Contacts of the helix formed by residues 167 - 181 (chain B) in PDB entry 1ML3
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 THR 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B SER* 3.3 2.7 - - - -
166B CYS* 1.3 75.3 - - - +
168B THR* 1.3 60.5 + - - +
170B CYS* 2.8 18.4 + - - +
171B LEU* 2.9 13.2 + - - +
190B MET* 3.4 24.0 - - + -
192B THR* 4.5 9.2 - - + +
194B HIS* 4.2 5.5 + - - -
226B THR* 5.1 2.8 + - - +
228B ALA* 3.3 24.9 - - + -
258B VAL* 4.2 6.5 - - + -
333B TYR* 3.1 26.6 + - - +
1166B CYX 3.4 18.8 - - - +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.4 7.4 - - + -
164B ALA* 4.1 19.0 - - + +
165B SER* 3.1 17.7 + - - -
167B THR* 1.3 78.6 - - - +
169B ASN* 1.3 57.8 + - - +
171B LEU* 4.5 4.3 - - - +
172B ALA* 2.9 42.9 + - + +
228B ALA* 3.1 30.6 + - - +
231B ALA* 3.5 12.3 - - + +
232B VAL* 4.0 24.9 - - + +
235B VAL* 4.7 2.7 - - + -
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Residues in contact with ASN 169 (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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145B VAL* 3.5 25.1 - - - +
146B MET 4.5 2.8 + - - +
163B ASN* 2.9 30.3 + - - +
164B ALA* 4.1 2.8 - - - +
165B SER 2.9 18.9 + - - +
166B CYS* 3.1 12.9 + - - +
167B THR 3.1 0.8 - - - -
168B THR* 1.3 77.1 - - - +
170B CYS* 1.3 55.8 + - - +
173B PRO* 3.0 18.8 - - - +
288B ILE* 6.0 0.2 - - - +
307B SER* 3.1 29.1 + - - +
339B TYR* 3.4 18.7 - - + -
342B ARG* 3.9 21.6 - - + +
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Residues in contact with CYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B CYS 3.2 3.6 + - - +
167B THR 2.8 9.0 + - - +
169B ASN* 1.3 79.3 - - - +
171B LEU* 1.3 64.5 + - - +
172B ALA 3.5 0.2 - - - -
173B PRO* 3.5 4.0 - - - +
174B ILE* 3.5 6.4 - - - +
258B VAL* 3.6 20.9 - - + -
307B SER 3.3 12.1 - - - +
308B SER* 2.9 34.1 + - - -
331B SER* 3.6 15.3 - - - -
332B TRP 3.9 4.9 - - - -
333B TYR* 3.4 36.6 - - + -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR 2.9 13.3 + - - +
168B THR* 4.6 0.7 - - - -
170B CYS* 1.3 77.3 - - - +
172B ALA* 1.3 67.7 + - - +
174B ILE* 2.8 18.1 + - + +
175B VAL* 2.9 30.7 + - + +
190B MET* 3.4 38.4 - - + -
229B ALA* 3.9 11.2 - - + -
232B VAL* 3.5 26.7 - - + -
243B LEU* 4.4 10.8 - - + -
258B VAL* 4.4 9.6 - - + +
260B LEU* 3.9 28.0 - - + -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.0 10.3 - - + -
148B VAL* 3.9 20.9 - - + -
168B THR* 2.9 33.0 + - + +
171B LEU* 1.3 73.6 - - - +
173B PRO* 1.3 58.3 - - + +
175B VAL* 3.7 0.7 - - - +
176B HIS* 2.7 37.1 + - - +
232B VAL* 4.3 19.6 - - + +
235B VAL* 4.8 3.1 - - + -
236B ILE* 3.9 1.5 - - + +
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Residues in contact with PRO 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.8 2.2 - - + -
148B VAL* 4.1 10.5 - - + -
169B ASN* 3.0 29.8 - - - +
170B CYS 3.5 8.7 - - - +
172B ALA* 1.3 92.5 - - + +
174B ILE* 1.3 62.5 + - - +
176B HIS* 3.4 1.8 + - + +
177B VAL* 3.1 30.5 + - - +
285B MET* 3.7 20.8 - - + +
288B ILE* 3.9 23.1 - - + -
289B LEU* 4.5 7.9 - - + -
307B SER* 4.4 2.5 - - - -
308B SER* 4.3 9.9 - - - -
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B CYS 3.5 15.9 - - - +
171B LEU* 2.8 17.5 + - + +
173B PRO* 1.3 71.8 - - - +
175B VAL* 1.3 62.0 + - - +
177B VAL* 3.3 4.7 + - - +
178B LEU* 3.1 28.1 + - + +
