Contacts of the helix formed by residues 178 - 193 (chain B) in PDB entry 2KOD
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 SER 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.6 33.0 + - - +
177B ALA* 1.3 75.7 - - - +
179B GLN* 1.3 59.9 + - - +
180B GLU* 3.5 12.9 + - - +
181B VAL* 2.7 36.0 + - - +
182B LYS* 3.4 2.8 + - - +
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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
----------------------------------------------------------
172B LEU* 5.3 3.3 - - - +
177B ALA 3.7 3.1 + - - +
178B SER* 1.3 74.0 + - - +
180B GLU* 1.3 63.7 + - - +
182B LYS* 2.8 55.0 + - - +
183B ASN* 3.1 25.6 + - - +
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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
----------------------------------------------------------
178A SER* 3.7 32.9 - - - +
180A GLU* 4.1 17.7 - - + -
181A VAL* 4.8 6.7 - - + +
178B SER* 3.0 12.5 + - - +
179B GLN* 1.3 79.4 - - - +
181B VAL* 1.3 60.8 + - - +
183B ASN* 3.4 17.6 + - - +
184B TRP* 3.3 20.8 + - - +
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Residues in contact with VAL 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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180A GLU* 4.8 11.9 - - + +
181A VAL* 5.3 5.4 - - - -
184A TRP* 4.2 35.7 - - + -
175B GLU* 5.9 0.2 - - - -
177B ALA* 4.2 13.5 - - + -
178B SER* 2.7 31.1 + - - +
180B GLU* 1.3 73.9 - - - +
182B LYS* 1.3 54.5 - - - +
184B TRP* 3.0 6.3 + - + -
185B MET* 2.4 71.3 + - + +
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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
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169B TYR* 3.4 32.5 - - - -
172B LEU* 3.4 36.5 - - + +
178B SER 3.4 2.9 + - - +
179B GLN* 2.8 45.0 + - - +
181B VAL* 1.3 80.0 - - - +
183B ASN* 1.3 59.6 + - - +
185B MET* 4.5 2.9 - - - -
186B THR* 2.3 54.0 + - - +
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Residues in contact with ASN 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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179B GLN* 3.1 26.0 + - - +
180B GLU* 3.7 23.0 + - - +
181B VAL 3.2 0.2 - - - -
182B LYS* 1.3 79.7 - - - +
184B TRP* 1.3 54.8 + - - +
186B THR* 5.0 0.2 - - - -
187B GLU* 2.6 48.9 - - - +
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Residues in contact with TRP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 5.3 7.2 + - - -
148A THR* 4.4 12.5 - - + -
151A LEU* 5.2 2.0 - - + -
175A GLU* 4.4 10.5 + - - -
176A GLN 5.7 1.3 + - - -
177A ALA* 4.9 9.9 - - + +
181A VAL* 4.3 27.4 - - + +
184A TRP* 4.7 17.0 - + - -
185A MET* 3.1 35.9 - - + -
189A LEU* 4.7 6.5 - - + -
180B GLU 3.3 10.2 + - - +
181B VAL* 3.0 9.5 + - + +
183B ASN* 1.3 79.1 - - - +
185B MET* 1.3 77.4 + - + +
187B GLU* 3.0 6.3 + - - +
188B THR* 2.6 71.6 + - + -
189B LEU* 3.4 25.1 - - + -
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Residues in contact with MET 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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184A TRP* 3.1 44.4 - - + -
150B ILE* 3.6 29.8 - - + -
168B PHE* 4.2 8.5 - - + -
172B LEU* 6.3 0.4 - - - -
175B GLU* 3.6 23.3 - - - +
181B VAL* 2.4 46.0 + - + +
182B LYS* 4.5 1.8 - - - -
184B TRP* 1.3 80.7 - - + +
186B THR* 1.3 57.5 + - - +
187B GLU 2.8 10.8 + - - -
188B THR 2.9 0.2 + - - -
189B LEU* 2.9 42.8 + - + -
190B LEU 3.3 4.9 + - - -
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.8 22.5 - - + -
169B TYR* 3.3 43.3 - - + +
172B LEU* 4.5 0.2 - - - +
182B LYS* 2.3 48.6 + - + +
183B ASN* 4.8 0.7 - - - -
185B MET* 1.3 70.8 - - - +
187B GLU* 1.3 60.1 + - - +
