Contacts of the helix formed by residues 291 - 304 (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 SER 291 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281G LEU 2.6 29.5 + - - -
282G PHE* 2.9 10.5 + - - -
283G SER 3.4 17.7 - - - -
284G GLY* 3.5 8.5 - - - +
286G LYS* 4.0 2.9 - - - -
290G LEU* 1.3 77.0 - - - +
292G GLU* 1.3 62.5 + - - +
293G GLN* 3.2 5.6 + - - +
294G ALA* 3.1 21.7 + - - +
295G LEU* 3.5 13.9 + - - +
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Residues in contact with GLU 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G LYS* 3.8 36.3 + - + +
291G SER* 1.3 74.4 - - - +
293G GLN* 1.3 67.5 + - + +
295G LEU* 3.2 12.4 + - + +
296G TYR* 3.1 56.5 + - + -
385G LYS* 5.0 5.7 + - - +
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Residues in contact with GLN 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ILE* 3.7 20.2 + - - +
274G LEU* 5.1 1.9 - - - +
281G LEU* 3.0 45.8 - - - +
282G PHE* 4.8 4.3 - - + -
291G SER* 3.3 12.1 - - - +
292G GLU* 1.3 85.8 - - + +
294G ALA* 1.3 60.3 + - - +
296G TYR* 3.4 5.1 + - - -
297G TYR* 3.1 19.8 + - - +
382G ILE* 3.5 31.3 - - + +
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Residues in contact with ALA 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G PHE* 3.7 37.4 - - + +
290G LEU* 3.7 22.2 - - + -
291G SER* 3.1 18.5 + - - +
293G GLN* 1.3 77.1 - - - +
295G LEU* 1.3 57.4 + - - +
297G TYR* 3.1 10.4 - - - +
298G ILE* 2.9 32.1 + - - +
356G ILE* 5.0 2.5 - - + -
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Residues in contact with LEU 295 (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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286G LYS* 4.0 29.6 - - + -
287G TYR* 4.9 6.1 - - + +
290G LEU* 3.8 27.8 - - + -
291G SER 3.6 9.4 - - - +
292G GLU* 3.2 12.0 + - + +
294G ALA* 1.3 77.3 - - - +
296G TYR* 1.3 58.8 + - + +
298G ILE* 3.2 6.6 + - + +
299G GLY 2.8 23.9 + - - -
334G TYR* 4.0 29.6 - - + +
387G HIS* 4.6 16.6 - - + +
388G PRO* 3.2 25.1 - - + +
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Residues in contact with TYR 296 (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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292G GLU* 3.1 43.8 + - + +
293G GLN* 3.4 8.5 + - - +
295G LEU* 1.3 75.7 - - + +
297G TYR* 1.3 64.1 - - - +
299G GLY* 3.3 1.0 + - - -
300G GLY 3.0 18.7 + - - -
381G GLY* 3.1 29.2 - - - +
382G ILE* 3.7 12.3 - - + -
385G LYS* 3.5 61.2 - - + +
386G ILE 3.4 19.7 - - - +
387G HIS* 4.2 22.2 - + + -
388G PRO* 4.6 0.2 - - + -
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Residues in contact with TYR 297 (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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124G VAL* 4.7 5.0 - - - +
126G PHE* 4.8 0.2 - - - -
272G MET* 3.6 30.5 - - + +
273G SER 6.1 0.2 - - - -
274G LEU* 3.8 27.1 - - + -
282G PHE* 3.6 22.0 - + + -
293G GLN 3.1 13.2 + - - +
294G ALA 3.1 12.1 + - - +
296G TYR* 1.3 76.2 - - - +
298G ILE* 1.3 62.3 + - - +
300G GLY 3.1 10.2 + - - -
301G VAL* 3.1 24.0 + - + +
356G ILE* 3.8 20.4 - - + -
374G LEU 4.2 1.8 - - - -
375G LEU* 3.3 35.3 + - + +
378G GLY* 3.5 40.9 - - - -
379G LEU 4.5 0.2 - - - -
382G ILE* 4.0 4.2 - - + +
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Residues in contact with ILE 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G LEU* 4.4 9.2 - - + -
294G ALA 2.9 19.0 + - - +
295G LEU* 3.3 13.2 - - + +
297G TYR* 1.3 75.3 - - - +
299G GLY* 1.3 67.3 + - - +
301G VAL* 3.0 10.0 + - - +
302G ILE* 2.9 38.0 + - + +
334G TYR* 4.1 24.0 - - + -
343G ILE* 4.0 15.3 - - + -
345G ILE* 4.0 27.4 - - + -
356G ILE* 4.0 21.8 - - + -
388G PRO* 3.8 14.8 - - + -
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Residues in contact with GLY 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G LEU 2.8 12.2 + - - -
296G TYR 3.3 0.4 + - - -
298G ILE* 1.3 76.0 - - - +
300G GLY* 1.3 57.1 + - - +
302G ILE* 3.3 5.9 + - - +
303G LYS* 2.9 30.1 + - - +
386G ILE* 3.6 31.9 - - - +
388G PRO* 3.9 15.3 - - - -
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Residues in contact with GLY 300 (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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296G TYR 3.0 10.5 + - - -
297G TYR 3.1 2.2 + - - -
299G GLY* 1.3 75.9 - - - +
301G VAL* 1.3 56.6 + - - +
303G LYS* 3.2 1.6 + - - +
304G HIS* 3.0 37.0 + - - +
377G ALA 3.2 24.9 - - - -
381G GLY* 3.7 12.7 - - - -
386G ILE* 4.4 7.2 - - - -
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Residues in contact with VAL 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297G TYR* 3.1 35.1 + - + +
298G ILE* 3.0 10.4 + - - +
300G GLY* 1.3 74.8 - - - +
302G ILE* 1.3 58.4 + - - +
304G HIS 3.6 0.3 - - - -
305G ALA* 2.8 29.8 + - - +
308G ILE* 3.9 17.7 - - + +
343G ILE* 4.3 17.9 - - + -
356G ILE* 5.2 0.9 - - + -
358G VAL* 4.4 18.4 - - + -
360G PHE* 4.5 8.3 - - + -
374G LEU* 4.2 28.3 - - + +
377G ALA* 4.2 0.4 - - + -
378G GLY 4.5 1.6 - - - +
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Residues in contact with ILE 302 (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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298G ILE* 2.9 39.2 + - + +
299G GLY* 3.7 5.6 - - - +
301G VAL* 1.3 77.0 - - - +
303G LYS* 1.3 63.1 + - - +
304G HIS 3.5 0.2 + - - -
305G ALA* 3.6 14.4 + - - +
332G LEU* 3.6 53.6 - - + +
333G ALA* 4.1 11.4 - - - -
334G TYR* 4.7 1.1 - - + -
343G ILE* 4.2 10.1 - - + -
388G PRO* 4.6 16.2 - - + +
408G PRO* 4.9 7.6 - - + +
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Residues in contact with LYS 303 (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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299G GLY 2.9 17.4 + - - +
300G GLY* 3.6 5.6 - - - +
302G ILE* 1.3 79.4 - - - +
304G HIS* 1.3 77.8 + - + +
305G ALA 3.7 0.7 + - - -
306G LYS 5.2 0.7 + - - -
380G ASP* 4.4 6.7 + - - -
384G ASN* 5.6 4.0 + - - +
386G ILE* 3.6 33.2 - - + +
424G ASP* 4.1 3.9 - - - +
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Residues in contact with HIS 304 (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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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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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