Contacts of the helix formed by residues 399 - 407 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B GLU* 3.6 33.9 - - + +
371B GLN* 4.5 0.2 - - - +
374B VAL* 3.6 16.8 - - + -
391B ILE* 5.0 0.2 - - + -
396B LEU* 3.0 17.3 + - + +
398B ARG* 1.3 78.0 - - - +
400B TYR* 1.3 64.7 + - - +
401B ASP 3.3 2.7 - - - -
402B GLN* 3.0 15.3 + - - +
403B VAL* 3.0 22.1 + - - +
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Residues in contact with TYR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLN* 3.6 27.6 - - + +
400A TYR* 4.0 15.7 - + + -
435A PHE* 4.8 0.2 - - - +
439A TYR* 3.6 35.3 - + + +
396B LEU* 3.4 5.1 + - - +
397B GLN 3.4 18.4 + - - +
398B ARG 3.4 1.4 - - - -
399B ALA* 1.3 77.5 - - - +
401B ASP* 1.3 62.6 + - - +
403B VAL* 3.3 6.2 + - + +
404B LEU* 3.0 34.6 + - + +
439B TYR* 2.7 61.7 + + + -
440B LEU* 4.9 2.9 - - + -
442B CYS* 3.3 17.5 - - - -
443B ILE* 3.8 18.5 - - + +
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Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A HIS* 2.7 42.5 + - - +
395A PHE* 5.7 0.2 - - - -
397A GLN* 3.0 20.8 + - - +
398A ARG* 3.0 60.7 + - + +
3001A TPP 5.0 0.2 - - - +
399B ALA 3.3 1.0 - - - -
400B TYR* 1.3 78.3 - - - +
402B GLN* 1.3 57.4 + - - +
404B LEU* 4.6 1.6 - - - +
405B HIS* 2.7 42.2 + - - +
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Residues in contact with GLN 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MSE 3.6 12.4 - - + +
398A ARG* 3.6 20.5 + - - +
371B GLN* 3.1 44.0 + - - +
374B VAL* 3.9 17.3 - - + -
375B THR* 3.1 27.1 - - - +
398B ARG 3.9 1.4 + - - -
399B ALA* 3.0 30.8 + - - +
401B ASP* 1.3 77.1 - - - +
403B VAL* 1.3 61.4 + - - +
406B ASP* 2.8 41.3 + - - +
407B VAL* 3.2 6.4 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 4.0 10.1 - - + -
396B LEU* 3.8 20.2 - - + -
399B ALA 3.0 17.1 + - - +
400B TYR* 3.6 9.6 - - + +
402B GLN* 1.3 77.1 - - - +
404B LEU* 1.3 58.1 + - - +
407B VAL* 3.3 7.2 - - - +
408B ALA* 2.9 26.3 + - - +
416B PHE* 3.8 32.3 - - + -
440B LEU* 4.2 18.4 - - + -
443B ILE* 4.2 5.8 - - + -
446B MSE 3.7 25.6 - - + -
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLN* 3.7 28.9 - - + +
435A PHE* 3.8 27.6 - - + -
591A PHE* 3.6 21.1 - - + -
400B TYR* 3.0 31.2 + - + +
401B ASP 4.0 1.6 - - - +
403B VAL* 1.3 78.9 - - - +
405B HIS* 1.3 60.3 + - + +
408B ALA* 3.4 7.9 - - - +
409B ILE* 3.1 35.4 + - + +
443B ILE* 3.9 34.1 - - + -
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Residues in contact with HIS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER 4.0 13.9 - - - -
120A VAL* 4.1 1.6 - - - -
121A GLY 3.4 14.3 + - - -
122A HIS* 3.0 61.2 + + + +
125A THR* 4.5 4.2 - - + +
398A ARG* 6.0 0.2 - - - -
430A THR* 3.6 24.8 - - + +
401B ASP* 2.7 32.9 + - - +
404B LEU* 1.3 76.9 - - + +
406B ASP* 1.3 82.6 + - - +
407B VAL 3.5 0.2 - - - -
409B ILE* 3.6 23.5 - - + +
410B GLN* 3.2 13.7 + - - -
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Residues in contact with ASP 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 5.0 4.7 - - + +
125A THR* 3.4 25.6 + - - +
398A ARG* 5.5 0.5 + - - -
375B THR* 2.7 39.1 + - + +
378B ALA* 3.4 22.9 - - + +
401B ASP 4.8 0.2 - - - +
402B GLN* 2.8 32.2 + - - +
405B HIS* 1.3 96.5 + - - +
407B VAL* 1.3 58.5 + - + +
410B GLN* 3.2 24.6 + - - +
412B LEU* 3.8 1.4 - - - +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 3.6 36.3 - - + +
378B ALA* 4.4 2.2 - - + -
402B GLN 3.2 3.6 + - - +
403B VAL* 3.3 9.6 + - - +
405B HIS 3.5 0.2 - - - -
406B ASP* 1.3 86.0 - - + +
408B ALA* 1.3 60.7 + - - +
409B ILE 3.5 0.4 - - - -
410B GLN* 3.4 2.1 + - - -
411B LYS* 2.9 23.4 + - - -
412B LEU* 3.0 36.1 + - - +
414B VAL* 3.9 25.6 - - + -
416B PHE* 4.2 7.0 - - + -
471B PRO* 3.4 20.9 - - + -
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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