D ILE* 3.7 30.3 - - + -
436D ASP* 3.1 28.2 + - + +
439D TYR* 1.3 97.0 - - + +
441D ARG* 1.3 65.5 + - - +
443D ILE* 3.1 38.2 + - + +
446D MSE 4.0 12.6 - - + +
448D ILE* 3.4 25.3 - - + +
473D ALA* 4.3 13.2 - - + -
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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