Contacts of the helix formed by residues 308 - 316 (chain G) in PDB entry 1O1F
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 ASN 308 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292G MET* 3.4 1.8 - - - -
306G THR* 3.6 4.0 + - - +
307G THR* 1.3 76.5 + - - +
309G PRO* 1.3 65.0 - - - +
310G TYR* 2.8 38.4 + - - +
311G ASP* 3.1 41.8 + - - +
312G TYR* 3.7 1.7 - - - -
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Residues in contact with PRO 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G TYR* 4.7 11.4 - - + -
292G MET* 3.0 30.5 - - + -
307G THR 3.1 7.9 - - - +
308G ASN* 1.3 84.4 - - - +
310G TYR* 1.3 60.0 + - + +
311G ASP 2.8 11.4 + - - -
312G TYR* 2.9 17.4 + - + +
315G VAL* 4.8 2.5 - - + -
316G SER* 3.3 17.4 - - - -
320G ILE* 3.5 45.1 - - + -
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Residues in contact with TYR 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G ASN* 2.8 28.5 + - - +
309G PRO* 1.3 77.9 - - + +
311G ASP* 1.3 58.3 + - - +
312G TYR 3.3 3.3 + - - -
313G HIS* 5.0 1.4 + - - -
316G SER* 3.8 28.8 + - - -
318G GLY 5.6 2.5 - - - -
319G GLU* 6.0 0.3 - - - -
320G ILE* 2.8 36.2 - - + +
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Residues in contact with ASP 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G THR* 2.5 29.9 + - - +
308G ASN* 3.1 19.1 + - - +
309G PRO 2.8 0.2 + - - -
310G TYR* 1.3 81.2 - - - +
312G TYR* 1.3 77.4 + - + +
313G HIS 3.8 1.3 - - - -
363G ASN* 2.6 35.3 + - - +
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Residues in contact with TYR 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G MET* 4.4 11.7 - - + -
304G LEU 4.3 0.7 + - - -
305G ILE* 2.9 31.6 - - + -
306G THR* 2.7 38.3 + - - +
308G ASN 3.7 6.7 - - - -
309G PRO* 2.9 18.2 + - + +
311G ASP* 1.3 105.9 - - + +
313G HIS* 1.3 55.9 - - - +
314G TYR* 3.2 2.5 - - - +
315G VAL* 2.8 40.3 + - + +
316G SER* 3.4 2.9 + - - -
359G MET* 3.6 35.2 - - + +
360G HIS* 4.2 13.0 + + - -
363G ASN* 3.8 15.5 - - - -
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Residues in contact with HIS 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G THR 5.6 0.2 + - - -
310G TYR 5.0 2.3 + - - -
311G ASP 3.8 1.8 - - - -
312G TYR* 1.3 72.4 - - - +
314G TYR* 1.3 80.7 + + - +
315G VAL 3.0 1.2 + - - -
316G SER* 3.4 12.0 + - - -
317G GLU* 3.2 46.2 + - + +
362G GLY 4.1 17.7 - - - +
363G ASN* 4.0 6.0 + - - +
365G LYS* 5.4 7.2 - - - +
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Residues in contact with TYR 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G ARG 4.1 0.2 - - - +
275G VAL 3.7 20.7 - - - +
276G THR* 3.8 36.7 - - + +
278G GLN* 3.1 20.7 + - - +
312G TYR 3.1 0.8 + - - +
313G HIS* 1.3 90.9 - + - +
315G VAL* 1.3 67.0 + - + +
317G GLU* 4.4 0.4 - - - -
358G VAL* 3.4 23.1 - - + +
359G MET* 4.5 6.3 + - - +
361G TYR* 4.1 1.1 + - + -
362G GLY* 3.1 38.2 - - - -
423G HIS 4.6 2.8 + - - -
426G VAL* 3.8 8.1 - - - +
427G GLY* 3.3 30.3 + - - -
430G ALA* 3.8 21.1 - - + -
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Residues in contact with VAL 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G VAL 4.7 3.4 - - - +
278G GLN* 2.8 9.6 - - - +
284G SER* 4.6 4.0 - - - -
288G PHE* 4.0 43.1 - - + -
289G TYR* 2.3 50.2 + - + +
292G MET* 4.8 3.8 - - - -
309G PRO* 4.5 9.0 - - + +
312G TYR* 2.8 27.3 + - + +
314G TYR* 1.3 89.6 - - + +
316G SER* 1.3 55.7 + - - +
359G MET* 4.7 10.3 - - + -
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Residues in contact with SER 316 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G PRO* 3.3 35.0 + - - -
310G TYR* 3.8 32.6 - - - -
312G TYR 3.4 5.0 + - - -
313G HIS* 3.4 9.3 + - - -
315G VAL* 1.3 81.0 - - - +
317G GLU* 1.3 62.7 + - - +
318G GLY 3.2 7.0 - - - +
319G GLU 5.0 2.0 - - - -
320G ILE* 4.5 7.4 - - - -
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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
------------------------------------------------------------
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