Contacts of the helix formed by residues 177 - 193 (chain B) in PDB entry 2Y0N
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 PRO 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLU 3.6 8.7 - - - +
176B ILE* 1.3 86.9 - - + +
178B GLU* 1.3 56.4 + - - +
179B VAL* 3.1 3.6 - - + +
180B LEU* 2.7 29.8 + - + -
181B LYS 2.9 9.7 + - - -
485B ASP 5.6 0.2 - - - +
488B LEU* 3.8 38.6 - - + +
489B ARG* 3.4 32.3 - - - +
492B ALA* 3.9 18.8 - - + -
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE 3.2 3.7 + - - +
177B PRO* 1.3 71.4 - - - +
179B VAL* 1.3 61.7 + - - +
181B LYS* 3.5 31.8 + - + +
182B LYS* 3.0 39.3 + - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 3.1 2.0 + - + -
178B GLU* 1.3 78.1 - - + +
180B LEU* 1.3 58.8 + - - +
182B LYS* 3.7 19.8 - - + +
183B GLN* 3.3 21.7 + - - +
492B ALA* 4.4 24.0 - - + +
495B HIS* 4.1 36.6 + - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 3.8 9.9 - - + -
177B PRO* 2.7 24.7 + - + +
179B VAL* 1.3 72.7 - - - +
181B LYS* 1.3 58.4 + - - +
182B LYS 3.3 0.4 - - - -
183B GLN* 3.4 5.5 - - + +
184B LEU* 2.9 32.6 + - - +
457B LEU* 3.8 15.8 - - + +
488B LEU* 3.4 48.9 - - + +
491B LEU* 3.8 26.5 - - + +
492B ALA* 3.9 13.0 - - + +
495B HIS* 4.6 8.1 - - + -
499B PHE* 4.0 19.5 - - + -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 3.5 41.0 - - + +
177B PRO 2.9 5.3 + - - -
178B GLU* 3.5 32.6 + - + +
180B LEU* 1.3 74.0 - - - +
182B LYS* 1.3 65.8 + - + +
184B LEU* 3.2 6.7 + - - +
185B GLU* 3.2 28.8 + - - +
593F TRP* 3.8 44.4 - - + +
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 3.0 30.5 + - + +
179B VAL* 3.7 18.4 - - + +
181B LYS* 1.3 72.8 - - + +
183B GLN* 1.3 56.9 + - - +
185B GLU* 2.8 37.3 + - - +
186B ASP* 2.8 22.8 + - - +
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Residues in contact with GLN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL 3.3 13.0 + - - +
180B LEU* 3.3 12.7 + - - +
182B LYS* 1.3 78.3 - - - +
184B LEU* 1.3 57.1 + - - +
186B ASP* 3.3 15.9 + - - +
187B ASP* 2.9 29.6 + - - +
190B TYR* 5.8 1.4 - - - -
454B GLN* 5.0 1.6 - - - +
457B LEU* 4.0 8.3 - - + -
495B HIS* 3.4 23.8 + - + +
499B PHE* 3.5 48.3 - - + +
501B GLU* 5.4 4.0 - - - +
504B TYR* 4.1 21.6 + - - -
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 4.0 19.1 - - + -
180B LEU 2.9 17.3 + - - +
181B LYS 3.4 8.1 - - - +
182B LYS 3.1 0.4 - - - -
183B GLN* 1.3 73.3 - - - +
185B GLU* 1.3 59.3 + - - +
187B ASP* 3.4 10.1 - - + +
188B CYS* 3.1 26.5 + - - +
275B TYR* 5.1 0.2 + - - -
454B GLN 5.1 0.7 - - - +
457B LEU* 3.8 29.4 - - + +
458B ARG* 4.1 33.0 - - + +
461B VAL* 3.8 24.2 - - + -
589F PHE* 4.8 4.3 - - + -
591F LEU* 3.7 25.0 - - + +
593F TRP* 4.5 3.8 - - + -
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B LYS* 3.2 15.8 + - - +
182B LYS* 2.8 23.1 + - - +
184B LEU* 1.3 69.4 - - - +
