Contacts of the helix formed by residues 291 - 304 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B LEU 2.6 29.3 + - - -
282B PHE* 2.9 10.2 + - - -
283B SER 3.4 17.7 - - - -
284B GLY* 3.5 9.4 - - - +
286B LYS* 4.0 2.5 - - - -
290B LEU* 1.3 77.1 - - - +
292B GLU* 1.3 64.0 + - - +
293B GLN* 3.2 6.0 + - - +
294B ALA* 3.1 22.9 + - - +
295B LEU* 3.5 12.8 + - - +
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B LYS* 3.8 37.6 + - - +
291B SER* 1.3 74.0 - - - +
293B GLN* 1.3 67.5 + - + +
295B LEU* 3.2 11.8 + - + +
296B TYR* 3.1 55.5 + - + +
385B LYS* 5.0 6.2 + - - +
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Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ILE* 3.7 20.2 + - - +
274B LEU* 5.1 2.1 - - - +
281B LEU* 3.0 45.8 - - - +
282B PHE* 4.8 5.4 - - + -
291B SER* 3.3 11.0 - - - +
292B GLU* 1.3 85.2 - - + +
294B ALA* 1.3 60.5 + - - +
296B TYR* 3.4 5.5 + - - -
297B TYR* 3.1 18.9 + - - +
382B ILE* 3.5 30.7 - - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.7 38.1 - - + +
290B LEU* 3.7 22.7 - - + -
291B SER* 3.1 18.7 + - - +
293B GLN* 1.3 75.4 - - - +
295B LEU* 1.3 59.5 + - - +
297B TYR* 3.1 10.0 - - - +
298B ILE* 2.9 31.7 + - - +
356B ILE* 5.0 2.2 - - + -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B LYS* 4.0 29.8 - - + -
287B TYR* 4.9 6.3 - - + +
290B LEU* 3.8 27.4 - - + -
291B SER 3.6 9.4 - - - +
292B GLU* 3.2 12.5 + - + +
294B ALA* 1.3 77.2 - - - +
296B TYR* 1.3 59.3 + - + +
298B ILE* 3.2 6.7 + - + +
299B GLY 2.8 23.0 + - - -
334B TYR* 4.0 28.5 - - + +
387B HIS* 4.6 16.4 - - + +
388B PRO* 3.2 26.0 - - + +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B GLU* 3.1 45.3 + - + +
293B GLN* 3.8 9.4 - - - +
295B LEU* 1.3 75.1 - - + +
297B TYR* 1.3 66.6 + - - +
299B GLY* 3.3 1.0 + - - -
300B GLY 3.0 18.2 + - - -
381B GLY* 3.1 29.2 - - - +
382B ILE* 3.7 12.6 - - + -
385B LYS* 3.5 61.0 + - + +
386B ILE 3.4 19.1 - - - -
387B HIS* 4.2 21.7 - + + -
388B PRO* 4.6 0.2 - - + -
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 4.7 5.0 - - - +
126B PHE* 4.8 0.2 - - - -
272B MET* 3.6 31.2 - - + +
273B SER 6.4 0.2 - - - -
274B LEU* 3.8 26.5 - - + -
282B PHE* 3.6 23.1 - + + -
293B GLN 3.1 12.6 + - - +
294B ALA 3.1 12.3 + - - +
296B TYR* 1.3 75.8 - - - +
298B ILE* 1.3 62.1 + - - +
300B GLY 3.1 10.4 + - - -
301B VAL* 3.1 23.2 + - + +
356B ILE* 3.8 20.0 - - + -
374B LEU 4.2 1.3 - - - -
375B LEU* 3.3 36.3 + - + +
378B GLY* 3.5 41.9 - - - -
379B LEU 4.5 0.2 - - - -
382B ILE* 4.0 4.2 - - + +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LEU* 4.4 9.4 - - + -
294B ALA 2.9 20.0 + - - +
295B LEU* 3.3 12.6 - - + +
297B TYR* 1.3 73.4 - - - +
299B GLY* 1.3 65.9 + - - +
301B VAL* 3.0 10.1 + - - +
302B ILE* 2.9 38.0 + - + +
334B TYR* 4.1 23.6 - - + -
343B ILE* 4.0 16.6 - - + -
345B ILE* 4.0 27.4 - - + -
356B ILE* 4.0 21.8 - - + -
388B PRO* 3.8 14.8 - - + -
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU 2.8 12.2 + - - -
296B TYR 3.3 0.4 + - - -
298B ILE* 1.3 75.6 - - - +
300B GLY* 1.3 57.3 + - - +
302B ILE* 3.3 5.4 + - - +
303B LYS* 2.9 30.0 + - - +
386B ILE* 3.6 31.7 - - - +
388B PRO* 3.9 15.7 - - - -
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR 3.0 10.5 + - - -
297B TYR 3.1 3.1 + - - -
299B GLY* 1.3 76.6 - - - +
301B VAL* 1.3 54.8 + - - +
303B LYS* 3.2 1.8 + - - -
304B HIS* 3.0 36.2 + - - +
377B ALA 3.2 25.6 - - - -
381B GLY* 3.7 13.5 - - - -
386B ILE* 4.4 7.0 - - - -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR* 3.1 35.5 + - + +
298B ILE* 3.0 10.0 + - - +
300B GLY* 1.3 75.6 - - - +
302B ILE* 1.3 59.3 + - - +
304B HIS 3.6 0.3 - - - -
305B ALA* 2.8 30.0 + - - +
308B ILE* 3.9 17.4 - - + +
343B ILE* 4.3 17.9 - - + -
356B ILE* 5.2 1.1 - - + -
358B VAL* 4.4 17.7 - - + -
360B PHE* 4.5 8.7 - - + -
374B LEU* 4.2 28.5 - - + +
377B ALA* 4.2 0.9 - - + -
378B GLY 4.5 0.9 - - - +
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ILE* 2.9 39.8 + - + +
299B GLY* 3.7 5.6 - - - +
301B VAL* 1.3 77.1 - - - +
303B LYS* 1.3 64.2 + - - +
305B ALA* 3.6 14.2 + - - +
332B LEU* 3.6 54.4 - - + +
333B ALA* 4.1 11.7 - - - +
334B TYR* 4.7 1.1 - - + -
343B ILE* 4.2 11.0 - - + -
388B PRO* 4.6 16.2 - - + +
408B PRO* 4.9 6.7 - - + -
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B GLY 2.9 16.8 + - - +
300B GLY* 3.2 6.3 + - - +
302B ILE* 1.3 79.9 - - - +
304B HIS* 1.3 78.2 + - + +
305B ALA 3.7 0.3 + - - -
306B LYS 5.2 0.5 + - - -
380B ASP* 4.4 6.7 + - - -
384B ASN* 5.6 4.0 + - - +
386B ILE* 3.6 34.8 - - + +
424B ASP* 4.1 3.1 - - - +
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLY* 3.0 24.0 + - - +
301B VAL 3.6 2.0 - - - -
303B LYS* 1.3 101.3 + - + +
305B ALA* 1.3 63.7 + - - +
306B LYS 3.4 2.0 - - - -
307B ALA* 3.1 6.0 + - - +
308B ILE* 2.9 22.2 + - - +
377B ALA* 4.0 13.2 - - + -
380B ASP* 2.9 30.9 + - - -
386B ILE* 5.1 0.2 - - - +
424B ASP* 2.7 40.3 + - - +
427B PHE* 3.6 43.5 - + + +
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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