Contacts of the helix formed by residues 281 - 292 (chain A) in PDB entry 2FY4
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A GLU* 3.1 10.2 + - - +
280A LEU* 1.3 76.2 - - - +
282A ASP* 1.3 67.0 + - - +
283A THR* 3.8 8.2 + - - -
284A HIS* 3.0 30.2 + - - -
285A ARG* 2.8 24.1 + - - +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A SER* 1.3 72.2 - - - +
283A THR* 1.3 61.5 + - - +
285A ARG* 2.8 31.9 + - - +
286A ALA* 3.0 24.3 + - - +
395A VAL* 3.8 27.1 - - + +
549A PHE* 3.7 20.7 - - + -
572A LEU* 5.4 4.2 - - - +
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A SER* 3.1 8.0 + - - -
282A ASP* 1.3 78.0 - - - +
284A HIS* 1.3 73.8 + - + +
286A ALA* 3.1 5.2 + - - +
287A LEU* 3.0 28.1 + - + +
393A PHE* 3.5 31.8 - - + +
394A ILE* 3.9 6.3 - - + +
395A VAL* 3.2 33.1 + - - +
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A VAL* 3.1 38.4 - - + +
279A GLU* 2.8 38.2 + - + +
280A LEU* 4.8 1.1 - - + -
281A SER* 3.0 17.2 + - - +
283A THR* 1.3 87.8 - - + +
285A ARG* 1.3 62.9 + - - +
287A LEU* 3.1 33.4 + - + +
288A GLN* 3.2 13.5 + - - +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.4 18.4 - - + +
102A PHE 2.6 30.5 + - - -
103A ALA* 3.3 4.9 + - - +
104A ARG* 3.3 39.6 - - - +
280A LEU* 3.6 28.6 + - + +
281A SER 2.8 19.7 + - - +
282A ASP* 2.8 32.8 + - - +
284A HIS* 1.3 73.1 - - - +
286A ALA* 1.3 58.9 + - - +
288A GLN* 3.6 3.1 + - - +
289A LEU* 3.1 32.1 + - - +
317A THR* 3.7 30.7 - - + +
318A CYS 4.7 5.7 + - - +
547A GLU 5.8 1.2 + - - -
549A PHE* 4.1 5.1 - - - -
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.7 25.5 - - + +
282A ASP 3.0 16.8 + - - +
283A THR 3.4 5.4 - - - +
284A HIS 3.1 0.2 - - - -
285A ARG* 1.3 77.7 - - - +
287A LEU* 1.3 59.8 + - - +
288A GLN 3.1 0.2 - - - -
289A LEU* 3.1 2.1 + - - +
290A LEU* 2.8 35.9 + - - +
393A PHE* 3.5 24.2 - - + -
549A PHE* 4.1 3.8 - - + -
551A CYS* 4.0 5.8 - - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A THR* 3.0 21.6 + - + +
284A HIS* 3.1 29.6 + - + +
286A ALA* 1.3 78.0 - - - +
288A GLN* 1.3 63.3 + - - +
290A LEU* 3.2 3.0 + - + -
291A HIS* 3.0 47.9 + - + +
293A GLY* 4.8 0.4 - - - -
391A LEU* 3.7 32.5 - - + +
393A PHE* 3.9 21.5 - - + +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 2.9 40.2 + - - +
274A ALA 4.5 2.6 + - - -
276A GLY* 4.1 18.1 - - - -
280A LEU* 5.3 1.9 - - - +
284A HIS 3.2 9.5 + - - +
285A ARG* 3.7 9.5 - - - +
286A ALA 3.1 0.2 - - - -
287A LEU* 1.3 80.0 - - - +
289A LEU* 1.3 58.1 + - + +
292A GLY* 2.7 40.0 + - - +
293A GLY* 4.5 0.7 - - - +
298A ASN* 3.6 14.7 - - - +
302A ARG* 3.2 10.1 + - - +
311A VAL* 4.4 3.4 - - - +
313A GLY* 4.8 1.2 - - - -
315A ASP* 4.4 2.7 + - - +
317A THR* 3.7 35.1 + - + +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 3.8 16.3 - - + +
100A VAL 4.3 3.8 - - - +
101A ILE* 4.0 15.9 - - + -
285A ARG 3.1 20.6 - - - +
286A ALA 3.1 7.5 + - - +
288A GLN* 1.3 77.7 - - + +
290A LEU* 1.3 63.1 + - - +
302A ARG* 4.8 2.3 + - - +
304A TYR* 5.2 0.2 + - - -
311A VAL* 3.7 27.8 - - + -
317A THR* 3.7 22.0 - - + -
318A CYS 4.3 9.6 - - - +
319A GLY* 3.7 8.1 - - - -
320A VAL 3.6 27.1 - - - +
321A VAL* 3.1 37.4 - - + +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 4.1 7.3 - - - +
94A VAL* 4.2 22.5 + - + -
97A SER 4.3 11.4 - - - +
99A ALA* 3.9 19.7 - - + +
286A ALA 2.8 23.6 + - - +
287A LEU* 3.2 4.7 + - - +
289A LEU* 1.3 80.9 - - - +
291A HIS* 1.3 63.2 + - + +
304A TYR* 3.6 17.3 + - - -
321A VAL* 5.0 2.4 - - - +
391A LEU* 3.7 25.1 - - + -
393A PHE* 4.5 16.8 - - + -
551A CYS* 3.9 31.2 - - - +
552A TYR* 4.3 12.6 - - - +
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Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 4.7 3.1 - - + -
94A VAL* 4.0 15.9 - - + -
287A LEU* 3.0 34.1 + - + +
290A LEU* 1.3 76.6 - - + +
292A GLY* 1.3 59.6 + - - +
293A GLY* 2.8 43.7 + - - -
294A GLY 3.5 8.1 + - - -
299A GLY* 3.6 10.7 - - - +
304A TYR* 3.7 15.1 + - - -
384A LEU* 4.4 16.6 - - + +
387A ILE* 4.6 1.6 - - + -
388A VAL* 3.6 41.9 + - + +
391A LEU* 3.8 29.3 - - + +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 3.4 0.2 + - - -
288A GLN* 2.7 37.1 + - - +
290A LEU 3.8 0.2 - - - -
291A HIS* 1.3 72.3 + - - +
293A GLY* 1.3 56.3 + - - +
294A GLY 3.3 0.7 - - - -
297A LYS* 3.3 4.7 - - - +
298A ASN* 3.0 30.8 + - - +
299A GLY* 3.9 9.9 - - - -
302A ARG* 3.9 14.7 - - - +
304A TYR* 4.5 0.6 + - - -
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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