Contacts of the helix formed by residues 291 - 304 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281J LEU 2.6 28.9 + - - -
282J PHE* 2.9 10.1 + - - -
283J SER 3.4 17.7 - - - -
284J GLY* 3.5 9.2 - - - +
286J LYS* 4.0 2.9 - - - -
290J LEU* 1.3 75.9 - - - +
292J GLU* 1.3 62.5 + - - +
293J GLN* 3.2 6.4 + - - -
294J ALA* 3.1 22.2 + - - +
295J LEU* 3.5 13.7 + - - +
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Residues in contact with GLU 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286J LYS* 3.8 36.7 + - + +
291J SER* 1.3 74.0 - - - +
293J GLN* 1.3 66.3 + - + +
295J LEU* 3.2 12.1 + - + +
296J TYR* 3.1 57.3 + - + +
385J LYS* 5.0 5.4 + - - +
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Residues in contact with GLN 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J ILE* 3.7 20.8 + - - +
274J LEU* 5.1 2.3 - - - +
281J LEU* 3.0 44.9 - - - +
282J PHE* 4.8 5.2 - - + -
291J SER* 3.1 11.8 - - - +
292J GLU* 1.3 85.4 - - + +
294J ALA* 1.3 60.9 + - - +
296J TYR* 3.4 5.5 + - - -
297J TYR* 3.1 19.2 + - - +
382J ILE* 3.5 31.3 - - + +
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Residues in contact with ALA 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282J PHE* 3.7 37.4 - - + +
290J LEU* 3.7 22.4 - - + -
291J SER* 3.1 18.6 + - - +
292J GLU 3.2 0.2 - - - -
293J GLN* 1.3 77.0 - - - +
295J LEU* 1.3 57.8 + - - +
297J TYR* 3.1 10.5 - - - +
298J ILE* 2.9 32.0 + - - +
356J ILE* 5.0 2.2 - - + +
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Residues in contact with LEU 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286J LYS* 4.0 29.6 - - + -
287J TYR* 4.9 7.0 - - + +
290J LEU* 3.8 26.5 - - + -
291J SER 3.6 9.4 - - - +
292J GLU* 3.2 11.1 + - + +
294J ALA* 1.3 77.8 - - - +
296J TYR* 1.3 61.4 + - + +
298J ILE* 3.2 6.7 + - + +
299J GLY 2.8 23.4 + - - -
334J TYR* 4.0 29.4 - - + +
387J HIS* 4.6 15.5 - - + +
388J PRO* 3.2 25.0 - - + +
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Residues in contact with TYR 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292J GLU* 3.1 43.9 + - + +
293J GLN* 3.8 8.3 - - - +
294J ALA 3.3 0.2 - - - -
295J LEU* 1.3 76.1 - - + +
297J TYR* 1.3 66.6 + - - +
299J GLY* 3.3 0.9 + - - -
300J GLY 3.0 18.4 + - - -
381J GLY* 3.1 29.2 - - - +
382J ILE* 3.7 12.1 - - + -
385J LYS* 3.5 61.2 + - + +
386J ILE 3.4 19.2 - - - +
387J HIS* 4.1 22.9 - + + -
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Residues in contact with TYR 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J VAL* 4.7 5.4 - - + +
126J PHE* 4.8 0.5 - - - -
272J MET* 3.6 30.9 - - + +
273J SER 6.4 0.4 - - - -
274J LEU* 3.8 26.5 - - + -
282J PHE* 3.6 24.5 - + + -
293J GLN 3.1 13.1 + - - +
294J ALA 3.1 11.6 + - - +
296J TYR* 1.3 76.9 - - - +
298J ILE* 1.3 62.2 + - - +
300J GLY 3.1 10.6 + - - -
301J VAL* 3.1 23.1 + - + +
356J ILE* 3.8 21.5 - - + -
374J LEU 4.2 1.6 - - - -
375J LEU* 3.3 35.6 - - + +
378J GLY* 3.5 41.1 - - - -
379J LEU* 4.8 0.2 - - + -
382J ILE* 4.0 4.4 - - + +
