Contacts of the helix formed by residues 183 - 195 (chain F) in PDB entry 2Y1M
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 LYS 183 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181F ILE* 2.7 10.4 + - - +
182F THR* 1.3 87.4 - - - +
184F ALA* 1.3 68.5 + - - +
185F ASP* 3.2 3.1 - - + +
186F ALA* 2.8 31.4 + - + +
187F ALA* 2.9 12.1 + - - +
242F ASP* 4.4 0.4 + - - +
245F THR* 4.2 19.5 - - - +
246F ARG* 4.5 12.3 - - + -
249F GLN* 2.9 45.1 + - + +
250F PRO* 6.2 0.2 - - + -
251F TRP* 5.8 4.7 - - + +
321F ASN 5.5 1.4 + - - -
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Residues in contact with ALA 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ILE 4.3 0.6 + - - -
182F THR 3.8 3.8 + - - -
183F LYS* 1.3 73.1 - - - +
185F ASP* 1.3 67.6 + - - +
187F ALA* 3.1 15.0 + - - +
188F GLU* 3.1 13.7 + - - +
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Residues in contact with ASP 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F LYS* 3.2 2.2 - - + +
184F ALA* 1.3 82.4 - - - +
186F ALA* 1.3 62.5 + - - +
188F GLU* 3.4 8.3 + - - +
189F PHE* 3.3 18.4 + - - +
251F TRP* 3.5 39.7 + - + +
252F SER* 4.7 9.4 + - - -
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Residues in contact with ALA 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ILE* 3.6 5.6 - - + -
183F LYS* 2.8 19.6 + - + +
185F ASP* 1.3 75.5 - - - +
187F ALA* 1.3 64.5 + - - +
189F PHE* 3.1 4.6 + - - +
190F TRP 3.0 19.1 + - - -
241F PHE* 3.3 30.6 - - + -
245F THR* 3.6 27.4 - - + +
251F TRP* 4.0 13.1 - - + -
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Residues in contact with ALA 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ILE* 3.8 34.1 - - + +
183F LYS 2.9 9.9 + - - +
184F ALA* 3.1 13.0 + - - +
186F ALA* 1.3 79.0 - - - +
188F GLU* 1.3 60.0 + - - +
190F TRP* 4.0 0.5 - - - +
191F ARG* 3.1 32.7 + - - +
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Residues in contact with GLU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F ALA 3.1 11.9 + - - +
185F ASP* 3.8 10.8 - - - +
186F ALA 3.2 0.4 - - - -
187F ALA* 1.3 74.6 - - - +
189F PHE* 1.3 65.6 + - - +
191F ARG* 4.9 4.0 - - - +
192F LYS* 3.2 37.4 + - + +
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Residues in contact with PHE 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F ASP 3.3 5.9 + - - +
186F ALA 3.1 9.0 + - - +
188F GLU* 1.3 79.6 - - - +
190F TRP* 1.3 69.3 + - - +
192F LYS* 3.9 1.9 - - - +
193F ALA* 2.9 34.3 + - + +
194F PHE* 3.7 21.3 - + - -
205F PHE* 4.5 6.5 - + - -
208F ALA* 3.5 15.9 - - + -
209F LEU* 3.5 31.4 - - + -
212F VAL* 3.5 32.1 - - + -
241F PHE* 3.9 15.7 - + - -
251F TRP* 3.5 39.0 - + + +
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Residues in contact with TRP 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ILE* 3.5 22.2 - - + -
186F ALA 3.0 8.9 + - - +
187F ALA 4.0 0.4 - - - +
189F PHE* 1.3 83.1 - - - +
191F ARG* 1.3 78.2 + - - +
194F PHE* 2.6 54.5 + + + +
195F GLY 4.3 1.9 + - - -
197F LYS* 3.0 28.5 + - + -
198F THR 4.0 6.7 - - - -
199F ILE* 4.6 0.7 - - - -
200F VAL* 3.8 14.4 - - + -
205F PHE* 3.8 19.7 - + - -
236F ILE* 3.6 23.3 - - + -
237F SER 3.8 0.2 - - - -
238F VAL* 3.8 29.9 - - + +
241F PHE* 3.5 41.3 - + + -
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Residues in contact with ARG 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F GLY 4.2 3.8 + - - -
177F ASP* 3.1 29.6 + - - +
178F THR* 4.4 2.4 - - - +
179F PHE 2.9 27.5 + - - +
181F ILE* 4.9 5.5 - - - +
187F ALA* 3.1 19.2 + - - +
188F GLU* 4.6 6.1 - - - +
190F TRP* 1.3 89.7 - - - +
192F LYS* 1.3 62.4 + - - +
195F GLY* 2.7 53.1 + - - +
196F GLU* 3.4 21.3 + - + +
197F LYS 3.9 7.3 + - - -
238F VAL* 4.8 6.4 - - - +
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Residues in contact with LYS 192 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188F GLU* 3.2 37.7 + - + +
189F PHE* 3.9 2.7 - - - +
191F ARG* 1.3 80.8 - - - +
193F ALA* 1.3 64.8 + - - +
195F GLY 4.3 1.4 + - - -
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Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F PHE* 2.9 26.8 + - + +
192F LYS* 1.3 82.3 - - - +
194F PHE* 1.3 88.5 + - + +
195F GLY 3.8 0.2 - - - -
197F LYS* 5.8 0.5 - - - -
208F ALA* 4.3 11.7 - - + -
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Residues in contact with PHE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F PHE* 3.7 18.2 - + - -
190F TRP* 2.6 51.4 + + + +
193F ALA* 1.3 90.5 - - + +
195F GLY* 1.3 65.8 + - - +
196F GLU 3.0 4.0 + - - -
197F LYS* 3.0 42.5 + - + +
200F VAL* 3.7 31.6 - - + -
204F SER* 4.0 6.5 - - - -
205F PHE* 4.0 25.4 - + - -
208F ALA* 3.2 29.2 - - + -
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Residues in contact with GLY 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F TRP* 4.3 1.2 - - - -
191F ARG* 2.7 56.7 + - - +
192F LYS 4.3 1.6 + - - -
193F ALA 3.8 0.8 - - - -
194F PHE* 1.3 70.5 - - - +
196F GLU* 1.3 62.7 + - - -
197F LYS 3.9 0.2 + - - -
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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