Contacts of the helix formed by residues 243 - 252 (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 HIS 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A SER* 3.3 21.7 + - - -
240A SER* 3.2 12.8 + - - +
242A GLY* 1.3 82.0 - - - +
244A TYR* 1.3 68.9 + + + +
245A GLY* 3.2 6.4 + - - +
246A ILE* 3.2 20.1 - - + +
247A HIS* 3.3 7.4 + - - -
306A ILE* 5.2 1.1 - - - -
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Residues in contact with TYR 244 (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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242A GLY 4.1 1.2 + - - -
243A HIS* 1.3 75.9 - + + +
245A GLY* 1.3 63.9 + - - +
247A HIS* 3.2 8.6 + - - +
248A GLU* 2.7 66.5 + - + +
306A ILE* 5.4 5.4 - - - -
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Residues in contact with GLY 245 (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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243A HIS* 3.1 5.5 - - - +
244A TYR* 1.3 96.5 - - - +
246A ILE* 1.3 56.5 + - - +
248A GLU* 3.3 4.0 + - - +
249A GLU* 2.8 30.9 + - - +
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Residues in contact with ILE 246 (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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240A SER* 3.5 25.4 - - - +
241A TYR* 3.4 40.6 - - + +
243A HIS* 3.2 18.4 - - + +
245A GLY* 1.3 73.8 - - - +
247A HIS* 1.3 76.0 + - + +
249A GLU* 3.4 16.7 + - - +
250A MET* 3.0 35.5 + - + +
496A HIS* 6.3 1.8 - - + -
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Residues in contact with HIS 247 (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* 2.7 37.7 - - + -
243A HIS 3.3 17.0 + - - -
244A TYR* 3.2 7.9 + - - +
246A ILE* 1.3 79.6 - - + +
248A GLU* 1.3 67.0 + - - +
250A MET* 3.2 25.2 + - + +
251A LEU* 2.8 34.4 + - + +
282A GLY* 3.7 18.9 - - - -
283A THR* 4.1 22.0 - - + -
306A ILE* 3.5 19.5 - - + +
549A SAH 3.4 22.1 + - + +
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Residues in contact with GLU 248 (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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244A TYR* 2.7 51.5 + - + +
245A GLY* 3.3 5.4 + - - +
247A HIS* 1.3 73.7 - - - +
249A GLU* 1.3 56.1 + - - +
251A LEU* 3.7 7.0 - - - +
252A LYS* 2.8 68.5 + - + +
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Residues in contact with GLU 249 (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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245A GLY 2.8 17.0 + - - +
246A ILE* 3.8 17.3 - - - +
248A GLU* 1.3 77.1 - - - +
250A MET* 1.3 61.3 + - - +
252A LYS* 3.5 7.5 + - - +
253A ASP* 3.1 20.3 + - - +
350A TYR* 5.2 4.7 + - - -
496A HIS* 3.5 45.6 - - + +
498A LYS* 5.3 6.1 - - - -
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Residues in contact with MET 250 (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* 4.7 6.7 - - - -
246A ILE* 3.0 20.2 + - + +
247A HIS* 3.2 42.1 + - + +
249A GLU* 1.3 75.8 - - - +
251A LEU* 1.3 58.0 + - + +
253A ASP* 3.0 19.8 + - - +
256A ARG* 3.0 30.0 + - - +
257A THR* 3.0 3.5 + - - -
346A GLU* 3.8 14.6 - - - +
496A HIS* 3.9 27.1 - - + +
549A SAH 3.5 43.1 - - + +
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Residues in contact with LEU 251 (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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247A HIS* 2.8 26.4 + - + +
248A GLU* 3.9 5.2 - - - +
250A MET* 1.3 78.3 - - - +
252A LYS* 1.3 61.4 + - + +
253A ASP 3.4 2.8 + - - +
254A LYS* 4.6 4.5 + - - +
256A ARG* 3.9 9.4 - - - +
257A THR* 3.7 18.5 + - + +
283A THR* 3.9 25.6 - - + +
285A ILE* 3.8 42.4 - - + -
549A SAH 4.5 2.5 - - - +
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Residues in contact with LYS 252 (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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248A GLU* 2.8 52.9 + - + +
249A GLU* 3.7 7.2 - - - +
251A LEU* 1.3 75.0 - - - +
253A ASP* 1.3 57.9 + - - +
254A LYS* 3.1 21.1 + - - +
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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