Contacts of the helix formed by residues 178 - 191 (chain A) in PDB entry 2P18
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A CYS* 3.6 6.5 - - - -
174A PHE* 3.7 12.7 - - - -
177A GLY* 1.3 75.7 - - - +
179A GLU* 1.3 75.8 + - - +
180A LYS* 2.8 42.9 + - - +
181A ASP* 3.0 31.1 + - - +
182A MET 3.1 16.3 + - - -
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Residues in contact with GLU 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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174A PHE* 3.6 20.2 - - + -
178A ASP* 1.3 81.0 - - - +
180A LYS* 1.3 75.2 + - - +
182A MET* 3.2 1.7 + - - +
183A CYS* 2.8 33.8 + - - -
284A HIS* 3.7 21.3 - - + +
287A MET* 3.8 18.6 - - + +
288A MET* 3.6 42.2 - - + +
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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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178A ASP* 2.8 31.4 + - - +
179A GLU* 1.3 87.2 + - - +
181A ASP* 1.3 66.2 + - - +
183A CYS* 3.3 3.1 + - - +
184A ARG* 3.0 23.7 + - - +
284A HIS* 3.8 43.5 + - + +
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Residues in contact with ASP 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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137A PRO* 3.3 34.6 - - - +
138A CYS* 3.7 6.6 - - + -
176A GLU 4.6 0.9 - - - +
177A GLY* 3.2 11.4 - - - -
178A ASP* 3.0 35.2 + - - +
180A LYS* 1.3 79.2 - - - +
182A MET* 1.3 61.8 + - - +
184A ARG* 3.2 10.0 + - - +
185A ALA* 3.0 21.3 + - - +
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Residues in contact with MET 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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138A CYS* 3.8 19.5 - - + -
139A HIS* 5.1 2.5 - - + +
165A THR* 3.6 39.0 - - + +
171A ILE* 3.9 23.1 - - + -
172A GLY* 3.9 12.6 - - - +
174A PHE* 3.6 42.2 - - + -
178A ASP 3.1 7.1 + - - +
179A GLU 3.2 4.2 + - - +
181A ASP* 1.3 72.9 - - - +
183A CYS* 1.3 67.9 + - - +
185A ALA* 3.2 4.3 + - - +
186A MET* 2.9 34.6 + - + +
287A MET* 4.0 12.6 - - + -
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Residues in contact with CYS 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 GLU 2.8 26.7 + - - +
180A LYS 3.6 5.6 - - - +
182A MET* 1.3 71.4 - - - +
184A ARG* 1.3 57.8 + - - +
186A MET* 3.2 4.4 + - - +
187A GLU* 2.9 40.4 + - + +
269A VAL* 4.1 9.0 - - + -
283A ALA* 3.7 18.6 - - + -
284A HIS* 3.7 23.1 - - + +
287A MET* 3.6 34.1 - - - -
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Residues in contact with ARG 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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137A PRO* 6.1 7.1 - - - +
180A LYS 3.0 13.4 + - - +
181A ASP* 3.5 11.7 - - - +
182A MET 3.2 0.2 - - - -
183A CYS* 1.3 77.8 - - - +
185A ALA* 1.3 61.7 + - - +
187A GLU* 3.3 13.3 + - - +
188A LYS* 3.1 59.5 + - + +
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Residues in contact with ALA 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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136A ALA* 4.1 22.0 - - + +
137A PRO 5.4 0.7 - - - +
138A CYS* 5.8 0.7 - - + -
145A LEU* 5.2 0.7 - - - +
165A THR* 3.9 27.8 - - + -
181A ASP 3.0 13.3 + - - +
182A MET* 3.6 12.6 - - - +
184A ARG* 1.3 78.1 - - - +
186A MET* 1.3 63.6 + - + +
188A LYS* 3.2 10.5 + - - +
189A VAL* 3.0 27.4 + - + +
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Residues in contact with MET 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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165A THR* 4.2 7.6 - - + -
166A MET* 4.0 38.8 - - + +
171A ILE* 4.1 11.0 - - + -
182A MET* 2.9 40.3 + - + +
183A CYS* 3.2 6.3 + - - +
185A ALA* 1.3 80.4 - - - +
187A GLU* 1.3 57.6 + - - +
189A VAL* 3.4 4.4 + - + -
190A TYR* 2.8 31.9 + - - +
266A PHE 3.6 19.7 - - - +
267A LEU* 3.4 34.5 - - - +
269A VAL* 5.5 0.7 - - + -
270A ALA* 4.1 6.7 - - + +
287A MET* 3.9 9.9 - - + -
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Residues in contact with GLU 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 CYS* 2.9 27.2 + - - +
184A ARG* 3.6 12.6 - - + +
186A MET* 1.3 76.4 - - - +
188A LYS* 1.3 62.5 + - + +
190A TYR* 3.4 0.4 + - - -
191A HIS* 3.1 40.9 + - + +
269A VAL 5.4 0.7 - - - +
270A ALA* 3.9 26.6 - - + +
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Residues in contact with LYS 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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120A GLU* 3.0 28.4 + - - +
134A ILE* 3.8 24.1 - - + +
135A ASP* 3.0 31.4 + - - +
137A PRO* 5.5 1.4 - - - +
145A LEU* 5.8 0.2 - - + -
184A ARG* 3.1 63.4 + - + +
185A ALA* 3.6 9.4 - - - +
187A GLU* 1.3 76.3 - - + +
189A VAL* 1.3 62.6 + - + +
191A HIS* 3.5 2.1 + - - -
192A ILE* 3.2 25.7 + - - +
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Residues in contact with VAL 189 (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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134A ILE* 5.9 0.2 - - - -
145A LEU* 3.6 29.8 - - + -
160A LEU* 4.2 15.5 - - + -
162A THR* 5.4 1.1 - - + -
165A THR* 5.9 0.4 - - + -
166A MET* 4.0 19.5 - - + -
185A ALA 3.0 17.8 + - - +
186A MET* 3.8 13.7 - - + +
188A LYS* 1.3 74.1 - - - +
190A TYR* 1.3 66.2 + - - +
191A HIS 3.2 0.7 + - - -
192A ILE* 3.3 23.8 + - + +
257A LEU* 3.7 30.4 - - + +
267A LEU* 4.0 12.1 - - + -
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Residues in contact with TYR 190 (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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186A MET 2.8 21.7 + - - +
187A GLU 3.6 4.7 - - - +
188A LYS 3.4 0.2 - - - -
189A VAL* 1.3 74.4 - - - +
191A HIS* 1.3 84.6 + + + +
192A ILE 3.5 1.1 + - - -
198A TYR* 3.6 8.4 - + - -
201A ASP* 4.8 2.1 - - - +
257A LEU* 5.2 0.2 - - - -
261A LYS* 2.8 68.7 + - + +
267A LEU* 3.7 31.6 - - + +
268A ARG* 4.7 6.1 - - + -
270A ALA* 3.7 15.0 - - + -
271A ASP* 3.7 35.1 + - + +
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Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 3.1 35.2 + - + +
188A LYS* 3.8 3.4 - - - +
190A TYR* 1.3 102.3 - + + +
192A ILE* 1.3 67.1 + - - +
193A HIS 3.0 4.0 + - - -
194A LYS* 3.0 28.4 + - + +
198A TYR* 2.8 30.1 + - - -
270A ALA* 4.3 12.7 + - - +
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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