Contacts of the helix formed by residues 253 - 265 (chain A) in PDB entry 2FY5
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 ASP 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LEU 3.1 5.4 + - - +
252A LYS* 1.3 80.2 - - + +
254A SER* 1.3 64.1 + - - +
255A THR* 2.4 41.5 + - - -
256A ASN* 3.1 24.8 + - - +
257A ARG* 3.2 25.6 + - - +
368A LYS* 3.0 34.2 + - + +
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Residues in contact with SER 254 (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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252A LYS 4.0 0.2 + - - -
253A ASP* 1.3 71.9 + - - +
255A THR* 1.3 66.1 + - - +
257A ARG* 3.3 33.0 + - - +
258A ASP* 3.2 30.8 + - - +
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Residues in contact with THR 255 (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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253A ASP* 2.4 25.5 + - - -
254A SER* 1.3 71.2 - - - +
256A ASN* 1.3 57.4 + - - -
258A ASP* 3.4 10.2 - - + +
259A SER* 3.3 21.5 + - - -
366A ARG* 3.2 51.3 + - + +
367A TRP* 4.3 1.8 - - - +
368A LYS* 3.4 33.5 + - + -
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Residues in contact with ASN 256 (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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250A LEU* 3.4 45.4 + - + +
253A ASP* 3.1 17.0 + - - +
254A SER 3.2 0.4 - - - -
255A THR* 1.3 72.5 - - - +
257A ARG* 1.3 68.1 + - - +
258A ASP 3.1 1.5 + - - -
259A SER* 3.3 1.0 + - - -
260A LEU* 2.9 29.0 + - - +
367A TRP* 3.1 29.4 - - + +
368A LYS 2.8 46.0 + - - -
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Residues in contact with ARG 257 (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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250A LEU 4.8 0.4 + - - -
251A VAL* 3.2 35.6 + - + +
252A LYS 3.8 15.6 + - - -
253A ASP 3.2 12.2 + - - +
254A SER* 3.5 30.6 + - - +
256A ASN* 1.3 77.5 - - - +
258A ASP* 1.3 56.1 + - - +
260A LEU* 3.2 10.9 + - - +
261A ASP* 2.8 36.3 + - - +
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Residues in contact with ASP 258 (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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254A SER* 3.2 17.7 + - - +
255A THR* 3.4 14.3 - - + +
257A ARG* 1.3 82.0 - - - +
259A SER* 1.3 58.4 + - - +
261A ASP* 3.2 9.3 + - - +
262A MET* 2.9 32.3 + - + +
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Residues in contact with SER 259 (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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255A THR 3.3 6.8 + - - -
256A ASN 3.3 1.6 + - - -
258A ASP* 1.3 74.6 - - - +
260A LEU* 1.3 66.2 + - - +
262A MET* 2.9 4.5 + - - +
263A ILE* 2.8 25.3 + - - +
365A LEU* 3.3 25.6 - - - +
366A ARG* 2.8 40.7 + - - +
367A TRP* 3.6 21.3 - - - -
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Residues in contact with LEU 260 (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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162A TYR* 5.3 2.0 - - - +
243A TRP* 4.6 6.3 - - + -
247A ARG* 4.2 21.3 - - + +
250A LEU* 4.5 17.5 - - + -
251A VAL* 4.1 26.2 - - + +
256A ASN 2.9 26.0 + - - +
257A ARG* 3.4 6.1 - - - +
259A SER* 1.3 75.9 - - - +
261A ASP* 1.3 58.4 + - - +
263A ILE* 3.1 6.1 + - - +
264A GLU* 2.8 43.7 + - + +
303A TRP* 3.4 37.0 - - + -
367A TRP* 3.9 12.3 - - + -
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Residues in contact with ASP 261 (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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257A ARG 2.8 17.6 + - - +
258A ASP* 3.3 12.4 - - - +
260A LEU* 1.3 71.9 - - - +
262A MET* 1.3 65.4 + - - +
264A GLU* 3.3 14.9 + - - +
265A ARG* 2.9 70.3 + - - +
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Residues in contact with MET 262 (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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183A PRO* 6.5 0.2 - - + -
185A HIS* 3.2 37.0 + - + +
187A ILE* 4.3 1.7 - - + +
196A VAL* 3.5 35.2 - - + -
258A ASP* 2.9 21.1 + - + +
259A SER 2.9 8.0 + - - +
261A ASP* 1.3 77.5 - - - +
263A ILE* 1.3 62.2 + - - +
265A ARG* 3.2 33.1 + - - +
266A CYS* 3.3 3.8 + - - +
363A ARG* 4.0 19.3 - - - +
365A LEU* 3.7 22.0 - - + -
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Residues in contact with ILE 263 (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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162A TYR* 4.1 7.7 - - + -
187A ILE* 4.2 14.1 - - + -
194A PHE* 4.8 5.4 - - + -
259A SER 2.8 13.9 + - - +
260A LEU* 3.5 5.8 - - - +
262A MET* 1.3 74.6 - - - +
264A GLU* 1.3 62.9 + - - +
265A ARG 3.3 0.7 + - - -
266A CYS* 3.3 19.9 - - - -
269A LEU* 4.7 11.0 - - + -
303A TRP* 3.5 74.3 - - + +
306A LYS* 4.2 3.6 - - + +
365A LEU* 3.6 16.4 - - + -
367A TRP* 3.8 21.1 - - + -
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Residues in contact with GLU 264 (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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161A SER 5.4 0.2 - - - -
162A TYR* 3.5 50.0 + - + +
164A LEU* 4.4 4.6 - - - +
247A ARG* 3.3 30.8 + - - -
260A LEU* 2.8 32.3 + - - +
261A ASP* 3.5 13.3 - - - +
263A ILE* 1.3 78.3 - - - +
265A ARG* 1.3 63.7 + - + +
266A CYS 3.7 0.3 + - - -
306A LYS* 3.9 13.0 + - - -
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Residues in contact with ARG 265 (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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181A PRO* 3.1 53.4 - - + +
182A GLU 5.0 2.2 + - - +
183A PRO 5.6 0.6 + - - -
185A HIS* 3.8 13.7 + - + -
261A ASP* 2.9 50.4 + - - +
262A MET* 3.2 25.5 + - - +
263A ILE 3.2 0.6 - - - -
264A GLU* 1.3 81.7 - - + +
266A CYS* 1.3 62.9 + - - +
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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