Contacts of the helix formed by residues 174 - 188 (chain A) in PDB entry 1LV2
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 HIS 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU 4.0 6.2 + - - +
173A ALA* 1.3 99.7 + - + +
175A ALA* 1.3 65.8 + - - +
176A GLY 3.0 4.2 + - - +
177A GLU* 3.0 43.0 + - - +
178A HIS* 3.3 10.4 + - - +
243A VAL* 3.8 29.2 + - + +
244A PHE* 4.9 7.6 + - + -
246A ASP* 3.3 39.1 + - + +
248A ASP* 3.5 15.7 + - - -
295A GLN* 6.1 1.3 - - - -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.7 25.2 - - + +
149A LEU* 4.0 8.1 - - + -
171A LEU 3.5 21.6 + - - +
172A ARG 4.5 0.4 + - - -
173A ALA 3.7 1.4 - - - -
174A HIS* 1.3 75.1 - - - +
176A GLY* 1.3 61.2 + - - +
178A HIS* 3.2 19.0 + - - +
179A LEU* 3.2 18.8 + - - +
323A MET* 3.9 21.3 + - + +
324A LEU* 4.2 4.3 - - + -
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A HIS* 3.0 1.8 - - - +
175A ALA* 1.3 79.1 - - - +
177A GLU* 1.3 61.9 + - - +
178A HIS 3.2 0.3 + - - -
179A LEU* 3.2 7.2 + - - +
180A LEU* 3.2 23.6 + - - +
298A THR* 3.8 20.4 - - - -
301A MET* 4.0 9.3 - - - +
302A ILE* 4.9 3.4 - - - +
323A MET 5.3 0.4 + - - -
324A LEU* 3.7 19.7 - - - +
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Residues in contact with GLU 177 (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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173A ALA 4.7 0.5 - - - +
174A HIS* 3.0 45.0 + - - +
176A GLY* 1.3 75.4 + - - +
178A HIS* 1.3 57.9 + - - +
181A LEU* 3.0 34.9 + - - +
243A VAL* 3.9 17.9 - - + +
294A LEU* 3.7 29.6 - - + +
295A GLN* 4.1 18.9 - - - +
298A THR* 3.3 33.0 - - - +
299A TRP* 5.2 3.2 + - - -
302A ILE* 5.9 0.2 - - - +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN 5.4 2.6 + - - -
148A VAL* 6.5 1.1 - - + -
149A LEU* 3.3 42.1 - - + +
152A TRP* 3.8 18.0 - + + -
174A HIS 3.3 7.4 + - - +
175A ALA* 3.2 17.4 + - - +
176A GLY 3.1 0.2 - - - -
177A GLU* 1.3 75.5 - - - +
179A LEU* 1.3 69.3 + - + +
181A LEU* 3.3 9.7 + - + +
182A GLY* 2.9 21.7 + - - -
236A TYR* 5.1 0.8 + - - -
240A LYS* 3.4 52.4 - - + +
243A VAL* 5.3 3.8 - - + +
244A PHE* 4.9 7.4 - + + -
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Residues in contact with LEU 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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142A MET* 4.1 23.1 - - + +
145A GLN* 3.6 35.0 - - + +
146A LEU* 4.0 31.4 - - + -
149A LEU* 6.1 0.4 - - + -
175A ALA 3.2 13.8 + - - +
176A GLY* 3.2 7.4 + - - +
178A HIS* 1.3 81.0 - - + +
180A LEU* 1.3 56.7 + - - +
182A GLY* 3.3 2.1 + - - -
183A ALA* 2.9 30.7 + - - +
301A MET* 4.9 8.1 - - + -
324A LEU* 4.3 23.6 - - + -
328A PLM 3.8 20.4 - - + +
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Residues in contact with LEU 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 GLY 3.2 8.9 + - - +
177A GLU 3.9 1.8 - - - +
179A LEU* 1.3 74.7 - - - +
181A LEU* 1.3 65.0 + - - +
183A ALA* 3.5 4.0 + - + +
184A THR* 2.8 31.2 + - - -
214A VAL* 5.1 0.9 - - + -
218A VAL* 3.7 26.9 - - + +
222A LEU* 4.7 5.2 - - + -
294A LEU* 3.8 19.5 - - + +
297A ILE* 4.2 15.9 - - + +
298A THR* 3.2 42.0 - - - +
301A MET* 4.3 16.8 - - + -
328A PLM 4.2 22.9 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU 3.0 23.9 + - - +
178A HIS* 3.6 9.0 - - + +
180A LEU* 1.3 76.2 - - - +
182A GLY* 1.3 58.1 + - - +
184A THR* 3.2 5.1 + - - -
185A LYS* 2.8 32.6 + - - +
222A LEU* 6.4 1.1 - - + -
226A PHE* 4.1 24.1 - - + -
236A TYR* 3.6 20.1 - - + +
239A LEU* 4.5 15.0 - - + +
240A LYS* 3.9 31.6 - - + +
243A VAL* 4.5 11.4 - - + -