258B VAL* 6.0 2.7 - - + -
260B LEU* 4.1 23.1 - - + -
277B LEU* 4.0 22.9 - - + +
289B LEU* 3.8 20.0 - - + -
308B SER* 3.6 14.4 - - - +
310B TYR* 4.6 3.6 - - + -
329B ILE* 4.1 19.7 - - + -
331B SER* 4.0 18.8 - - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 2.9 39.3 + - + +
172B ALA 3.8 4.9 - - - +
174B ILE* 1.3 75.4 - - - +
176B HIS* 1.3 58.1 + - - +
178B LEU* 3.0 10.6 + - + +
179B VAL* 2.8 30.9 + - + +
185B VAL* 4.0 15.9 - - + -
232B VAL* 4.5 4.9 - - + -
236B ILE* 3.8 16.4 - - + -
239B THR* 3.9 24.0 - - + -
243B LEU* 4.0 17.9 - - + -
260B LEU* 4.5 9.0 - - + -
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Residues in contact with HIS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLY 3.3 26.0 + - - -
148B VAL* 3.6 30.1 + - + -
172B ALA 2.7 21.3 + - - +
173B PRO* 3.5 7.4 - - + +
174B ILE 3.2 0.2 - - - -
175B VAL* 1.3 73.1 - - - +
177B VAL* 1.3 51.4 + - - +
179B VAL* 3.5 5.7 + - + +
180B LYS* 2.7 65.8 + - + +
236B ILE* 3.6 18.9 - - + +
284B TYR* 4.8 2.8 - + - -
285B MET* 3.9 14.1 - - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO 3.1 15.4 + - - +
174B ILE 3.8 0.4 - - - +
176B HIS* 1.3 73.1 - - - +
178B LEU* 1.3 61.9 - - + +
180B LYS* 4.5 0.2 - - - -
181B GLU* 2.9 46.3 + - + +
183B PHE* 5.4 1.1 - - + -
276B ALA* 4.2 3.4 - - + +
277B LEU* 3.7 32.5 - - + +
280B ALA* 3.9 16.2 - - + -
284B TYR* 3.9 11.7 - - + +
285B MET* 3.8 28.5 - - + -
289B LEU* 4.0 10.8 - - + -
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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
----------------------------------------------------------
174B ILE* 3.1 18.7 + - + +
175B VAL* 3.0 14.2 + - - +
177B VAL* 1.3 80.0 - - + +
179B VAL* 1.3 59.3 + - - +
182B GLY 3.6 0.5 + - - -
183B PHE* 3.0 36.4 + - + +
184B GLY 3.0 22.0 + - - +
185B VAL* 4.2 18.2 - - + -
260B LEU* 4.3 12.8 - - + -
262B PHE* 3.6 44.6 - - + -
273B ILE* 4.1 11.2 - - + -
277B LEU* 5.7 3.6 - - + -
329B ILE* 4.1 17.3 - - + -
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Residues in contact with VAL 179 (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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175B VAL* 2.8 29.2 + - + +
176B HIS* 3.9 7.6 - - + +
178B LEU* 1.3 76.6 - - - +
180B LYS* 1.3 67.1 + - + +
182B GLY* 3.2 13.0 + - - -
184B GLY* 4.3 12.1 + - - +
185B VAL* 4.5 12.8 - - + +
236B ILE* 4.6 11.7 - - + -
238B SER* 4.5 19.7 - - - +
239B THR* 4.7 3.1 - - + -
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Residues in contact with LYS 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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176B HIS* 2.7 44.2 + - + +
177B VAL 4.3 0.2 - - - +
179B VAL* 1.3 75.7 - - - +
181B GLU* 1.3 62.3 + - - +
182B GLY 3.3 0.8 + - - -
284B TYR* 3.5 55.5 - - + +
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Residues in contact with GLU 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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177B VAL* 2.9 33.2 + - + +
180B LYS* 1.3 78.2 + - - +
182B GLY* 1.3 59.3 + - - +
183B PHE* 3.5 21.1 + - + -
266B ARG* 4.1 10.4 + - - -
276B ALA* 4.1 6.3 - - + -
279B ARG* 2.6 36.4 + - - -
280B ALA* 4.6 1.7 - - - +
284B TYR* 2.6 37.4 + - - +
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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