Contacts of the helix formed by residues 195 - 209 (chain B) in PDB entry 1ESQ
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 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.3 28.0 - - - +
31B PHE* 4.0 6.3 - - - -
194B THR* 1.3 77.8 + - - +
196B ALA* 1.3 65.6 + - - +
197B GLY 3.1 2.5 - - - -
199B LEU* 2.8 28.6 + - - +
325B TZP 3.1 20.3 + - - -
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Residues in contact with ALA 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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31B PHE* 4.4 6.5 - - - -
190B LEU* 3.3 36.6 - - + +
193B VAL* 3.1 21.9 + - + +
194B THR 3.3 0.8 + - - -
195B GLY* 1.3 78.7 - - - +
197B GLY* 1.3 60.8 + - - +
200B LEU* 3.3 13.2 + - - +
225B TYR* 2.8 29.9 + - - +
305B ATP 4.3 7.6 - - - +
325B TZP 3.7 0.8 + - - -
360B MG 4.6 3.4 - - - -
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 3.1 31.5 + - - -
195B GLY 3.1 0.8 - - - -
196B ALA* 1.3 77.9 - - - +
198B SER* 1.3 59.0 + - - +
200B LEU* 3.2 5.2 + - - +
201B THR* 2.9 24.6 + - - -
305B ATP 3.5 20.8 + - - -
325B TZP 3.4 9.0 + - - -
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Residues in contact with SER 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.7 0.7 - - - -
25B ASN* 3.7 10.0 + - - -
28B VAL* 3.6 26.2 - - - +
32B THR* 4.5 2.0 - - - -
63B VAL* 5.6 0.2 - - - +
65B ASN* 2.9 24.5 + - - +
94B ASP* 3.7 8.9 + - - -
96B VAL* 4.6 0.3 - - - +
121B ARG* 3.9 0.2 - - - +
195B GLY 3.1 4.7 + - - -
197B GLY* 1.3 70.5 - - - +
199B LEU* 1.3 65.9 + - - +
201B THR* 3.3 3.6 + - - -
202B SER* 3.1 25.5 + - - -
325B TZP 2.5 28.6 + - - -
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Residues in contact with LEU 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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31B PHE* 3.5 34.5 - - + -
32B THR* 4.0 19.4 + - + +
35B GLY* 3.7 31.9 - - - -
36B LEU* 3.9 7.2 - - + +
195B GLY 2.8 18.7 + - - +
198B SER* 1.3 73.5 - - - +
200B LEU* 1.3 52.4 + - - +
202B SER* 3.2 4.4 + - - -
203B VAL* 2.8 47.5 + - + +
225B TYR* 3.6 27.6 - - + +
248B LEU* 4.0 1.8 - - + -
252B LEU* 3.9 15.3 - - + -
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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
----------------------------------------------------------
121B ARG* 4.3 9.6 - - + +
168B THR* 3.7 30.5 - - + -
196B ALA 3.3 12.2 + - - +
197B GLY 3.2 9.4 + - - +
199B LEU* 1.3 79.2 - - - +
201B THR* 1.3 50.7 + - - +
203B VAL* 2.7 14.2 + - + +
204B VAL* 2.7 40.2 + - + +
221B ALA 4.6 0.9 - - - +
222B ILE* 3.8 28.3 - - + +
225B TYR* 3.4 30.3 - - + -
305B ATP 3.7 26.7 - - - +
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Residues in contact with THR 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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63B VAL* 3.4 25.7 - - + +
65B ASN* 5.3 0.4 - - - -
92B ILE* 3.8 20.1 - - + +
93B LEU 4.5 1.3 - - - -
94B ASP* 2.7 40.4 + - + +
121B ARG* 3.2 19.2 + - + +
197B GLY 2.9 10.0 + - - -
198B SER 3.3 8.7 + - - -
200B LEU* 1.3 73.6 - - - +
202B SER* 1.3 58.1 + - - +
204B VAL* 3.0 14.0 + - - +
205B GLY* 2.9 23.7 + - - -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.0 3.9 - - - +
22B SER* 3.4 13.9 + - - -
24B THR* 5.9 1.0 - - - +
32B THR* 3.3 27.0 - - - +
36B LEU* 3.9 20.3 - - - +