190B LEU* 3.0 36.2 - - + +
211B LEU* 5.0 0.9 - - + -
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Residues in contact with GLU 187 (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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145A TYR* 3.2 31.4 - - + +
146A SER* 3.3 9.3 + - - +
183B ASN* 2.6 35.6 - - - +
184B TRP* 3.0 6.0 + - - +
185B MET 2.8 0.8 - - - -
186B THR* 1.3 85.3 - - + +
188B THR* 1.3 59.3 + - - +
190B LEU* 4.6 3.6 - - - -
191B VAL* 4.5 3.5 - - - +
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Residues in contact with THR 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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145A TYR* 3.7 13.3 - - + -
146A SER* 3.4 28.9 + - - +
147A PRO* 5.1 0.2 - - + -
148A THR* 4.7 0.2 - - + -
151A LEU* 4.1 16.4 - - + -
184B TRP* 2.6 59.0 + - + -
185B MET 2.9 1.0 + - - -
187B GLU* 1.3 79.8 - - - +
189B LEU* 1.3 74.9 + - + +
190B LEU 3.0 4.5 + - - -
191B VAL 3.5 2.6 + - - -
192B GLN* 3.2 20.4 + - - +
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Residues in contact with LEU 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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151A LEU* 5.3 2.0 - - + -
184A TRP* 4.8 7.0 - - + -
189A LEU* 5.3 9.2 - - + -
150B ILE* 4.7 6.3 - - + -
151B LEU* 3.6 32.1 - - + -
164B TYR* 3.1 12.9 + - - -
168B PHE* 4.6 7.3 - - + -
184B TRP* 3.4 34.8 - - + -
185B MET* 2.9 31.7 + - + +
188B THR* 1.3 78.6 - - + +
190B LEU* 1.3 63.7 + - - +
191B VAL 3.3 0.2 - - - -
192B GLN* 3.7 24.9 - - - +
193B ASN* 3.3 23.1 + - - +
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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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161B PHE* 3.9 18.9 - - + -
164B TYR* 3.1 39.9 + - + -
165B VAL* 4.9 3.4 - - - -
168B PHE* 3.5 42.1 - - + -
169B TYR* 4.7 4.9 - - + -
185B MET 3.3 3.6 + - - -
186B THR* 3.0 35.9 - - + +
187B GLU* 4.2 0.7 - - - +
188B THR 3.0 0.6 - - - -
189B LEU* 1.3 78.7 - - - +
191B VAL* 1.3 64.5 + - + +
194B ALA* 3.9 6.2 + - - +
211B LEU* 4.0 23.3 - - + -
214B MET* 4.2 13.9 - - + -
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Residues in contact with VAL 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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145A TYR* 3.5 48.4 + - + -
161B PHE* 5.4 1.1 - - + -
187B GLU 4.5 5.8 - - - +
188B THR 3.5 1.6 + - - -
190B LEU* 1.3 88.7 - - + +
192B GLN* 1.3 64.1 + - - +
193B ASN 3.7 0.2 - - - -
194B ALA* 3.4 15.2 - - + +
199B LYS* 4.0 36.2 + - + +
202B LEU* 4.5 20.9 - - + -
203B LYS* 5.2 0.7 - - + -
214B MET* 4.5 20.6 - - + -
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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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145A TYR* 4.4 10.7 + - + +
151A LEU* 3.3 41.3 - - - +
151B LEU* 5.7 2.4 - - - +
188B THR* 3.2 17.1 + - + +
189B LEU* 3.7 26.8 - - - +
190B LEU 3.4 0.4 - - - -
191B VAL* 1.3 76.9 - - - +
193B ASN* 1.3 70.5 + - - +
194B ALA 2.9 14.5 + - - +
199B LYS* 4.7 8.7 + - - +
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Residues in contact with ASN 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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150B ILE* 4.0 9.1 + - - +
151B LEU* 3.9 27.7 + - - +
153B ILE 3.1 26.7 + - - +
154B ARG* 2.8 35.9 + - + +
155B GLN 3.2 7.6 + - - -
164B TYR* 3.6 15.1 + - - +
168B PHE* 6.1 0.6 - - - -
189B LEU* 3.3 15.6 + - - +
192B GLN* 1.3 90.8 + - - +
194B ALA* 1.3 64.3 + - - +
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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