Contacts of the helix formed by residues 186 - 201 (chain B) in PDB entry 2Y96
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 ASN 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ASP* 2.9 28.9 + - - +
116B LEU 3.3 16.8 - - - +
117B PRO* 3.5 15.7 - - + +
152B SER* 3.1 9.2 + - - +
184B LEU* 3.5 1.7 + - - -
185B PRO* 1.3 77.5 - - - +
187B ARG* 1.3 64.0 + - - +
188B GLY* 2.7 30.1 + - - -
189B PHE* 2.8 35.5 + - - -
190B LEU* 3.0 17.2 + - - +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 4.8 13.0 + - - +
117B PRO* 3.9 23.8 - - + -
185B PRO 4.6 0.2 - - - -
186B ASN* 1.3 74.0 - - - +
188B GLY* 1.3 60.6 + - - +
190B LEU* 3.7 7.6 + - - +
191B LYS* 3.2 24.9 + - - +
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 3.8 23.7 - - - +
186B ASN* 2.7 14.2 + - - -
187B ARG* 1.3 74.7 - - - +
189B PHE* 1.3 57.8 + - - -
190B LEU 3.1 1.3 - - - -
191B LYS* 3.2 10.2 + - - +
192B GLN* 2.9 39.6 + - - +
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Residues in contact with PHE 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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114B ASP 3.5 21.5 - - - -
115B ASP* 3.5 4.0 - - - -
116B LEU 3.7 5.2 - - - -
119B PHE* 3.5 23.1 - + + -
121B LEU* 3.9 21.1 - - + -
152B SER* 3.3 25.1 - - - -
153B ARG* 3.5 22.9 - - + -
156B THR* 3.5 27.7 - - + +
185B PRO* 4.0 3.6 - - + -
186B ASN* 2.8 38.9 + - - +
188B GLY* 1.3 71.4 - - - -
190B LEU* 1.3 57.0 + - - +
192B GLN* 3.2 19.7 + - - +
193B LEU* 2.8 32.9 + - - +
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Residues in contact with LEU 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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38A ALA* 4.1 17.9 - - + +
41A LEU* 3.8 30.3 - - + -
42A GLU* 3.6 34.5 - - + +
45A PHE* 4.2 24.5 - - + -
170B LEU* 4.7 5.6 - - + -
174B ILE* 5.2 0.4 - - + -
184B LEU* 6.0 0.2 - - + -
185B PRO* 4.4 9.4 - - + +
186B ASN 3.0 15.1 + - - +
187B ARG* 3.8 6.7 - - - +
189B PHE* 1.3 74.9 - - - +
191B LYS* 1.3 60.0 + - - +
193B LEU* 3.1 15.5 + - + +
194B ARG* 2.8 32.7 + - - +
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Residues in contact with LYS 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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38A ALA* 6.1 1.5 - - - +
187B ARG 3.2 12.3 + - - +
188B GLY* 3.2 12.5 + - - +
190B LEU* 1.3 79.0 - - - +
192B GLN* 1.3 63.8 + - + +
194B ARG* 3.2 14.9 + - - +
195B GLU* 3.1 54.1 + - + +
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Residues in contact with GLN 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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117B PRO 4.2 6.1 + - - -
119B PHE 2.9 22.6 + - - -
120B ASP* 3.4 22.1 - - - +
121B LEU* 2.8 30.1 + - - +
122B SER* 3.3 11.2 + - - -
125B PHE* 3.9 16.4 - - + -
188B GLY* 2.9 27.5 + - - +
189B PHE* 3.3 13.1 - - - +
190B LEU 3.2 0.2 - - - -
191B LYS* 1.3 78.2 - - + +
193B LEU* 1.3 56.3 + - - +
195B GLU* 3.2 15.0 + - - +
196B LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 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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45A PHE* 5.4 0.4 - - + -
125B PHE* 4.1 9.6 - - + -
156B THR* 3.7 43.1 - - + +
159B LEU* 3.8 27.8 - - + -
160B ALA* 4.0 16.4 - - + +
163B MET* 3.6 16.8 - - - +
170B LEU* 3.8 18.4 - - + -
185B PRO* 4.4 7.4 - - + -
189B PHE 2.8 18.5 + - - +
190B LEU* 3.6 14.6 - - + +
