Contacts of the helix formed by residues 435 - 440 (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 PHE 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A SER* 4.4 0.6 + - - -
397A GLN* 3.9 11.8 - - - +
429A GLN 6.2 0.2 - - - -
432A GLN* 5.0 3.8 - - + -
433A GLY 3.5 0.4 - - - -
434A ALA* 1.3 102.2 - - + +
436A ASP* 1.3 61.5 + - - +
437A LEU 3.2 2.9 - - - -
438A SER* 2.9 21.0 + - - -
439A TYR* 3.0 30.2 + - + -
559A ASN* 3.4 3.4 - - - +
560A ALA* 3.9 15.0 - - + -
588A PRO 6.1 0.9 - - - -
590A PHE 5.7 1.1 - - - -
591A PHE* 4.2 13.2 - + - -
400B TYR* 4.8 1.1 - - - +
404B LEU* 3.8 35.0 - - + -
442B CYS* 3.3 40.4 - - - -
443B ILE* 4.8 0.4 - - - -
444B PRO* 3.7 25.1 - - + -
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Residues in contact with ASP 436 (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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393A SER* 2.4 34.0 + - - +
418A ILE* 4.6 10.5 - - + +
433A GLY 3.5 2.3 - - - +
435A PHE* 1.3 75.6 - - - +
437A LEU* 1.3 62.1 + - - +
438A SER 3.0 0.9 + - - -
439A TYR* 3.3 29.4 - - + +
440A LEU* 2.9 42.7 + - + +
448A ILE* 5.6 0.2 - - - +
475A ARG* 2.7 52.0 + - - +
559A ASN* 3.5 0.2 - - - +
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Residues in contact with LEU 437 (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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436A ASP* 1.3 78.1 - - - +
438A SER* 1.3 58.7 + - - +
440A LEU* 5.1 0.4 - - - -
441A ARG* 3.4 30.3 - - - +
448A ILE* 3.8 22.4 - - + +
450A THR* 3.7 18.8 - - + -
475A ARG* 3.5 38.6 - - - +
511A PHE* 5.2 2.9 - - + +
535A VAL* 3.9 19.1 - - + +
557A GLU* 3.5 30.7 - - + +
559A ASN* 2.9 31.7 - - + +
563A GLY 3.8 1.7 - - - +
564A GLY* 3.9 2.0 - - - -
565A ALA* 4.6 2.7 - - + +
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Residues in contact with SER 438 (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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435A PHE* 2.9 10.2 + - - -
437A LEU* 1.3 78.2 - - - +
439A TYR* 1.3 66.9 + - - +
440A LEU 3.1 2.0 + - - -
441A ARG* 3.1 15.1 + - - +
442A CYS* 3.7 8.5 + - - +
559A ASN* 3.4 11.4 + - - -
560A ALA* 3.9 1.7 + - - +
562A MSE 2.9 26.3 + - - -
563A GLY* 3.6 11.5 - - - +
564A GLY 3.1 11.3 + - - -
438B SER* 5.5 5.0 - - - +
442B CYS* 3.8 18.1 - - - +
563B GLY* 6.0 1.4 - - - -
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Residues in contact with TYR 439 (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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393A SER 2.8 23.6 + - - -
396A LEU* 3.5 22.9 - - + +
397A GLN* 3.8 24.7 + - + -
400A TYR* 2.5 57.8 + + + -
435A PHE* 3.0 28.8 + - + -
436A ASP* 3.3 30.9 - - + +
438A SER* 1.3 79.0 - - - +
440A LEU* 1.3 81.5 + - + +
442A CYS* 3.3 10.4 - - - -
443A ILE* 3.6 1.4 - - - +
400B TYR* 3.6 32.3 - + + +
439B TYR* 4.4 7.2 - - + +
442B CYS* 4.6 0.6 - - - -
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Residues in contact with LEU 440 (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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396A LEU* 4.4 8.3 - - + -
400A TYR* 4.8 1.3 - - + -
403A VAL* 4.4 14.8 - - + -
418A ILE* 3.7 29.2 - - + -
436A ASP* 2.9 28.4 + - + +
438A SER 3.1 0.6 - - - -
439A TYR* 1.3 100.7 - - + +
441A ARG* 1.3 63.4 + - - +
442A CYS 3.3 1.1 - - - -
443A ILE* 3.1 37.2 + - + +
446A MSE 4.0 19.0 - - + +
448A ILE* 3.7 20.6 - - + +
473A ALA* 4.4 11.4 - - + -
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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