Contacts of the helix formed by residues 167 - 181 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.2 3.2 + - - -
166A CYS* 1.3 78.3 - - - +
168A THR* 1.3 64.7 + - - +
170A CYS* 2.9 4.2 + - - +
171A LEU* 2.9 20.4 + - - +
190A MET* 3.7 26.7 - - + -
192A THR* 4.5 6.5 - - + +
194A HIS* 3.8 14.2 + - - -
226A THR* 5.4 1.3 - - - +
228A ALA* 3.5 25.4 - - + -
258A VAL* 4.6 3.1 - - + -
333A TYR* 2.8 32.5 + - + +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 6.2 0.2 - - + -
145A VAL* 4.5 6.7 - - + -
164A ALA* 4.2 17.3 - - + -
165A SER* 3.2 17.5 + - - -
167A THR* 1.3 78.1 - - - +
169A ASN* 1.3 57.0 + - - +
170A CYS 3.0 0.2 - - - -
171A LEU* 4.4 3.8 - - - +
172A ALA* 2.8 43.2 + - + +
228A ALA* 2.9 39.1 + - - +
231A ALA* 3.7 17.7 - - + +
232A VAL* 4.1 14.6 - - + +
235A VAL* 5.1 2.5 - - + -
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.3 28.2 - - - +
146A MET 4.4 2.4 + - - +
163A ASN* 2.9 29.8 + - - +
164A ALA* 4.0 4.8 - - - +
165A SER 3.0 23.6 + - - +
166A CYS* 3.6 9.9 - - - +
167A THR 3.1 0.2 - - - -
168A THR* 1.3 75.9 - - - +
170A CYS* 1.3 57.0 + - - +
173A PRO* 3.1 24.6 - - - +
307A SER* 3.1 23.9 + - - +
339A TYR* 3.5 16.0 - - + -
342A ARG* 3.9 20.0 - - + +
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Residues in contact with CYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS 3.4 3.9 + - - +
167A THR 2.9 10.2 + - - +
169A ASN* 1.3 80.0 - - - +
171A LEU* 1.3 64.2 + - - +
173A PRO* 3.5 3.1 - - - +
174A ILE* 3.7 6.1 - - - +
258A VAL* 3.2 26.2 - - + -
307A SER 3.5 7.9 - - - +
308A SER* 2.9 33.0 + - - -
331A SER* 3.6 12.8 - - - -
332A TRP 3.8 1.6 - - - -
333A TYR* 3.3 40.8 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR 2.9 12.9 + - - +
168A THR* 4.1 3.4 - - - +
170A CYS* 1.3 77.0 - - - +
172A ALA* 1.3 66.0 + - - +
174A ILE* 2.8 19.4 + - + +
175A VAL* 3.1 30.0 + - + -
190A MET* 4.1 28.9 - - + -
229A ALA* 4.0 20.2 - - + +
232A VAL* 3.6 24.0 - - + -
243A LEU* 4.7 6.7 - - + -
258A VAL* 4.4 12.5 - - + +
260A LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.3 9.6 - - + -
148A VAL* 4.1 21.1 - - + -
168A THR* 2.8 28.5 + - + +
171A LEU* 1.3 73.2 - - - +
173A PRO* 1.3 56.4 - - + +
175A VAL* 3.1 1.8 + - - +
176A HIS* 2.6 36.4 + - - +
232A VAL* 4.0 25.4 - - + +
235A VAL* 5.0 3.6 - - + -
236A ILE* 4.0 2.1 - - + +
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.8 2.0 - - + -
148A VAL* 4.1 11.0 - - + -
169A ASN* 3.1 29.8 - - - +
170A CYS 3.5 9.4 - - - +
172A ALA* 1.3 95.6 - - + +
174A ILE* 1.3 60.1 + - - +
176A HIS* 3.9 1.5 - - + +
177A VAL* 3.1 29.1 + - - +
285A MET* 3.8 22.1 - - + +
288A ILE* 4.0 20.4 - - + -
289A LEU* 4.5 8.4 - - + +
307A SER* 4.6 0.2 - - - -
308A SER* 4.3 11.9 - - - -
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Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A CYS 3.7 15.9 - - - +