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Residues in contact with ILE 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J LEU* 4.4 8.7 - - + -
294J ALA 2.9 19.0 + - - +
295J LEU* 3.3 12.6 - - + +
297J TYR* 1.3 74.7 - - - +
299J GLY* 1.3 67.1 + - - +
301J VAL* 3.0 9.3 + - - +
302J ILE* 2.9 38.1 + - + +
334J TYR* 4.1 23.8 - - + -
343J ILE* 4.0 15.9 - - + -
345J ILE* 4.0 26.5 - - + -
356J ILE* 4.0 22.2 - - + -
388J PRO* 3.8 14.1 - - + -
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Residues in contact with GLY 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295J LEU 2.8 12.2 + - - -
296J TYR 3.3 0.6 + - - -
298J ILE* 1.3 75.5 - - - +
300J GLY* 1.3 57.1 + - - +
302J ILE* 3.3 5.1 + - - +
303J LYS* 2.9 30.1 + - - +
386J ILE* 3.6 31.5 - - - +
388J PRO* 3.9 16.2 - - - -
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Residues in contact with GLY 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296J TYR 3.0 10.5 + - - -
297J TYR 3.1 2.6 + - - -
299J GLY* 1.3 75.7 - - - +
301J VAL* 1.3 55.0 + - - +
303J LYS* 3.2 1.7 + - - -
304J HIS* 3.0 37.0 + - - +
377J ALA 3.2 25.1 - - - -
381J GLY* 3.7 13.1 - - - -
386J ILE* 4.4 7.4 - - - -
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Residues in contact with VAL 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297J TYR* 3.1 35.8 + - + +
298J ILE* 3.0 9.7 + - - +
300J GLY* 1.3 74.6 - - - +
302J ILE* 1.3 57.3 + - - +
304J HIS 3.6 0.5 - - - -
305J ALA* 2.8 29.8 + - - +
308J ILE* 4.1 17.5 - - + -
343J ILE* 4.3 17.9 - - + -
356J ILE* 5.2 1.1 - - + -
358J VAL* 4.4 18.6 - - + -
360J PHE* 4.5 8.1 - - + -
374J LEU* 4.2 27.6 - - + +
377J ALA* 4.2 0.9 - - + -
378J GLY 4.5 1.1 - - - +
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Residues in contact with ILE 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298J ILE* 2.9 38.5 + - + +
299J GLY* 3.7 4.9 - - - +
301J VAL* 1.3 77.8 - - - +
303J LYS* 1.3 63.6 + - - +
304J HIS 3.5 0.3 + - - -
305J ALA* 3.6 15.0 + - - +
332J LEU* 3.6 55.1 - - + +
333J ALA* 4.1 11.9 - - - +
334J TYR* 4.7 0.9 - - + -
343J ILE* 4.2 10.1 - - + -
388J PRO* 4.6 17.3 - - + +
408J PRO* 4.9 6.7 - - + +
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Residues in contact with LYS 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299J GLY 2.9 17.0 + - - +
300J GLY* 3.2 6.0 + - - +
302J ILE* 1.3 79.3 - - - +
304J HIS* 1.3 79.6 + - + +
305J ALA 3.7 0.5 + - - -
306J LYS 5.2 0.5 + - - -
380J ASP* 4.4 6.7 + - - -
384J ASN* 5.6 4.0 + - - +
386J ILE* 3.6 32.8 - - + +
424J ASP* 4.1 3.6 - - - +
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Residues in contact with HIS 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300J GLY* 3.0 23.8 + - - +
301J VAL 3.6 2.0 - - - -
303J LYS* 1.3 102.5 - - + +
305J ALA* 1.3 64.6 + - - +
306J LYS 3.4 2.7 - - - -
307J ALA* 3.1 5.7 + - - +
308J ILE* 2.9 21.7 + - - +
377J ALA* 4.0 13.5 - - + -
380J ASP* 2.9 29.2 + - - -
386J ILE* 5.1 0.2 - - - +
424J ASP* 2.7 39.5 + - - +
427J PHE* 3.6 42.4 - + + +
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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