Contacts of the helix formed by residues 187 - 206 (chain Z) in PDB entry 6CP3
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 187 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Z GLY 4.3 2.9 - - - +
186Z ASN* 1.3 86.9 - - + +
188Z LYS* 1.3 53.3 + - - +
189Z PHE* 3.0 2.5 - - + +
190Z GLN* 2.9 20.0 + - + +
191Z GLU* 2.6 34.6 + - - +
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Residues in contact with LYS 188 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 ASP 4.9 3.1 - - - -
66 LEU* 4.2 7.4 + - - +
96 ARG* 3.4 37.0 - - + +
106 GLU* 3.9 14.8 + - - +
136 ASP* 5.6 2.0 - - - +
183Z GLU* 2.4 42.4 + - - +
186Z ASN* 3.1 21.6 - - + +
187Z PRO* 1.3 76.3 - - - +
189Z PHE* 1.3 56.2 + - - +
190Z GLN 3.1 0.2 - - - -
191Z GLU* 3.9 18.8 - - + +
192Z LYS* 2.6 48.2 + - + +
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Residues in contact with PHE 189 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Y ALA* 4.7 12.1 - - + -
127Y GLU* 4.8 17.9 - - + -
164Y LYS 3.4 26.5 - - - -
165Y GLY* 3.7 16.6 - - - -
166Y GLY 5.4 1.0 + - - -
183Z GLU 5.8 0.2 + - - -
184Z LEU* 5.8 3.6 - - + +
186Z ASN 3.3 16.8 + - - +
187Z PRO* 4.6 0.9 - - + -
188Z LYS* 1.3 77.5 - - - +
190Z GLN* 1.3 58.9 + - + +
192Z LYS* 4.7 11.0 + - - +
193Z VAL* 3.5 17.8 - - - +
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Residues in contact with GLN 190 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Z PRO* 2.9 21.5 + - + +
189Z PHE* 1.3 80.0 - - + +
191Z GLU* 1.3 78.1 + - - +
192Z LYS 3.2 3.5 + - - -
193Z VAL* 3.3 20.4 + - - +
194Z LEU* 4.3 1.6 + - - +
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Residues in contact with GLU 191 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 ASP* 4.7 8.3 - - - +
96 ARG* 5.7 4.0 - - - +
187Z PRO 2.6 19.3 + - - +
188Z LYS* 3.4 17.7 + - + +
190Z GLN* 1.3 83.7 - - - +
192Z LYS* 1.3 65.0 + - - +
193Z VAL 3.3 0.2 - - - -
194Z LEU* 3.3 30.9 - - + +
195Z GLN* 3.8 24.4 + - - +
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Residues in contact with LYS 192 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66 LEU* 3.7 29.2 - - + -
164Y LYS 4.8 0.8 + - - -
165Y GLY* 3.7 2.4 - - - -
166Y GLY* 2.9 31.5 - - - +
180Y ILE* 3.0 30.8 - - - +
188Z LYS* 2.6 38.6 + - + +
189Z PHE* 4.7 8.6 + - - +
191Z GLU* 1.3 76.1 - - - +
193Z VAL* 1.3 55.7 + - - +
194Z LEU 3.2 1.6 - - - -
195Z GLN* 3.0 14.1 + - + +
196Z GLN* 2.5 70.7 + - - +
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Residues in contact with VAL 193 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129Y LEU* 5.4 10.5 - - + -
133Y SER* 5.6 6.1 - - - -
166Y GLY* 5.0 7.0 - - - +
167Y LEU* 3.2 33.9 - - + -
189Z PHE 3.5 22.7 - - - +
190Z GLN* 3.6 11.0 - - - +
191Z GLU 3.3 0.2 - - - -
192Z LYS* 1.3 77.8 - - + +
194Z LEU* 1.3 51.2 + - - +
196Z GLN* 3.4 11.1 + - - +
197Z SER* 2.6 40.8 + - - +
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Residues in contact with LEU 194 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Y ARG* 6.5 0.9 - - - -
190Z GLN 4.3 1.2 + - - +
191Z GLU* 3.3 27.0 + - + +
193Z VAL* 1.3 76.5 - - - +
195Z GLN* 1.3 64.7 + - - +
197Z SER* 3.2 10.3 + - - -
198Z ILE* 3.0 47.7 + - + +
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Residues in contact with GLN 195 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46 GLN* 4.4 9.3 - - + +
56 ASP* 2.8 54.2 + - + +
66 LEU* 4.5 11.9 - - + +
191Z GLU* 3.8 18.8 + - - +
192Z LYS* 3.0 25.9 + - + +
194Z LEU* 1.3 80.0 - - - +
196Z GLN* 1.3 61.7 + - - +
198Z ILE* 3.3 22.5 - - - +
199Z SER* 2.6 40.6 + - - +
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Residues in contact with GLN 196 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46 GLN* 5.4 0.9 + - - -
66 LEU* 3.8 4.9 - - - +
166Y GLY* 3.6 13.3 - - - -
167Y LEU* 3.8 22.1 - - + +
178Y LEU* 2.8 44.3 - - + +
192Z LYS* 2.5 66.7 + - - +
193Z VAL* 3.4 10.1 - - - +
195Z GLN* 1.3 77.9 - - - +
197Z SER* 1.3 57.9 + - - +
199Z SER* 3.6 6.0 - - - -
200Z GLU* 2.8 44.5 + - - +
