Contacts of the helix formed by residues 304 - 313 (chain G) in PDB entry 1F1H
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 HIS 304 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G GLY* 3.0 24.0 + - - +
301G VAL 3.6 2.0 - - - -
303G LYS* 1.3 102.1 + - + +
305G ALA* 1.3 65.0 + - - +
306G LYS 3.4 2.2 - - - -
307G ALA* 3.1 5.9 + - - +
308G ILE* 2.9 22.1 + - - +
377G ALA* 4.0 14.1 - - + -
380G ASP* 2.9 29.4 + - - -
386G ILE* 5.1 0.2 - - - +
424G ASP* 2.7 40.5 + - - +
427G PHE* 3.6 43.4 - + + +
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Residues in contact with ALA 305 (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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301G VAL 2.8 18.4 + - - +
302G ILE* 3.6 1.5 + - - +
303G LYS 3.4 2.8 + - - -
304G HIS* 1.3 74.9 - - - +
306G LYS* 1.3 59.7 + - - +
308G ILE* 2.8 11.4 + - - +
309G ASN* 2.8 34.3 + - - +
332G LEU* 3.6 42.6 - - + -
360G PHE* 4.6 11.2 - - + -
410G VAL* 5.1 0.7 - - + -
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Residues in contact with LYS 306 (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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303G LYS 5.2 0.8 + - - -
304G HIS 3.4 0.4 - - - -
305G ALA* 1.3 77.1 - - + +
307G ALA* 1.3 61.2 + - - +
309G ASN* 3.2 23.2 + - - +
332G LEU* 5.5 2.5 - - + -
409G GLN* 3.2 29.7 + - - +
410G VAL 4.0 7.5 + - - -
411G ALA* 3.9 15.7 - - + +
416G GLU* 3.1 30.9 + - + +
417G ALA* 3.5 16.1 - - - -
420G ALA* 3.5 18.2 - - + -
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Residues in contact with ALA 307 (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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304G HIS 3.1 9.8 + - - +
306G LYS* 1.3 75.5 - - - +
308G ILE* 1.3 65.9 + - - +
310G ALA* 3.1 19.9 + - - +
311G LEU* 3.8 9.3 - - - +
417G ALA 4.3 0.2 - - - -
420G ALA* 3.6 5.6 - - - +
421G LEU* 3.8 34.2 - - + +
424G ASP* 3.8 19.0 + - + +
427G PHE* 4.0 17.0 - - + -
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Residues in contact with ILE 308 (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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301G VAL* 3.9 21.5 - - + +
304G HIS 2.9 19.3 + - - +
305G ALA* 2.8 8.8 + - - +
307G ALA* 1.3 76.2 - - - +
309G ASN* 1.3 56.7 + - - +
311G LEU* 2.8 26.4 + - + +
312G ALA* 2.8 19.5 + - + +
360G PHE* 4.1 13.0 - - + -
370G CYS 4.9 1.3 - - - +
373G ALA* 4.1 20.6 - - + +
374G LEU* 3.5 36.3 - - + -
377G ALA* 3.6 28.3 - - + -
427G PHE* 4.4 6.7 - - + -
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Residues in contact with ASN 309 (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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305G ALA 2.8 11.5 + - - +
306G LYS* 3.2 18.0 - - - +
308G ILE* 1.3 76.5 - - - +
310G ALA* 1.3 58.4 - - - +
313G ASN* 2.7 58.3 + - - +
319G TYR* 3.7 17.3 - - - +
322G LEU* 4.7 1.2 - - - +
360G PHE* 3.4 21.2 - - - -
410G VAL* 3.4 14.3 - - - +
411G ALA* 2.7 33.0 + - + +
417G ALA* 3.8 4.0 - - + -
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Residues in contact with ALA 310 (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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306G LYS 3.7 0.2 + - - -
307G ALA 3.1 15.0 + - - +
309G ASN* 1.3 77.4 - - - +
311G LEU* 1.3 50.7 + - + +
313G ASN 4.7 1.6 - - - -
314G PRO* 3.7 9.9 - - - +
414G LEU* 5.0 1.7 - - - +
417G ALA* 3.5 33.8 - - - +
418G LEU* 4.1 12.8 - - + +
421G LEU* 3.8 23.6 - - + -
442G TYR* 2.6 30.0 + - - -
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Residues in contact with LEU 311 (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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307G ALA 3.8 15.9 - - - +
308G ILE* 2.8 7.2 + - - +
310G ALA* 1.3 81.1 - - + +
312G ALA* 1.3 58.0 + - - +
313G ASN 3.4 1.3 - - - -
314G PRO* 3.8 4.0 - - - +
365G ALA* 3.2 22.5 - - - +
366G ASN* 4.0 4.7 + - - +
369G LEU* 3.5 31.6 - - + +
370G CYS* 3.7 21.1 - - - +
373G ALA* 3.7 24.2 - - + -
421G LEU* 4.3 17.9 - - + -
428G LEU* 4.9 5.2 - - + -
434G PHE* 4.9 11.0 - - + -
442G TYR* 3.7 28.1 + - + -
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Residues in contact with ALA 312 (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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308G ILE* 2.8 19.4 + - + +
311G LEU* 1.3 72.7 - - - +
313G ASN* 1.3 68.9 + - - +
314G PRO* 3.4 3.6 - - - +
360G PHE* 4.1 5.4 - - + -
361G PRO* 3.4 31.2 - - + -
362G ASP* 3.0 28.6 + - - +
365G ALA* 3.5 7.9 - - - +
370G CYS* 3.5 19.1 - - - -
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Residues in contact with ASN 313 (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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309G ASN* 2.7 39.2 + - - +
312G ALA* 1.3 82.0 - - - +
314G PRO* 1.3 58.8 - - - +
315G THR 3.3 4.6 + - - -
318G SER* 3.6 17.0 - - - -
319G TYR* 2.8 38.5 + - + +
321G ARG* 4.1 0.3 + - - -
322G LEU* 3.3 19.4 - - + +
360G PHE* 2.7 36.8 + - - +
362G ASP* 3.3 11.1 - - - +
414G LEU* 4.0 1.6 - - - +
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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