Contacts of the helix formed by residues 170 - 186 (chain B) in PDB entry 6JKG
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 ASP 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PRO 3.5 11.8 - - - +
169B ILE* 1.3 91.6 - - - +
171B TYR* 1.3 64.6 + - - +
172B TYR* 3.5 10.3 - - + +
173B THR* 3.6 10.7 + - - +
174B GLU* 3.2 10.9 + - - +
209B PRO* 5.2 15.6 - - + +
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Residues in contact with TYR 171 (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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113B ASN 6.1 1.3 - - - +
114B LYS* 3.1 67.7 + - + +
117B PHE* 4.3 12.3 - + + -
118B TYR* 3.8 14.3 - - - -
170B ASP* 1.3 71.5 - - - +
172B TYR* 1.3 68.6 + - - +
173B THR 3.0 2.0 - - - -
174B GLU* 2.9 49.2 + - + +
175B THR* 3.1 32.8 + - + +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER* 3.7 24.7 + - - -
107B PRO* 5.2 8.3 - - + -
117B PHE* 4.4 37.9 - + + -
121B ASN* 3.2 26.7 - - - -
145B SER* 5.6 5.8 - - - -
170B ASP* 3.5 6.8 - - + +
171B TYR* 1.3 77.0 - - - +
173B THR* 1.3 64.7 + - - +
175B THR* 2.7 21.6 + - - -
176B LYS* 3.1 44.7 + - + +
203B ILE* 5.2 12.9 - - + +
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 4.6 2.9 - - - +
147B SER* 3.5 43.0 + - - +
148B VAL* 4.0 14.6 - - + +
169B ILE* 3.7 25.2 - - + +
170B ASP* 3.6 11.8 + - - +
171B TYR 3.0 0.8 - - - -
172B TYR* 1.3 82.0 - - - +
174B GLU* 1.3 65.9 + - - +
175B THR 3.1 1.6 - - - -
176B LYS* 3.1 14.1 + - + +
177B ILE* 3.2 17.1 + - + +
209B PRO* 5.3 4.9 - - - +
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Residues in contact with GLU 174 (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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169B ILE* 4.1 14.2 - - + +
170B ASP 3.2 19.2 + - - +
171B TYR* 2.9 49.4 + - + +
173B THR* 1.3 76.6 - - - +
175B THR* 1.3 55.6 + - - +
177B ILE* 3.1 26.6 - - + +
178B LEU* 3.4 17.5 - - + +
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Residues in contact with THR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.8 23.1 + - + +
118B TYR* 4.2 11.4 - - + -
121B ASN* 3.3 25.6 + - - +
122B TYR* 5.1 2.0 + - - -
171B TYR* 3.1 40.8 + - + +
172B TYR* 2.7 21.8 + - - -
174B GLU* 1.3 78.3 - - - +
176B LYS* 1.3 58.8 + - - +
177B ILE 3.4 0.7 - - - -
178B LEU* 3.9 10.3 - - + +
179B GLN* 3.0 28.1 + - - +
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Residues in contact with LYS 176 (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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105B ALA 5.1 5.1 + - - -
106B SER* 5.3 1.4 - - - -
121B ASN* 3.7 16.7 + - - +
143B THR 3.0 26.3 + - - -
144B SER* 3.5 33.5 + - - +
145B SER* 3.9 8.7 - - - +
148B VAL* 3.9 11.9 - - + -
172B TYR* 3.1 52.3 + - + +
173B THR* 3.1 11.4 + - + +
175B THR* 1.3 76.7 - - - +
177B ILE* 1.3 59.9 + - - +
179B GLN* 3.6 19.6 + - - +
180B GLU* 3.0 28.8 + - - +
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Residues in contact with ILE 177 (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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148B VAL* 3.7 35.0 - - + +
150B PHE 5.8 1.6 - - - +
151B GLU 5.8 3.6 - - - +
169B ILE* 5.9 3.8 - - + -
173B THR* 3.2 13.4 + - + +
174B GLU* 3.1 21.8 - - + +
176B LYS* 1.3 74.3 - - - +
178B LEU* 1.3 79.5 + - + +
180B GLU* 3.2 5.6 + - - +
181B ARG* 2.9 69.7 + - - +
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Residues in contact with LEU 178 (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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118B TYR* 3.9 30.3 - - + -
122B TYR* 3.9 29.3 - - + +
171B TYR* 5.7 1.6 - - + +
174B GLU* 3.4 20.4 + - + +
175B THR* 3.9 11.9 - - + +
177B ILE* 1.3 88.6 - - + +
179B GLN* 1.3 63.2 + - - +
