Contacts of the helix formed by residues 305 - 317 (chain A) in PDB entry 2FYT
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 GLU 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A GLY* 4.6 12.5 - - - +
303A GLN 4.1 0.2 + - - -
304A SER* 1.3 69.1 + - - +
306A ILE* 1.3 65.3 + - - +
307A LEU 3.0 3.3 + - - -
308A TYR* 3.1 53.0 + - + +
309A GLN* 4.0 2.8 + - - +
327A LYS* 3.3 18.9 + - - -
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Residues in contact with ILE 306 (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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241A TYR 3.4 15.3 - - - +
242A GLY* 4.2 14.2 - - - +
243A HIS 5.0 3.8 - - - +
244A TYR* 5.4 3.6 - - - -
247A HIS* 3.5 27.4 - - + +
282A GLY* 3.7 34.9 - - - +
283A THR* 4.1 10.8 - - + +
302A ASP* 3.7 16.8 - - - +
304A SER* 3.1 14.2 + - - +
305A GLU* 1.3 78.5 - - - +
307A LEU* 1.3 65.3 + - - +
309A GLN* 3.0 25.0 + - + +
310A ALA 3.0 17.0 + - - -
549A SAH 3.9 2.2 - - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A CYS* 3.7 19.5 - - - -
282A GLY 4.5 0.9 - - - -
300A GLY 3.9 5.2 - - - +
302A ASP* 3.6 19.3 - - + +
304A SER 3.1 13.4 + - - +
305A GLU 3.0 0.8 - - - -
306A ILE* 1.3 84.2 - - - +
308A TYR* 1.3 56.6 + - + +
310A ALA* 3.1 6.7 + - - +
311A MET* 3.0 38.9 + - - +
325A LEU* 3.9 21.1 - - + +
326A ILE 3.3 22.4 - - - +
327A LYS* 3.8 38.4 - - + +
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Residues in contact with TYR 308 (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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305A GLU* 3.1 51.1 + - + +
307A LEU* 1.3 75.1 - - + +
309A GLN* 1.3 66.5 + - - +
311A MET* 3.4 25.8 + - - +
312A ASP* 3.3 22.6 + - - +
327A LYS* 3.5 37.3 + - + +
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Residues in contact with GLN 309 (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* 5.7 0.4 - - + -
305A GLU 5.3 1.1 - - - +
306A ILE* 3.0 30.3 + - + +
308A TYR* 1.3 75.8 - - + +
310A ALA* 1.3 54.5 + - - +
312A ASP* 3.1 15.1 + - - +
313A ILE* 2.7 56.1 + - + +
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Residues in contact with ALA 310 (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 CYS* 4.7 1.3 - - - -
282A GLY 3.3 24.0 + - - +
283A THR 3.6 20.2 - - - +
284A GLY* 4.1 1.6 - - - +
306A ILE 3.0 6.6 + - - +
307A LEU* 3.1 12.3 + - - +
309A GLN* 1.3 75.8 - - - +
311A MET* 1.3 57.5 + - - +
313A ILE* 4.1 0.8 - - - +
314A ILE* 2.8 36.4 + - - +
325A LEU* 3.6 22.7 - - + -
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Residues in contact with MET 311 (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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307A LEU* 3.0 20.8 + - - +
308A TYR* 3.4 33.0 - - - +
310A ALA* 1.3 78.0 - - - +
312A ASP* 1.3 61.4 + - - +
314A ILE* 3.5 3.8 + - - +
315A ARG* 3.2 27.8 + - - +
325A LEU* 3.2 30.1 - - + +
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Residues in contact with ASP 312 (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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308A TYR 3.3 9.1 + - - +
309A GLN* 3.1 20.0 + - - +
311A MET* 1.3 76.7 - - - +
313A ILE* 1.3 61.3 + - - +
315A ARG* 3.3 12.0 + - - +
316A LEU* 2.9 31.9 + - + +
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Residues in contact with ILE 313 (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* 3.4 41.3 - - + +
288A MET* 3.5 31.0 - - + -
309A GLN* 2.7 41.0 + - + +
310A ALA 3.6 3.6 - - - +
312A ASP* 1.3 73.2 - - + +
314A ILE* 1.3 63.7 + - + +
316A LEU* 3.3 12.1 + - + +
317A ASN* 2.8 35.5 + - - +
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Residues in contact with ILE 314 (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 4.1 3.4 - - - +
284A GLY* 4.0 23.1 - - - +
288A MET* 3.7 26.2 - - + -
310A ALA 2.8 26.2 + - - +
311A MET 3.9 4.9 - - - +
313A ILE* 1.3 74.5 - - - +
315A ARG* 1.3 61.7 + - - +
317A ASN* 3.4 2.4 + - - -
318A LYS 3.2 4.0 + - - -
319A LEU* 3.1 33.0 + - - +
320A GLU* 3.6 29.8 - - + +
323A ILE* 3.7 41.3 - - + +
325A LEU* 4.0 12.3 - - + -
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Residues in contact with ARG 315 (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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311A MET 3.2 17.2 + - - +
312A ASP* 3.7 14.6 - - - +
313A ILE 3.2 0.2 - - - -
314A ILE* 1.3 73.3 - - + +
316A LEU* 1.3 63.0 + - - +
318A LYS* 2.9 23.6 + - - +
320A GLU* 3.6 48.5 + - + +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASP* 2.9 16.9 + - + +
313A ILE* 3.4 13.9 - - + +
315A ARG* 1.3 78.4 - - - +
317A ASN* 1.3 62.6 + - - +
318A LYS* 3.3 12.4 + - - +
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Residues in contact with ASN 317 (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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288A MET* 3.5 19.4 - - - +
292A LYS* 5.5 4.3 + - - -
313A ILE* 2.8 33.5 + - - +
314A ILE 3.9 1.6 - - - +
315A ARG 3.1 0.6 - - - -
316A LEU* 1.3 80.9 - - - +
318A LYS* 1.3 71.6 + - - +
319A LEU* 3.3 29.6 + - + +
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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