Contacts of the helix formed by residues 162 - 179 (chain A) in PDB entry 6EVL
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ALA* 3.0 18.9 + - + +
158A TYR 4.3 0.2 + - - -
160A GLU* 3.2 9.6 - - + +
161A GLY* 1.3 73.2 - - - +
163A TYR* 1.3 60.8 + - - +
164A TYR* 3.5 7.4 + - - +
165A HIS* 2.5 47.7 + - - +
166A THR* 2.9 25.0 + - - -
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Residues in contact with TYR 163 (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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158A TYR* 3.4 46.9 + + - -
161A GLY* 3.3 32.1 + - - -
162A ASP* 1.3 71.6 + - - +
164A TYR* 1.3 66.9 + - - +
166A THR* 3.3 6.0 + - - -
167A VAL* 3.0 26.0 + - - +
197A ALA* 3.7 20.8 - - - +
200A GLN* 3.5 42.7 + - + +
201A LEU* 3.9 10.3 - - + -
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Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.3 7.0 + - - +
163A TYR* 1.3 78.2 - - - +
165A HIS* 1.3 79.7 + + + +
167A VAL* 3.1 10.9 + - + +
168A LEU* 3.1 56.6 + - + +
201A LEU* 3.8 29.7 - - + +
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Residues in contact with HIS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA* 4.0 10.3 - - + -
162A ASP* 2.5 38.4 + - - +
164A TYR* 1.3 85.7 - + - +
166A THR* 1.3 66.3 + - - +
168A LEU* 3.2 25.2 + - + +
169A TRP* 3.0 40.7 + - + +
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Residues in contact with THR 166 (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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154A GLY* 4.0 13.7 - - - +
157A ALA* 3.7 5.3 - - - +
158A TYR* 3.1 38.7 + - + +
162A ASP 2.9 20.8 + - - -
163A TYR* 3.3 11.6 - - - -
165A HIS* 1.3 76.4 - - - +
167A VAL* 1.3 55.3 + - - +
169A TRP* 3.4 0.9 + - - +
170A MET* 2.9 47.6 + - + +
193A TYR* 4.1 8.5 - - + +
194A LEU* 5.2 0.2 - - - -
197A ALA* 3.6 21.1 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR 3.0 19.7 + - - +
164A TYR* 3.1 11.6 + - + +
166A THR* 1.3 74.0 - - - +
168A LEU* 1.3 66.1 + - + +
171A GLU* 2.8 55.3 + - + +
194A LEU* 3.7 17.5 - - + -
197A ALA* 3.8 14.4 - - + -
198A VAL* 4.0 16.2 - - + -
201A LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.1 54.1 + - + +
165A HIS* 3.2 23.3 + - + +
167A VAL* 1.3 84.6 - - + +
169A TRP* 1.3 63.8 + - + +
171A GLU* 4.0 4.6 - - + +
172A GLN* 3.3 19.8 + - - +
302A DMS 3.8 27.8 - - + +
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Residues in contact with TRP 169 (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 LEU* 3.6 33.0 - - + -
150A CYS* 3.6 23.6 - - - +
153A MET* 3.4 49.9 + - + +
154A GLY* 3.5 20.4 - - - +
157A ALA* 4.6 1.9 - - + +
165A HIS* 3.0 40.3 + - + +
168A LEU* 1.3 77.1 - - + +
170A MET* 1.3 62.7 + - - +
172A GLN* 3.0 5.4 + - - +
173A VAL* 3.0 25.7 + - - +
302A DMS 3.5 42.5 - - + +
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Residues in contact with MET 170 (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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151A PHE* 3.6 43.3 - - + +
154A GLY* 3.6 9.0 - - - +
155A ARG* 3.6 28.0 - - + +
166A THR* 2.9 30.6 + - + +
169A TRP* 1.3 77.4 - - - +
171A GLU* 1.3 63.8 + - - +
173A VAL* 3.2 8.4 + - - +
174A LEU* 3.0 21.2 + - - +
190A VAL* 3.5 23.7 - - + +
193A TYR* 3.7 28.5 - - + -
194A LEU* 3.9 19.3 - - + +
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Residues in contact with GLU 171 (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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167A VAL* 2.8 41.0 + - + +
168A LEU* 4.0 5.2 - - + +
170A MET* 1.3 73.4 - - - +
172A GLN* 1.3 61.2 + - - +
174A LEU* 3.3 11.6 + - - +
175A LYS* 3.1 41.2 + - - +
