Contacts of the helix formed by residues 399 - 406 (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 ALA 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A GLU* 3.5 32.3 - - + +
374A VAL* 3.6 17.0 - - + -
391A ILE* 4.8 0.2 - - + -
395A PHE 4.2 0.4 + - - -
396A LEU* 3.1 17.1 + - + +
398A ARG* 1.3 79.0 - - - +
400A TYR* 1.3 64.6 + - - +
402A GLN* 3.0 19.8 + - - +
403A VAL* 3.0 22.8 + - - +
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Residues in contact with TYR 400 (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 3.6 5.2 + - - +
397A GLN 3.7 13.2 - - - +
398A ARG 3.5 2.4 + - - -
399A ALA* 1.3 77.1 - - - +
401A ASP* 1.3 57.4 + - - +
403A VAL* 3.2 7.7 + - + +
404A LEU* 3.0 42.3 + - + +
439A TYR* 2.5 63.9 + + + -
440A LEU* 5.0 2.0 - - + -
442A CYS* 3.2 18.5 - - - -
443A ILE* 3.7 19.3 - - + +
397B GLN* 3.6 27.3 + - + +
400B TYR* 4.0 16.2 - + + -
435B PHE* 4.7 0.2 - - - +
439B TYR* 3.5 34.3 - + + +
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Residues in contact with ASP 401 (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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399A ALA 3.3 0.4 - - - -
400A TYR* 1.3 80.1 - - - +
402A GLN* 1.3 63.7 + - - +
404A LEU 4.7 0.2 - - - +
405A HIS* 2.8 37.6 + - - +
406A ASP* 4.5 0.7 - - - +
122B HIS* 2.8 42.0 + - - -
394B THR 4.4 0.2 - - - -
397B GLN* 3.2 22.6 + - - +
398B ARG* 3.1 56.7 + - + +
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Residues in contact with GLN 402 (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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371A GLN* 3.4 45.1 + - - +
374A VAL* 3.7 16.8 - - + -
375A THR* 2.9 28.3 - - - +
398A ARG 3.8 1.2 + - - -
399A ALA* 3.0 33.9 - - - +
401A ASP* 1.3 78.1 - - - +
403A VAL* 1.3 66.3 + - - +
406A ASP* 3.0 31.7 + - - +
407A VAL* 3.1 10.9 + - - +
159B MSE 3.7 16.4 - - + +
398B ARG* 3.7 12.0 + - - +
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Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 4.0 16.6 - - + -
396A LEU* 3.9 28.3 - - + -
399A ALA 3.0 15.5 + - - +
400A TYR* 3.4 9.4 - - - +
402A GLN* 1.3 77.6 - - - +
404A LEU* 1.3 52.7 + - - +
407A VAL* 3.3 7.5 - - - +
408A ALA* 2.8 32.4 + - - +
416A PHE* 4.1 13.7 - - + -
440A LEU* 4.4 8.5 - - + -
443A ILE* 4.0 12.6 - - + -
446A MSE 3.4 30.7 - - + +
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Residues in contact with LEU 404 (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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400A TYR* 3.0 26.2 + - + +
401A ASP 4.3 1.3 - - - +
403A VAL* 1.3 79.8 - - - +
405A HIS* 1.3 64.0 + - + +
408A ALA* 3.1 9.8 + - - +
409A ILE* 3.0 35.8 + - + +
443A ILE* 4.1 32.1 - - + -
397B GLN* 3.8 23.8 - - - +
429B GLN 6.0 0.4 - - - +
435B PHE* 3.5 36.6 - - + -
591B PHE* 3.5 23.8 - - + -
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Residues in contact with HIS 405 (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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401A ASP* 2.8 35.2 + - - +
404A LEU* 1.3 77.4 - - + +
406A ASP* 1.3 85.9 + - - +
407A VAL 3.6 0.2 - - - -
409A ILE* 3.6 32.4 - - + +
410A GLN* 4.5 6.1 + - - +
119B SER 4.5 3.8 + - - +
120B VAL* 4.0 6.5 - - - -
121B GLY 3.9 6.0 + - - -
122B HIS* 3.3 52.8 + + + +
125B THR* 4.6 1.7 + - - -
397B GLN* 5.1 0.2 - - - +
398B ARG* 5.6 0.2 - - - -
430B THR* 3.3 40.9 + - + +
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Residues in contact with ASP 406 (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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375A THR* 3.1 30.2 + - + +
378A ALA* 3.6 5.5 - - + +
401A ASP* 4.5 1.2 - - - +
402A GLN* 3.0 26.9 + - - +
405A HIS* 1.3 93.2 + - - +
407A VAL* 1.3 63.2 + - + +
410A GLN* 2.8 29.1 + - - +
412A LEU* 3.2 9.9 - - - +
118B LEU* 6.1 0.2 - - + -
119B SER 4.8 2.6 - - - +
125B THR* 3.0 40.3 + - + +
159B MSE 4.3 1.6 - - - +
398B ARG* 5.2 2.1 + - - -
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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