186B ASP* 1.3 64.6 + - - +
188B CYS* 3.3 7.8 + - - +
189B TYR* 3.1 22.4 + - - +
591F LEU* 4.8 7.0 - - + -
593F TRP* 2.8 35.7 + - + +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LYS* 2.8 20.2 + - - +
183B GLN* 3.4 22.4 - - - +
185B GLU* 1.3 75.7 - - - +
187B ASP* 1.3 64.7 + - - +
189B TYR* 3.1 9.8 + - - +
190B TYR* 3.0 44.3 + - + -
501B GLU* 5.6 2.4 - - - +
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Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLN* 2.9 18.5 + - - +
184B LEU* 3.4 16.5 - - + +
186B ASP* 1.3 76.8 - - - +
188B CYS* 1.3 64.4 + - - +
190B TYR* 3.3 12.8 + - - +
191B ILE* 3.4 19.8 + - - +
198B VAL* 5.0 0.2 - - - +
275B TYR* 4.9 0.3 - - - -
454B GLN* 4.0 13.8 - - - +
458B ARG* 2.5 39.0 + - - +
504B TYR* 2.5 38.9 + - - +
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Residues in contact with CYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LEU 3.1 9.6 + - - +
185B GLU* 3.5 9.6 - - - +
186B ASP 3.2 0.2 - - - -
187B ASP* 1.3 79.6 - - - +
189B TYR* 1.3 63.6 + - - +
191B ILE* 3.0 12.1 + - - -
192B ASN* 2.8 34.6 + - - +
193B ARG* 6.3 1.3 - - - -
275B TYR* 3.4 36.1 - - - +
591F LEU* 3.9 13.0 - - + -
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B GLU 3.1 8.8 + - - +
186B ASP* 3.1 13.1 + - - +
188B CYS* 1.3 77.6 - - - +
190B TYR* 1.3 65.5 + + - +
192B ASN* 4.6 0.4 - - - -
193B ARG* 3.2 45.3 + - + +
194B ARG* 3.0 68.3 + - + +
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLN* 5.8 2.2 - - - -
186B ASP* 3.0 44.0 + - + -
187B ASP* 3.5 11.7 - - - +
188B CYS 3.1 0.2 + - - -
189B TYR* 1.3 78.8 - + + +
191B ILE* 1.3 53.0 + - - +
194B ARG* 3.4 34.5 + - - -
195B LYS 3.2 9.2 + - - -
196B ARG* 2.7 59.7 + - + +
501B GLU* 2.8 40.1 + - + +
504B TYR* 3.9 42.2 - + + -
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ASP* 3.4 33.0 - - - +
188B CYS 3.0 4.4 + - - +
190B TYR* 1.3 79.5 - - - +
192B ASN* 1.3 60.0 + - - +
193B ARG 3.5 0.4 - - - -
195B LYS* 3.4 18.0 - - - +
196B ARG 3.2 21.4 + - - +
197B LEU* 4.6 3.7 - - + +
198B VAL* 5.1 3.6 - - + -
275B TYR* 4.2 19.5 - - + -
277B TYR* 4.3 19.0 - - + +
278B GLU* 3.4 43.3 - - + +
458B ARG* 3.5 12.3 - - - +
504B TYR* 4.2 13.0 - - + -
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Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B CYS* 2.8 31.1 + - - +
189B TYR 4.4 0.2 + - - -
191B ILE* 1.3 74.9 - - + +
193B ARG* 1.3 69.3 + - - +
195B LYS* 4.7 5.7 - - - +
275B TYR* 3.1 49.5 - - - +
276B PRO* 5.6 0.6 - - + +
277B TYR* 3.9 34.2 + - + -
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B CYS* 6.3 1.0 - - - -
189B TYR* 3.2 50.1 + - + +
191B ILE 3.5 0.8 - - - -
192B ASN* 1.3 91.0 + - - +
194B ARG* 1.3 60.6 + - - +
195B LYS* 3.0 13.8 + - - +
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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