192B GLN* 1.3 70.4 - - - +
194B ARG* 1.3 60.9 + - - +
196B LEU* 3.4 4.8 + - + -
197B ASP* 2.9 28.9 + - - +
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 3.3 20.4 + - + +
36A PRO 2.2 39.8 + - - -
37A GLY* 3.5 7.4 - - - -
38A ALA* 4.1 19.7 - - - +
41A LEU* 3.4 28.3 - - + -
170B LEU* 4.0 5.2 - - - -
190B LEU* 2.8 17.6 + - - +
191B LYS* 3.2 15.3 + - - +
193B LEU* 1.3 76.4 - - - +
195B GLU* 1.3 59.7 + - + +
197B ASP* 3.1 4.0 + - - +
198B LYS* 2.9 62.6 + - - +
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Residues in contact with GLU 195 (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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191B LYS* 3.1 44.6 + - + +
192B GLN* 3.7 16.4 - - - +
193B LEU 3.2 0.2 - - - -
194B ARG* 1.3 78.1 - - + +
196B LEU* 1.3 62.0 + - - +
198B LYS* 3.3 16.0 + - + +
199B GLN* 3.1 37.4 + - - +
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Residues in contact with LEU 196 (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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125B PHE* 3.9 28.3 - - + -
126B TYR* 3.8 32.8 - - + +
160B ALA* 4.0 21.5 - - + -
163B MET* 3.9 19.3 - - + -
164B ILE* 4.2 11.4 - - + -
192B GLN 3.0 14.5 + - - +
193B LEU* 3.6 7.6 - - + +
194B ARG 3.3 0.2 - - - -
195B GLU* 1.3 75.4 - - - +
197B ASP* 1.3 57.7 + - - +
199B GLN* 3.3 20.1 + - + +
200B LEU* 2.9 38.2 + - + +
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Residues in contact with ASP 197 (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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33A TYR* 2.7 28.6 + - - -
35A THR* 2.7 24.6 + - + +
163B MET* 3.6 11.7 - - + +
168B MET 4.6 0.9 - - - +
169B THR* 3.6 8.0 - - - -
170B LEU* 2.8 33.8 + - + +
193B LEU 2.9 15.1 + - - +
194B ARG 3.3 8.3 - - - +
196B LEU* 1.3 74.9 - - - +
198B LYS* 1.3 62.9 + - - +
200B LEU* 3.4 5.3 + - - +
201B VAL* 3.0 32.4 + - - +
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Residues in contact with LYS 198 (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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35A THR* 3.9 17.0 - - - +
194B ARG* 2.9 49.1 + - - +
195B GLU* 3.6 17.3 - - + +
197B ASP* 1.3 72.9 - - - +
199B GLN* 1.3 66.4 + - + +
201B VAL* 3.3 21.1 + - - +
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Residues in contact with GLN 199 (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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126B TYR* 5.3 4.4 + - - +
195B GLU* 3.1 27.7 + - - +
196B LEU* 3.5 27.3 - - + +
198B LYS* 1.3 76.3 - - + +
200B LEU* 1.3 65.0 + - + +
201B VAL 4.0 5.2 - - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.8 21.8 - - + +
163B MET* 3.4 47.8 - - + +
164B ILE* 4.0 10.8 - - + +
168B MET 4.8 3.6 - - - +
196B LEU* 2.9 32.7 + - + +
197B ASP* 3.9 5.8 - - - +
199B GLN* 1.3 77.8 - - + +
201B VAL* 1.3 65.0 + - + +
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Residues in contact with VAL 201 (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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33A TYR* 4.2 41.5 - - + +
34A CYS* 5.8 1.1 - - - -
35A THR* 5.3 1.3 - - - +
169B THR* 5.4 4.7 - - + -
197B ASP* 3.0 23.0 + - - +
198B LYS* 3.3 14.6 + - - +
199B GLN 3.3 4.2 - - - +
200B LEU* 1.3 83.0 - - + +
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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