171A LEU* 2.8 18.3 + - + +
173A PRO* 1.3 69.8 - - - +
175A VAL* 1.3 67.4 + - - +
177A VAL* 3.2 6.1 + - - +
178A LEU* 3.1 25.8 + - + +
258A VAL* 5.9 2.9 - - + -
260A LEU* 4.2 13.9 - - + -
277A LEU* 4.0 19.9 - - + +
289A LEU* 3.8 18.6 - - + -
308A SER* 3.8 14.4 - - - +
310A TYR* 4.7 6.5 - - + -
329A ILE* 4.0 36.8 - - + -
331A SER* 4.0 17.5 - - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.1 31.9 + - + +
172A ALA 3.7 4.7 - - - +
174A ILE* 1.3 75.9 - - - +
176A HIS* 1.3 57.6 + - - +
178A LEU* 3.0 10.0 + - + +
179A VAL* 2.9 34.0 + - + +
185A VAL* 4.2 11.4 - - + -
232A VAL* 4.2 12.1 - - + -
236A ILE* 4.2 7.4 - - + -
239A THR* 3.8 28.9 - - + -
243A LEU* 4.1 17.7 - - + -
260A LEU* 4.3 10.3 - - + -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLY 3.8 13.2 + - - -
148A VAL* 3.3 42.8 + - + -
172A ALA 2.6 21.5 + - - +
173A PRO* 3.9 4.5 - - + +
175A VAL* 1.3 73.4 - - - +
177A VAL* 1.3 57.4 + - - +
179A VAL* 4.0 3.2 - - + +
180A LYS* 3.0 63.3 + - + +
236A ILE* 3.7 19.6 - - + +
284A TYR* 4.6 2.5 - + - -
285A MET* 3.9 20.4 - - - -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PRO 3.1 15.5 + - - +
174A ILE 3.2 7.7 + - - +
175A VAL 3.1 0.4 - - - -
176A HIS* 1.3 77.2 - - - +
178A LEU* 1.3 62.0 + - + +
180A LYS* 4.5 0.7 - - - -
181A GLU* 2.8 46.0 + - + +
276A ALA* 3.9 21.5 - - + +
277A LEU* 4.0 15.9 - - + -
280A ALA* 3.8 20.2 - - + -
284A TYR* 3.7 18.4 - - + +
285A MET* 3.9 15.5 - - + -
289A LEU* 3.9 9.9 - - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.1 18.6 + - + +
175A VAL* 3.0 14.6 + - - +
177A VAL* 1.3 80.5 - - + +
179A VAL* 1.3 59.2 + - - +
182A GLY 3.4 2.1 + - - -
183A PHE* 2.9 41.0 + - + -
184A GLY 2.8 21.7 + - - +
185A VAL* 4.4 16.2 - - + -
260A LEU* 4.5 4.9 - - + -
262A PHE* 3.8 32.8 - - + -
273A ILE* 4.2 23.3 - - + -
276A ALA* 6.2 0.4 - - + -
277A LEU* 5.2 6.3 - - + -
329A ILE* 4.0 13.9 - - + -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 2.9 33.9 + - + +
176A HIS* 4.3 2.9 - - + +
178A LEU* 1.3 78.8 - - - +
180A LYS* 1.3 62.0 + - - +
182A GLY* 3.7 8.3 + - - -
184A GLY* 4.3 7.5 + - - +
185A VAL* 4.4 15.3 - - + +
236A ILE* 4.5 10.8 - - + -
238A SER* 3.7 20.2 - - - +
239A THR* 4.2 15.3 - - + -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A HIS* 3.0 46.2 + - + +
177A VAL* 4.0 3.4 - - - +
179A VAL* 1.3 79.7 - - - +
181A GLU* 1.3 61.5 + - - +
182A GLY* 3.2 1.2 + - - -
284A TYR* 3.3 43.8 - - + +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 2.8 34.8 + - + +
180A LYS* 1.3 78.7 - - - +
182A GLY* 1.3 60.2 + - - +
183A PHE* 3.5 23.2 + - + -
266A ARG* 4.6 6.9 + - - -
276A ALA* 4.0 7.5 - - + +
279A ARG* 2.5 37.6 + - - +
284A TYR* 2.6 36.3 + - - +
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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