Contacts of the helix formed by residues 239 - 252 (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 GLY 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ARG 3.6 9.9 - - - -
91A ALA* 3.9 12.0 - - - +
238A ASP* 1.3 90.8 + - - +
240A ARG* 1.3 60.3 + - - -
242A GLU* 3.0 18.6 + - - -
243A TRP* 2.9 25.1 + - - +
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Residues in contact with ARG 240 (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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88A ASN 3.4 15.3 - - - +
89A ARG* 3.0 30.2 + - - +
90A LEU 3.4 21.1 - - - +
92A LEU* 3.0 39.9 - - - +
163A ARG* 3.3 21.4 + - - +
165A PRO* 3.7 17.7 - - - +
166A GLY 3.6 0.7 - - - +
170A ASP* 2.7 30.1 + - - +
236A THR 3.9 9.3 + - - -
238A ASP 4.4 4.0 + - - -
239A GLY* 1.3 72.8 - - - +
241A SER* 1.3 57.0 - - - +
243A TRP* 3.7 16.4 - - - -
244A ALA* 3.0 29.6 + - - +
305A ASP* 2.8 27.7 + - - -
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Residues in contact with SER 241 (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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89A ARG* 3.3 22.8 + - - +
166A GLY 3.9 4.9 - - - -
167A HIS* 2.6 41.6 + - - +
239A GLY 3.4 0.4 - - - -
240A ARG* 1.3 76.8 - - - +
242A GLU* 1.3 73.5 + - - +
244A ALA* 3.5 3.6 + - - +
245A GLU* 3.2 22.0 + - - +
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Residues in contact with GLU 242 (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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89A ARG 4.7 1.6 - - - +
238A ASP* 3.5 31.2 - - - +
239A GLY* 3.0 25.0 - - - +
241A SER* 1.3 84.5 + - - +
243A TRP* 1.3 57.6 + - - +
245A GLU* 3.1 9.5 + - - +
246A ALA* 3.0 27.5 + - - +
376A HIS* 5.0 2.8 + - - -
383A LYS* 5.3 11.4 + - - +
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Residues in contact with TRP 243 (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* 4.6 0.9 - - - -
165A PRO* 3.0 25.0 - - + +
235A LEU* 3.5 55.0 - - + +
236A THR* 3.7 21.6 - - + +
238A ASP* 4.5 4.0 - - - +
239A GLY 2.9 17.3 + - - +
240A ARG* 3.7 11.9 - - - +
242A GLU* 1.3 72.5 - - - +
244A ALA* 1.3 60.1 - - - +
246A ALA* 4.0 4.0 - - + +
247A ARG* 2.8 64.7 + - + +
250A LEU* 4.0 14.1 - - + -
260A LEU* 4.6 2.0 - - + -
303A TRP* 3.9 20.6 - + - -
305A ASP* 2.6 35.5 + - - -
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Residues in contact with ALA 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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165A PRO* 3.6 13.4 - - - +
166A GLY* 3.4 35.4 - - - +
167A HIS* 3.9 4.9 - - + +
240A ARG 3.0 18.8 + - - +
241A SER 3.6 6.1 - - - +
242A GLU 3.3 0.2 - - - -
243A TRP* 1.3 76.2 - - - +
245A GLU* 1.3 51.5 + - - +
247A ARG* 3.6 3.6 + - - +
248A THR* 2.8 35.0 + - - -
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Residues in contact with GLU 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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167A HIS* 5.9 4.1 - - - +
241A SER 3.2 9.6 + - - +
242A GLU* 3.1 10.9 + - - +
243A TRP 3.1 0.6 - - - -
244A ALA* 1.3 79.1 - - - +
246A ALA* 1.3 66.0 + - - +
248A THR* 3.1 17.7 + - - -
249A VAL* 3.2 15.6 + - + +
376A HIS* 3.6 21.0 - - + +
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Residues in contact with ALA 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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235A LEU* 3.9 24.7 - - + -
242A GLU 3.0 13.4 + - - +
243A TRP* 3.9 11.2 - - + +
245A GLU* 1.3 76.8 - - - +
247A ARG* 1.3 62.4 + - - +
249A VAL* 3.1 6.6 + - - +
250A LEU* 3.1 23.4 + - - +
373A ILE* 3.8 1.7 - - + +
376A HIS* 3.8 37.2 - - + +
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Residues in contact with ARG 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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162A TYR* 5.2 2.8 + - - -
164A LEU* 3.8 22.6 - - - +
165A PRO* 3.9 26.5 + - - +
243A TRP* 2.8 45.9 + - + +
244A ALA* 3.8 6.1 - - - +
246A ALA* 1.3 73.6 - - - +
248A THR* 1.3 60.9 + - - +
250A LEU* 3.1 5.5 + - - +
251A VAL* 2.9 54.8 + - + +
260A LEU* 4.0 19.2 - - + +
264A GLU* 3.1 25.3 + - - -
305A ASP* 5.5 0.2 - - - -
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Residues in contact with THR 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 ALA 2.8 20.2 + - - -
245A GLU* 3.1 13.1 + - - -
247A ARG* 1.3 78.0 - - - +
249A VAL* 1.3 64.1 + - + +
251A VAL* 3.5 15.3 + - + +
252A LYS* 3.7 17.3 + - - +
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Residues in contact with VAL 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 GLU* 3.5 15.7 - - + +
246A ALA 3.1 8.0 + - - +
247A ARG 3.1 0.6 - - - -
248A THR* 1.3 78.7 - - + +
250A LEU* 1.3 62.6 + - - +
252A LYS* 3.3 32.2 + - + +
253A ASP* 4.5 0.3 + - - +
370A SER* 4.6 2.2 - - - +
372A GLU* 3.5 41.5 - - + +
373A ILE* 3.4 23.6 - - + -
376A HIS* 3.9 19.1 - - - +
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Residues in contact with LEU 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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232A ILE* 4.1 21.5 - - + -
235A LEU* 3.9 19.7 - - + -
243A TRP* 4.0 22.9 - - + -
246A ALA 3.1 14.1 + - - +
247A ARG* 3.1 7.8 + - - +
249A VAL* 1.3 78.4 - - - +
251A VAL* 1.3 57.4 + - - +
252A LYS 3.0 5.9 + - - -
253A ASP 3.1 12.0 + - - -
256A ASN* 3.4 44.0 + - + +
260A LEU* 4.6 15.0 - - + -
367A TRP* 4.7 4.0 - - + -
368A LYS 5.2 2.0 - - - +
369A CYS* 5.9 0.7 - - - -
373A ILE* 3.4 34.5 - - + -
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Residues in contact with VAL 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 ARG* 2.9 53.4 + - + +
248A THR* 3.7 10.5 - - + +
249A VAL 3.3 0.4 - - - -
250A LEU* 1.3 74.4 - - - +
252A LYS* 1.3 56.6 + - - +
253A ASP 3.1 0.7 - - - -
257A ARG* 2.8 50.0 + - + +
260A LEU* 4.2 9.6 - - + -
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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 THR* 3.7 11.2 + - - +
249A VAL* 3.4 27.1 - - + +
250A LEU 3.0 1.0 + - - -
251A VAL* 1.3 77.9 - - - +
253A ASP* 1.3 58.1 + - + +
254A SER 4.0 0.5 + - - -
257A ARG* 3.4 9.3 + - - +
372A GLU* 3.8 26.9 + - - +
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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