294A LEU* 3.7 28.9 - - + -
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Residues in contact with GLY 182 (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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145A GLN* 6.3 0.7 - - - -
178A HIS 2.9 14.7 + - - -
179A LEU* 3.6 4.0 - - - -
181A LEU* 1.3 76.9 - - - +
183A ALA* 1.3 60.6 + - - +
185A LYS* 3.3 2.3 + - - +
186A ARG* 3.0 37.6 + - - +
236A TYR* 3.4 15.1 + - - -
328A PLM 5.2 1.1 - - - -
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Residues in contact with ALA 183 (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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179A LEU 2.9 19.0 + - - +
180A LEU* 4.1 5.2 - - + +
182A GLY* 1.3 72.1 - - - +
184A THR* 1.3 59.1 + - - +
186A ARG* 3.5 15.7 + - - +
187A SER* 2.6 33.8 + - - +
194A LEU* 5.1 7.3 - - + +
195A LEU 4.6 4.5 - - - +
196A LEU* 5.2 2.9 - - + -
218A VAL* 5.6 4.3 - - + -
328A PLM 4.0 34.3 - - + +
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Residues in contact with THR 184 (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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180A LEU 2.8 23.8 + - - -
181A LEU* 3.6 6.0 - - - -
183A ALA* 1.3 72.9 - - - +
185A LYS* 1.3 61.3 + - - +
187A SER 3.3 1.4 + - - -
188A MET* 2.9 28.9 + - - +
218A VAL* 3.8 9.6 - - - +
222A LEU* 3.6 42.5 - - + +
223A VAL* 3.8 15.8 - - + +
226A PHE* 3.6 34.5 - - + -
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Residues in contact with LYS 185 (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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181A LEU 2.8 16.2 + - - +
182A GLY* 3.6 4.7 - - - +
184A THR* 1.3 77.8 - - - +
186A ARG* 1.3 60.9 + - - +
188A MET* 3.2 31.0 + - - +
189A MET* 4.2 7.1 - - - +
226A PHE* 4.4 8.3 - - + -
231A ILE* 5.2 2.6 + - - -
232A ASP 5.1 1.3 - - - -
233A ASP* 2.7 36.9 + - - +
236A TYR* 3.2 57.2 - - + +
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Residues in contact with ARG 186 (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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145A GLN* 3.8 22.2 + - - +
182A GLY* 3.0 22.6 + - - +
183A ALA* 3.7 15.2 - - - +
185A LYS* 1.3 76.8 - - - +
187A SER* 1.3 58.5 + - - +
188A MET 3.3 0.2 - - - -
189A MET* 2.8 34.6 - - + +
190A TYR* 3.8 5.9 - - - -
195A LEU* 3.0 30.7 + - + +
196A LEU 3.4 14.7 - - - -
197A GLY* 3.3 12.3 - - - +
328A PLM 2.6 43.2 + - - -
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Residues in contact with SER 187 (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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183A ALA* 2.6 23.1 + - - +
184A THR 3.7 2.7 - - - -
186A ARG* 1.3 74.5 - - - +
188A MET* 1.3 63.5 + - - +
189A MET 2.9 8.4 + - - -
190A TYR* 2.9 28.0 + - - +
193A ILE 3.6 21.7 - - - +
194A LEU* 3.5 13.3 - - - +
195A LEU 2.8 27.4 + - - +
223A VAL* 4.5 7.9 - - - +
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Residues in contact with MET 188 (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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184A THR 2.9 13.3 + - - +
185A LYS* 3.2 29.4 + - - +
186A ARG 3.3 0.2 - - - -
187A SER* 1.3 77.7 - - - +
189A MET* 1.3 59.8 + - - +
190A TYR 3.2 0.2 - - - -
191A LYS* 5.3 1.0 + - - -
223A VAL* 4.4 9.4 - - - -
226A PHE* 3.3 40.2 - - + +
227A GLN* 3.1 29.3 + - + +
230A GLN* 4.2 9.4 - - + -
231A ILE* 3.7 37.9 - - - +
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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