194A LEU* 3.8 17.0 - - + +
198A VAL* 5.4 1.6 - - - +
206A ARG* 3.0 32.9 + - - -
301A SO4 5.1 0.9 + - - -
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Residues in contact with GLN 172 (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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144A MET 6.0 1.2 - - - +
150A CYS* 4.1 10.8 - - - -
168A LEU 3.3 10.9 + - - +
169A TRP* 3.0 10.3 + - - +
171A GLU* 1.3 77.9 - - - +
173A VAL* 1.3 62.6 + - - +
175A LYS* 3.1 16.7 + - - +
176A GLN* 2.9 58.3 + - - +
302A DMS 3.8 31.6 - - + +
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Residues in contact with VAL 173 (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 VAL* 3.6 24.4 - - + +
150A CYS* 3.6 12.1 - - + -
151A PHE* 3.5 37.2 - - + +
169A TRP 3.0 16.2 + - - +
170A MET* 3.2 10.1 + - - +
172A GLN* 1.3 76.2 - - - +
174A LEU* 1.3 56.9 + - - +
176A GLN* 3.2 4.1 + - - +
177A LEU* 2.8 33.5 + - + +
185A THR* 5.0 1.6 - - + -
190A VAL* 3.5 29.8 - - + -
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Residues in contact with LEU 174 (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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170A MET 3.0 14.5 + - - +
171A GLU* 3.6 14.8 - - - +
173A VAL* 1.3 75.6 - - - +
175A LYS* 1.3 70.6 + - - +
177A LEU* 3.9 4.3 - - + +
178A ASP* 3.0 34.1 + - - +
187A LYS* 3.9 37.9 - - + +
190A VAL* 3.9 20.4 - - + -
191A LEU* 4.3 15.5 - - + -
194A LEU* 3.9 25.1 - - + -
206A ARG* 4.8 1.6 - - - +
210A LEU* 5.2 0.2 - - + -
213A ARG* 4.9 4.3 - - - +
301A SO4 4.5 16.2 - - - +
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Residues in contact with LYS 175 (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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171A GLU* 3.1 31.7 + - - +
172A GLN* 3.1 23.5 + - - +
174A LEU* 1.3 82.6 - - - +
176A GLN* 1.3 57.9 + - + +
178A ASP* 3.3 15.0 + - + +
179A ALA* 2.9 27.5 + - - +
301A SO4 4.6 16.8 + - - -
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Residues in contact with GLN 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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144A MET 5.3 4.1 + - - -
145A LEU 3.3 25.7 + - - +
146A SER 4.0 0.2 - - - -
147A VAL* 3.5 24.1 - - + +
150A CYS* 3.9 6.9 - - - -
172A GLN* 2.9 50.3 + - - +
173A VAL* 4.0 1.8 - - - +
175A LYS* 1.3 75.6 - - + +
177A LEU* 1.3 66.1 + - - +
179A ALA* 3.2 11.2 + - - +
181A GLU* 2.9 64.2 + - - +
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Residues in contact with LEU 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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147A VAL* 3.9 19.5 - - + +
173A VAL* 2.8 33.3 + - + +
174A LEU* 3.9 5.6 - - + +
176A GLN* 1.3 76.1 - - - +
178A ASP* 1.3 60.5 + - - +
180A GLY* 2.9 22.3 + - - -
181A GLU 4.2 11.7 - - - +
183A ALA* 4.0 9.4 - - + +
185A THR 3.8 17.7 - - - +
186A THR* 4.2 2.0 - - - -
187A LYS* 3.9 43.1 - - + +
190A VAL* 4.2 5.8 - - + -
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Residues in contact with ASP 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 LEU* 3.0 23.9 + - - +
175A LYS* 3.6 15.6 + - + +
177A LEU* 1.3 70.7 - - - +
179A ALA* 1.3 57.3 + - - +
180A GLY* 3.0 9.8 + - - -
187A LYS* 2.5 33.3 + - - -
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Residues in contact with ALA 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 LYS 2.9 16.5 + - - +
176A GLN* 3.6 9.6 - - - +
177A LEU 3.2 0.8 - - - -
178A ASP* 1.3 74.4 - - - +
180A GLY* 1.3 59.9 + - - +
181A GLU* 3.2 10.2 + - + +
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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