Contacts of the helix formed by residues 399 - 407 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C GLU* 3.3 33.7 - - + +
371C GLN* 4.0 0.4 - - - -
374C VAL* 3.7 16.6 - - + -
395C PHE 4.2 0.2 + - - -
396C LEU* 3.0 16.4 + - + +
398C ARG* 1.3 78.2 - - - +
400C TYR* 1.3 66.1 + - - +
401C ASP 3.2 0.4 - - - -
402C GLN* 2.9 28.2 + - - +
403C VAL* 3.1 13.9 + - - +
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Residues in contact with TYR 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C LEU* 3.4 6.6 + - - +
397C GLN 3.8 13.9 - - - +
398C ARG 3.5 2.0 + - - -
399C ALA* 1.3 77.2 - - - +
401C ASP* 1.3 57.1 + - - +
403C VAL* 3.4 5.6 + - + +
404C LEU* 3.0 41.4 + - + +
439C TYR* 2.6 59.0 + + + -
440C LEU* 5.2 1.6 - - + -
442C CYS* 3.1 20.8 - - - -
443C ILE* 3.7 19.1 - - + +
397D GLN* 3.7 25.5 + - + +
398D ARG 6.3 0.2 - - - -
400D TYR* 4.1 17.9 - + + -
439D TYR* 3.5 34.3 - + + +
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Residues in contact with ASP 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ALA 3.1 0.8 + - - -
400C TYR* 1.3 76.2 - - - +
402C GLN* 1.3 67.1 + - - +
404C LEU 4.6 0.2 - - - +
405C HIS* 2.8 36.9 + - - +
406C ASP* 6.0 0.3 - - - -
122D HIS* 2.6 45.2 + - - -
394D THR 4.5 0.2 - - - -
397D GLN* 2.9 27.9 + - - +
398D ARG* 3.0 56.5 + - + +
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Residues in contact with GLN 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C GLN* 3.3 31.2 + - - +
374C VAL* 3.8 18.4 - - + -
375C THR* 3.1 26.7 - - - +
398C ARG 3.8 0.3 - - - +
399C ALA* 2.9 37.2 + - - +
401C ASP* 1.3 82.2 + - - +
403C VAL* 1.3 59.2 + - - +
406C ASP* 2.8 36.6 + - - +
407C VAL* 3.0 9.4 + - - +
159D MSE 2.6 36.4 - - + +
398D ARG* 3.8 9.5 - - - +
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Residues in contact with VAL 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C VAL* 4.0 10.1 - - + -
396C LEU* 3.9 20.0 - - + -
399C ALA 3.1 14.8 + - - +
400C TYR* 3.6 9.6 - - + +
402C GLN* 1.3 77.7 - - - +
404C LEU* 1.3 58.7 + - - +
407C VAL* 3.3 6.1 - - + +
408C ALA* 2.8 28.1 + - - +
416C PHE* 3.8 31.2 - - + -
440C LEU* 4.2 9.0 - - + -
443C ILE* 4.0 11.7 - - + -
446C MSE 3.4 30.3 - - + -
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Residues in contact with LEU 404 (chain C).
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* 3.0 31.8 + - + +
401C ASP 4.1 1.1 - - - +
403C VAL* 1.3 80.8 - - - +
405C HIS* 1.3 61.8 + - + +
408C ALA* 3.3 10.0 - - - +
409C ILE* 3.1 35.4 + - + +
443C ILE* 4.1 27.4 - - + -
397D GLN* 3.9 26.5 - - - +
429D GLN 6.0 0.7 - - - +
435D PHE* 3.6 43.3 - - + -
591D PHE* 3.8 15.0 - - + -
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Residues in contact with HIS 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C ASP* 2.8 24.5 + - - +
404C LEU* 1.3 76.8 - - + +
406C ASP* 1.3 86.6 + - - +
409C ILE* 3.4 33.7 - - + +
410C GLN* 4.4 4.9 + - - +
119D SER 4.1 13.1 - - - +
120D VAL* 4.2 2.0 - - - -
121D GLY* 3.0 22.7 + - - -
122D HIS* 2.9 62.5 + + + +
125D THR* 4.7 2.7 - - - -
430D THR* 3.5 21.4 - - + +
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Residues in contact with ASP 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C THR* 2.5 37.2 + - + +
378C ALA* 4.0 7.2 - - + +
401C ASP* 6.0 0.4 - - - -
402C GLN* 2.8 32.2 + - - +
405C HIS* 1.3 102.0 + - - +
407C VAL* 1.3 58.1 + - + -
410C GLN* 3.0 27.8 + - - +
412C LEU* 3.7 11.4 - - - +
118D LEU* 5.7 0.4 - - + -
119D SER 5.2 0.2 - - - +
125D THR* 3.3 30.2 + - + +
159D MSE 4.8 1.6 - - - +
398D ARG* 5.3 2.3 + - - -
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Residues in contact with VAL 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C VAL* 3.6 39.5 - - + +
378C ALA* 4.3 6.3 - - + -
402C GLN 3.0 3.6 + - - +
403C VAL* 3.3 10.8 - - + +
405C HIS 3.5 0.2 - - - -
406C ASP* 1.3 82.0 - - + +
408C ALA* 1.3 61.5 + - - +
409C ILE 3.5 0.4 - - - -
410C GLN* 3.4 2.6 + - - -
411C LYS* 3.0 7.8 + - - -
412C LEU* 2.9 51.2 + - + +
414C VAL* 4.0 21.8 - - + -
416C PHE* 4.3 5.8 - - + -
471C PRO* 3.6 18.6 - - + -
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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