Contacts of the helix formed by residues 403 - 411 (chain C) in PDB entry 3OMA
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 GLN 403 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C MET* 3.8 11.0 - - - +
353C MET* 3.1 30.9 - - - +
399C ILE* 3.5 14.7 + - + +
400C VAL 3.3 9.8 - - - +
401C LEU 3.2 1.5 - - - -
402C SER* 1.3 92.1 + - - +
404C ALA* 1.3 65.1 + - - +
405C SER* 3.2 2.2 - - - -
406C VAL* 2.9 15.8 + - + +
407C ASP* 2.9 20.8 + - - +
61D ILE* 3.8 19.7 - - + -
115D ILE* 3.5 15.4 - - + +
119D SER* 2.6 38.7 + - - +
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Residues in contact with ALA 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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336C TYR* 3.7 38.3 - - + +
345C GLN* 3.7 15.0 - - + +
349C MET* 3.9 6.2 - - - -
402C SER 3.1 6.1 + - - -
403C GLN* 1.3 70.3 - - - +
405C SER* 1.3 56.4 + - - +
407C ASP* 3.8 1.1 - - - +
408C ARG* 3.1 35.9 + - - +
123D LEU* 3.7 27.8 - - + -
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Residues in contact with SER 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C MET* 5.5 0.2 - - - -
403C GLN 4.5 1.0 - - - -
404C ALA* 1.3 76.9 - - - +
406C VAL* 1.3 59.8 + - - +
408C ARG* 3.6 6.1 - - - +
54D ILE* 3.4 10.8 - - - +
57D LEU* 3.4 23.1 - - - +
119D SER* 3.7 15.1 + - - -
122D VAL* 3.7 20.4 - - - -
123D LEU* 4.0 15.6 - - - +
126D GLN* 2.8 41.8 + - - +
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Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C VAL* 4.0 13.0 - - + +
403C GLN* 2.9 13.2 + - + +
405C SER* 1.3 76.1 + - - +
407C ASP* 1.3 60.6 + - - +
408C ARG 3.0 2.0 - - - -
409C TYR* 3.0 21.7 + - - +
410C TYR* 3.2 40.0 + - + -
43D PHE* 5.1 0.2 - - + -
54D ILE* 4.5 15.3 - - + +
57D LEU* 3.8 32.1 - - + -
58D ASP* 3.8 26.2 - - + +
61D ILE* 4.7 4.7 - - + -
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Residues in contact with ASP 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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2C HEA 2.6 33.8 - - - +
333C HIS 4.4 1.2 - - - +
334C HIS 6.1 0.2 - - - -
336C TYR* 3.3 34.2 + - + +
337C THR* 4.8 0.4 - - - +
400C VAL 4.7 1.2 + - - -
401C LEU* 3.3 39.0 + - - +
403C GLN 2.9 10.1 + - - +
404C ALA 3.8 1.8 - - - +
406C VAL* 1.3 72.2 - - - +
408C ARG* 1.3 61.6 + - - +
410C TYR* 3.6 7.2 - - - +
411C HIS* 2.7 41.8 + - - +
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Residues in contact with ARG 408 (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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336C TYR* 2.9 34.6 + - - +
337C THR* 4.1 13.5 - - - +
345C GLN* 2.6 24.0 + - - -
404C ALA 3.1 16.7 + - - +
405C SER 3.6 15.5 - - - +
406C VAL 3.0 0.2 - - - -
407C ASP* 1.3 77.2 - - - +
409C TYR* 1.3 56.4 + - - +
54D ILE* 4.8 0.7 - - + -
123D LEU* 3.5 11.1 - - - +
126D GLN* 2.9 28.5 + - - +
127D GLN* 3.3 27.7 + - - +
220D THR* 5.2 0.2 + - - -
225D GLY 3.7 21.1 - - - +
226D VAL* 4.4 1.7 - - - -
227D LYS* 3.1 64.6 + - - +
228D GLN* 5.8 3.0 - - - +
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Residues in contact with TYR 409 (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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405C SER 4.6 0.4 + - - -
406C VAL 3.0 10.0 + - - +
408C ARG* 1.3 79.9 - - - +
410C TYR* 1.3 67.9 + + + +
413C THR* 3.4 7.6 - - - +
475C GLY 3.5 13.5 - - - -
476C ARG 2.7 29.4 + - - -
478C GLY* 4.0 7.4 + - - -
43D PHE* 3.5 34.1 - + + -
44D GLN* 3.3 20.1 + - - +
54D ILE* 4.3 21.9 - - + +
55D HIS* 5.1 4.7 - + - -
222D PRO* 3.5 51.1 - - + +
225D GLY* 5.0 8.5 - - - -
227D LYS* 2.8 18.2 + - - +
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Residues in contact with TYR 410 (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 VAL* 3.7 13.2 - - + -
401C LEU* 3.6 20.4 - - + -
406C VAL* 3.2 31.9 + - + +
407C ASP* 4.4 1.3 - - - -
409C TYR* 1.3 80.8 - + - +
411C HIS* 1.3 68.0 + - - +
412C ASP 3.3 0.3 + - - -
413C THR* 2.6 25.9 + - - +
415C TYR* 3.4 49.8 - + + -
416C VAL* 3.4 7.5 - - - +
475C GLY 4.2 4.7 - - - -
476C ARG* 2.9 39.5 + - + +
43D PHE* 3.3 17.0 - + - -
58D ASP* 2.7 28.3 + - - -
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Residues in contact with HIS 411 (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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2C HEA 2.8 41.2 + - - +
6C MG 2.1 32.2 - - - -
175C TYR* 5.9 1.1 - - - -
334C HIS 4.2 18.7 - - - -
335C MET* 5.9 0.4 - - - -
336C TYR 6.0 1.0 + - - -
337C THR* 3.3 33.7 + - + -
407C ASP* 2.7 32.4 + - - +
409C TYR 3.5 0.6 - - - -
410C TYR* 1.3 72.2 - - - +
412C ASP* 1.3 80.2 + - + +
413C THR 3.3 0.3 + - - -
416C VAL* 4.2 0.4 - - - -
481C ARG* 5.9 1.8 - - - -
227D LYS* 2.8 33.1 + - + -
229D ASP* 4.7 1.5 + - - -
253D SER 4.9 0.9 - - - -
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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