63B VAL* 3.9 16.5 - - - +
198B SER 3.1 12.2 + - - -
199B LEU 3.5 7.9 - - - -
201B THR* 1.3 74.9 - - - +
203B VAL* 1.3 66.0 + - - +
205B GLY* 3.0 2.8 + - - +
206B ALA* 2.9 21.5 + - - +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY 5.8 0.2 - - - +
36B LEU* 4.4 3.8 - - + -
39B LEU* 3.9 20.9 - - + -
199B LEU* 2.8 44.2 + - + +
200B LEU* 2.7 15.3 + - + +
202B SER* 1.3 75.8 - - - +
204B VAL* 1.3 60.8 + - - +
206B ALA* 2.9 18.4 + - - +
207B PHE* 3.0 35.6 + - + -
221B ALA* 4.0 16.4 - - + +
224B SER* 6.0 0.4 - - - -
225B TYR* 4.0 17.3 - - + +
252B LEU* 5.4 4.7 - - + -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.9 20.6 - - + -
119B ALA* 4.7 6.5 - - + -
121B ARG* 4.7 11.4 - - + -
166B ALA* 5.9 0.9 - - + -
200B LEU* 2.7 36.3 + - + +
201B THR* 3.0 15.0 - - - +
203B VAL* 1.3 72.8 - - - +
205B GLY* 1.3 60.8 + - - +
207B PHE* 3.1 4.5 + - - +
208B CYS* 2.9 34.3 + - - -
218B ALA* 4.5 18.4 - - + -
221B ALA* 3.7 16.6 - - + -
222B ILE* 4.3 11.2 - - + -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.4 6.3 - - - -
61B ALA* 3.1 23.0 - - - +
63B VAL* 5.5 1.6 - - - -
92B ILE* 3.7 25.1 - - - +
201B THR 2.9 12.0 + - - -
202B SER* 3.0 5.3 + - - -
204B VAL* 1.3 75.6 - - - +
206B ALA* 1.3 62.4 + - - +
208B CYS* 3.2 1.8 + - - +
209B ALA* 3.1 17.5 + - - +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.9 15.9 - - + +
18B PRO* 3.7 10.0 - - + +
20B VAL* 3.7 21.0 - - + +
36B LEU* 4.3 3.8 - - + -
39B LEU* 4.1 19.3 - - + -
41B ALA* 4.4 3.8 - - + -
202B SER 2.9 11.4 + - - +
203B VAL* 2.9 17.9 + - - +
205B GLY* 1.3 76.3 - - - +
207B PHE* 1.3 60.1 + - + +
209B ALA* 3.2 17.2 + - - +
210B VAL* 4.0 2.1 + - - +
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Residues in contact with PHE 207 (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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6B ALA 4.4 0.2 - - - -
9B CYS* 3.6 22.2 - - + -
10B LEU* 3.6 22.9 - - + -
13B VAL* 3.8 18.8 - - + -
39B LEU* 4.6 10.1 - - + -
203B VAL* 3.0 24.4 + - + -
204B VAL 3.1 5.6 + - - +
206B ALA* 1.3 77.1 - - + +
208B CYS* 1.3 59.0 + - - +
210B VAL* 3.2 5.1 + - + +
211B GLU* 2.9 30.1 + - - +
217B ALA* 3.5 20.2 - - + +
220B ALA* 3.4 36.8 - - + -
221B ALA* 3.3 25.4 - - + -
224B SER* 3.5 23.3 - - - -
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Residues in contact with CYS 208 (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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90B PRO* 3.8 27.9 - - + +
92B ILE* 3.7 22.9 - - + -
118B ALA* 4.8 6.5 - - - -
119B ALA* 5.3 2.9 - - - -
204B VAL* 2.9 24.6 + - - +
205B GLY 3.2 9.8 + - - +
207B PHE* 1.3 76.0 - - - +
209B ALA* 1.3 59.9 + - - +
210B VAL 3.2 1.5 + - - -
211B GLU 3.5 14.1 + - - +
212B GLU* 5.5 0.2 - - - -
214B PRO* 4.6 13.0 - - - -
217B ALA* 3.7 21.3 - - - -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 3.3 26.6 - - + +
20B VAL* 5.5 0.7 - - + -
60B GLY* 3.5 31.3 - - - +
61B ALA* 4.2 0.9 - - + -
90B PRO* 4.5 1.1 - - - +
205B GLY 3.1 9.9 + - - +
206B ALA* 3.3 13.9 - - - +
207B PHE 3.0 0.8 - - - -
208B CYS* 1.3 77.8 - - - +
210B VAL* 1.3 60.7 + - - +
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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
------------------------------------------------------------
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