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Residues in contact with SER 197 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Y SER* 4.7 12.0 - - - -
136Y ARG* 4.5 18.2 - - - -
137Y ILE* 4.3 15.6 - - - +
167Y LEU* 5.4 3.3 - - - +
193Z VAL* 2.6 29.2 + - - +
194Z LEU* 3.2 15.4 + - - -
196Z GLN* 1.3 76.8 - - - +
198Z ILE* 1.3 59.9 + - - +
200Z GLU* 3.3 3.2 + - - +
201Z ILE* 3.0 33.7 + - - +
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Residues in contact with ILE 198 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Y ARG* 6.5 0.2 - - - -
194Z LEU* 3.0 31.2 + - + +
195Z GLN* 3.3 39.7 - - - +
197Z SER* 1.3 76.0 - - - +
199Z SER* 1.3 58.4 + - - +
201Z ILE* 3.4 17.1 + - + +
202Z GLU* 2.9 33.5 + - + +
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Residues in contact with SER 199 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46 GLN* 5.4 8.7 + - - +
178Y LEU* 3.0 32.9 - - - +
195Z GLN* 2.6 26.5 + - - +
196Z GLN 3.6 2.2 - - - -
197Z SER 3.2 0.4 - - - -
198Z ILE* 1.3 80.0 - - - +
200Z GLU* 1.3 55.6 + - - +
202Z GLU* 3.1 6.9 + - - +
203Z GLN* 2.4 40.6 + - - +
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Residues in contact with GLU 200 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Y VAL* 5.2 3.6 - - - +
137Y ILE* 2.9 37.9 - - + +
140Y ALA* 5.1 3.2 - - + +
141Y LEU* 6.1 3.1 - - + -
167Y LEU* 4.2 25.0 - - - +
168Y ILE* 4.8 0.3 - - - -
169Y VAL* 4.3 22.4 + - + +
176Y VAL* 4.5 18.6 - - + +
178Y LEU* 5.2 7.4 - - + +
196Z GLN* 2.8 27.1 + - + +
197Z SER* 3.8 2.6 - - - +
199Z SER* 1.3 72.6 - - - +
201Z ILE* 1.3 59.7 + - - +
203Z GLN* 4.3 6.7 - - - +
204Z LEU* 2.9 36.9 + - + +
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Residues in contact with ILE 201 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Y ARG* 3.7 39.5 - - + +
137Y ILE* 5.3 2.2 - - + -
140Y ALA* 4.9 12.6 - - + -
197Z SER 3.0 18.1 + - - +
198Z ILE* 3.4 22.0 - - + +
200Z GLU* 1.3 76.3 - - - +
202Z GLU* 1.3 69.5 + - - +
205Z LEU* 3.3 43.9 + - + +
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Residues in contact with GLU 202 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198Z ILE* 2.9 21.3 + - + +
199Z SER* 3.1 10.9 + - - +
201Z ILE* 1.3 83.6 - - - +
203Z GLN* 1.3 65.4 + - - +
205Z LEU* 4.6 1.1 - - - +
206Z SER* 2.4 33.4 + - - -
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Residues in contact with GLN 203 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER 4.1 4.6 + - - +
23B ASP* 3.0 48.3 - - - +
24B GLU* 5.1 1.3 - - - -
25B ALA 5.2 7.4 - - - +
176Y VAL* 5.3 13.0 - - + -
178Y LEU* 3.6 24.5 - - + +
199Z SER* 2.4 42.0 + - - +
200Z GLU* 4.0 6.1 - - - +
202Z GLU* 1.3 85.9 - - - +
204Z LEU* 1.3 64.4 + - + +
206Z SER* 3.1 20.2 + - - -
207Z LYS* 4.2 8.0 + - - +
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Residues in contact with LEU 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN* 5.7 3.1 - - - +
140Y ALA* 3.7 8.7 - - + +
141Y LEU* 3.3 55.6 - - + +
143Y ALA 4.8 0.2 - - - -
144Y SER* 3.2 36.1 - - - -
145Y LYS* 4.5 3.3 + - + +
146Y LEU* 3.7 27.1 - - + -
171Y LEU* 6.2 0.2 - - + -
200Z GLU* 2.9 21.7 + - + +
203Z GLN* 1.3 74.6 - - + +
205Z LEU* 1.3 62.9 + - - +
206Z SER 3.4 0.3 + - - -
207Z LYS* 3.8 10.2 + - + +
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Residues in contact with LEU 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140Y ALA* 4.4 20.2 - - + -
143Y ALA* 4.0 22.7 - - + +
201Z ILE* 3.3 43.9 + - + +
202Z GLU* 4.6 1.6 - - - +
203Z GLN 3.3 0.8 - - - -
204Z LEU* 1.3 80.8 - - - +
206Z SER* 1.3 58.7 + - - +
207Z LYS 3.1 10.4 + - - -
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Residues in contact with SER 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202Z GLU* 2.4 24.1 + - - -
203Z GLN* 3.1 13.9 + - - -
205Z LEU* 1.3 76.2 - - - +
207Z LYS* 1.3 76.1 + - - +
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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
------------------------------------------------------------
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