181B ARG* 3.8 11.4 - - - +
182B ALA* 3.1 23.7 + - - +
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Residues in contact with GLN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 3.5 13.5 + - - -
105B ALA 5.1 1.6 + - - -
121B ASN* 3.2 48.6 + - - +
122B TYR* 4.6 2.4 - - - -
125B THR* 3.2 20.3 + - + +
142B LEU* 2.8 37.7 - - + +
143B THR 5.0 0.6 + - - -
175B THR 3.0 16.3 + - - +
176B LYS* 3.6 24.7 + - - +
177B ILE 3.2 0.2 - - - -
178B LEU* 1.3 75.2 - - - +
180B GLU* 1.3 62.7 + - - +
182B ALA* 3.2 9.7 - - - +
183B VAL* 2.9 24.3 + - - +
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Residues in contact with GLU 180 (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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142B LEU* 3.5 15.2 - - + +
144B SER* 3.2 23.1 + - - +
148B VAL* 3.9 7.5 - - - +
176B LYS 3.0 18.6 + - - +
177B ILE* 3.7 4.7 - - - +
179B GLN* 1.3 75.2 - - - +
181B ARG* 1.3 53.9 + - + +
183B VAL* 3.1 2.3 + - - +
184B LEU* 2.5 50.7 + - + +
197B ALA* 3.7 17.4 - - + +
199B ARG* 2.6 46.6 + - - +
264B ALA* 3.8 8.8 - - - +
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Residues in contact with ARG 181 (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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151B GLU 5.3 9.9 + - - -
177B ILE* 2.9 59.4 + - - +
178B LEU* 3.8 11.9 - - - +
180B GLU* 1.3 72.3 - - + +
182B ALA* 1.3 54.1 + - - +
184B LEU* 2.9 6.1 + - - +
185B GLY* 2.4 37.9 + - - -
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Residues in contact with ALA 182 (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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122B TYR* 4.5 14.6 - - + -
125B THR* 4.9 3.6 - - + -
126B LYS* 4.7 13.0 - - + -
129B ILE* 3.9 17.3 - - + +
178B LEU 3.1 11.5 + - - +
179B GLN* 3.2 11.9 - - - +
181B ARG* 1.3 79.2 - - - +
183B VAL* 1.3 64.8 + - - +
185B GLY* 3.2 1.5 + - - -
186B ALA* 3.0 22.5 + - - +
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Residues in contact with VAL 183 (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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103B HIS* 5.7 0.2 - - - +
125B THR* 3.6 24.7 - - + -
129B ILE* 4.0 11.0 - - + -
140B LEU* 4.4 16.4 - - + +
142B LEU* 3.8 39.9 - - + -
179B GLN 2.9 19.6 + - - +
180B GLU 3.5 5.8 - - - +
182B ALA* 1.3 74.0 - - - +
184B LEU* 1.3 64.6 + - + +
186B ALA* 3.4 6.7 + - - +
195B THR* 2.6 40.8 + - - +
196B THR 4.1 10.1 - - - +
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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
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180B GLU* 2.5 45.1 + - + +
181B ARG* 3.7 4.7 - - - +
183B VAL* 1.3 72.2 - - + +
185B GLY* 1.3 65.5 + - - +
186B ALA 3.2 0.7 + - - -
187B ASN* 3.2 19.1 + - - +
195B THR* 3.8 7.9 - - - +
196B THR* 4.3 2.2 - - - -
197B ALA* 3.9 25.6 - - + +
262B GLY* 3.2 41.4 - - - +
263B LYS 3.8 2.7 - - - +
264B ALA* 3.7 18.4 - - + +
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Residues in contact with GLY 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 ARG 2.4 25.9 + - - -
182B ALA* 3.6 2.7 - - - -
184B LEU* 1.3 69.6 - - - +
186B ALA* 1.3 58.5 + - - +
187B ASN 3.2 6.1 + - - +
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Residues in contact with ALA 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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129B ILE* 3.7 31.0 - - + -
133B LYS* 5.7 1.6 + - + +
182B ALA 3.0 15.4 + - - +
183B VAL* 3.8 6.1 - - - +
184B LEU 3.1 1.0 - - - -
185B GLY* 1.3 72.7 - - - +
187B ASN* 1.3 66.9 + - - +
188B ASP* 3.2 12.5 + - - +
193B PHE* 3.7 12.6 - - + -
195B THR* 4.0 8.3 - - + -
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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