Contacts of the helix formed by residues 235 - 249 (chain A) in PDB entry 1YCH
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASP* 3.2 16.5 + - - +
232A TRP* 4.2 8.4 - - - -
234A LYS* 1.3 81.9 - - + +
236A PRO* 1.3 63.4 - - - +
237A GLY* 3.2 7.1 + - - -
238A ARG* 2.8 69.1 + - + +
239A ILE 4.2 1.9 + - - -
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Residues in contact with PRO 236 (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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221A ILE* 4.4 15.3 - - + +
222A LYS* 3.5 28.3 - - - +
223A THR* 3.9 0.9 - - - -
224A ILE* 4.0 20.9 - - + -
232A TRP* 3.4 32.1 - - + +
234A LYS 3.6 5.6 - - - +
235A ASP* 1.3 89.6 - - - +
237A GLY* 1.3 65.7 + - - +
239A ILE* 3.3 5.6 + - + +
240A ILE* 3.0 29.9 + - + +
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Residues in contact with GLY 237 (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 ASP* 3.1 7.5 + - - -
236A PRO* 1.3 80.5 - - - +
238A ARG* 1.3 53.1 + - - +
240A ILE* 3.0 8.6 + - - +
241A GLU* 2.7 49.1 + - - +
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Residues in contact with ARG 238 (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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185A ALA* 3.5 30.5 - - - +
189A MET* 4.0 23.5 - - + +
232A TRP* 5.6 3.1 - - + -
235A ASP* 2.8 46.4 + - - +
236A PRO 3.3 0.2 - - - -
237A GLY* 1.3 74.1 - - - +
239A ILE* 1.3 59.6 + - + +
241A GLU* 3.3 13.8 + - - +
242A ALA* 2.8 30.2 + - - +
245A ARG* 5.4 0.3 + - - -
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Residues in contact with ILE 239 (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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169A PHE* 3.9 11.9 - - + +
189A MET* 4.7 4.7 - - + -
192A ALA* 4.4 13.7 - - + -
224A ILE* 3.8 22.9 - - + -
232A TRP* 3.1 56.8 - - + +
235A ASP 4.2 0.2 + - - -
236A PRO 3.3 12.3 + - - +
238A ARG* 1.3 76.3 - - - +
240A ILE* 1.3 67.7 + - - +
242A ALA* 4.1 9.4 - - + -
243A TYR* 3.1 48.6 + - + -
246A TRP* 4.5 1.3 - - + -
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Residues in contact with ILE 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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169A PHE* 4.2 12.6 - - + -
211A LEU* 3.8 24.5 - - + +
221A ILE* 4.0 26.5 - - + -
224A ILE* 3.9 24.9 - - + -
236A PRO* 3.0 24.9 + - + +
237A GLY* 3.6 8.3 - - - +
239A ILE* 1.3 75.8 - - + +
241A GLU* 1.3 65.9 + - + +
243A TYR* 3.3 3.8 + - - +
244A ALA* 3.0 21.9 + - + +
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Residues in contact with GLU 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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237A GLY* 2.7 33.4 + - - +
238A ARG* 3.7 11.4 + - - +
240A ILE* 1.3 73.7 - - + +
242A ALA* 1.3 62.7 + - - +
244A ALA* 3.2 8.7 + - - +
245A ARG* 3.0 25.9 + - - +
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Residues in contact with ALA 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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189A MET* 4.1 11.7 - - - -
238A ARG 2.8 17.3 + - - +
239A ILE* 3.6 7.2 - - - +
241A GLU* 1.3 74.2 - - - +
243A TYR* 1.3 61.2 + - - +
245A ARG* 3.2 28.9 + - - +
246A TRP* 2.9 59.9 + - + -
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Residues in contact with TYR 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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168A ALA* 4.7 4.3 - - + -
169A PHE* 2.8 55.1 + + + -
170A GLY 4.0 2.3 + - - -
192A ALA* 5.0 3.7 + - + -
195A TYR* 4.1 9.5 - - - -
196A TYR* 3.6 26.5 - + + +
200A LEU* 3.4 31.9 - - + +
207A ILE* 4.1 14.8 - - + +
211A LEU* 4.0 13.2 - - + -
239A ILE* 3.1 47.4 + - + +
240A ILE 3.3 4.7 + - - +
242A ALA* 1.3 75.4 - - - +
244A ALA* 1.3 58.0 + - - +
246A TRP* 3.9 16.0 - + - +
247A ALA* 2.8 35.0 + - - +
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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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208A THR* 4.2 8.3 - - + +
211A LEU* 3.8 15.8 - - + +
240A ILE* 3.0 13.6 + - + +
241A GLU* 3.3 13.9 - - - +
243A TYR* 1.3 77.6 - - - +
245A ARG* 1.3 56.9 - - - +
247A ALA* 3.7 3.1 - - - +
248A GLU* 2.9 34.2 + - - +
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Residues in contact with ARG 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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189A MET* 5.4 4.4 - - - +
238A ARG 5.4 0.2 + - - -
241A GLU 3.0 13.2 + - - +
242A ALA* 3.6 31.6 + - - +
244A ALA* 1.3 76.1 - - - +
246A TRP* 1.3 81.5 + - + +
248A GLU* 3.3 14.6 + - - +
249A GLY* 3.1 18.5 + - - -
250A GLN* 4.3 9.0 + - + +
251A GLY 5.3 2.6 + - - +
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Residues in contact with TRP 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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189A MET* 4.0 18.8 - - + -
192A ALA* 4.2 6.1 - - + -
193A ALA* 3.6 37.7 - - + +
196A TYR* 3.9 40.4 + + + -
204A SER* 4.7 2.6 - - - -
239A ILE* 4.5 2.5 - - + -
242A ALA* 2.9 46.7 + - + +
243A TYR* 3.9 20.0 - + - +
245A ARG* 1.3 93.7 - - + +
247A ALA* 1.3 62.6 + - - +
249A GLY* 3.3 13.0 + - - -
302A LEU* 3.5 36.2 - - + +
303A ASP* 3.7 21.3 + - - -
335A LYS* 5.5 0.5 - - - +
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Residues in contact with ALA 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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196A TYR* 3.3 16.5 + - - +
204A SER* 3.4 33.4 - - - +
207A ILE* 3.7 14.1 - - + -
208A THR* 3.8 12.6 - - + -
243A TYR 2.8 19.5 + - - +
244A ALA 3.7 2.7 - - - +
246A TRP* 1.3 73.9 - - - +
248A GLU* 1.3 55.6 + - - +
249A GLY 3.4 0.3 + - - -
335A LYS* 2.6 29.0 + - - +
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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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208A THR* 4.3 8.9 - - + +
244A ALA* 2.9 20.4 + - - +
245A ARG* 3.3 15.0 - - - +
247A ALA* 1.3 76.2 - - - +
249A GLY* 1.3 59.8 + - - +
250A GLN* 3.4 30.7 + - + +
335A LYS* 2.8 26.5 + - - +
336A ASN* 5.5 0.9 + - - +
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Residues in contact with GLY 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 ARG 3.1 6.8 + - - -
246A TRP 3.3 10.7 + - - -
247A ALA 3.3 2.9 - - - -
248A GLU* 1.3 78.5 - - - +
250A GLN* 1.3 67.1 + - - +
251A GLY* 3.1 4.6 + - - -
302A LEU 5.7 2.7 - - - -
335A LYS* 4.2 18.8 - - - +
336A ASN* 3.0 24.6 + - - +
337A LYS* 4.7 6.9 + - - -
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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