Contacts of the helix formed by residues 187 - 198 (chain A) in PDB entry 1P22
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 MET 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A SER 3.3 23.2 + - - +
185A ASP* 3.4 9.7 - - - +
186A GLY* 1.3 80.3 - - - +
188A LEU* 1.3 59.3 + - - +
189A TRP 3.2 3.1 - - - -
190A LYS* 3.7 30.5 - - + -
191A LYS* 2.8 29.1 + - + +
227A PRO* 5.3 6.7 - - - +
228A PRO 3.7 9.9 - - - +
229A ASN* 3.5 41.5 - - + +
232A TYR* 5.3 3.8 - - - -
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Residues in contact with LEU 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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158A GLU* 4.0 19.5 - - + +
161A LEU* 3.2 35.4 - - + +
162A SER* 3.5 20.9 - - - +
169A LEU* 3.3 27.0 - - + +
182A VAL 3.9 13.5 - - - +
183A THR* 3.1 18.7 + - - +
186A GLY* 2.8 31.3 + - - +
187A MET* 1.3 70.9 - - - +
189A TRP* 1.3 63.2 + - + +
191A LYS* 4.2 9.2 - - + -
192A LEU* 3.2 26.0 + - + +
229A ASN* 3.9 0.2 - - - +
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Residues in contact with TRP 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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166A ALA* 3.5 41.1 - - + -
169A LEU* 3.3 33.9 - - + +
170A CYS* 4.1 19.5 - - - -
173A GLU* 3.2 26.2 + - - +
183A THR* 5.2 5.1 + - - -
187A MET 3.2 0.8 - - - -
188A LEU* 1.3 78.4 - - + +
190A LYS* 1.3 68.9 + - - +
191A LYS 3.1 0.4 - - - -
192A LEU* 2.8 6.7 + - + -
193A ILE* 2.6 27.9 + - + +
229A ASN* 3.8 17.4 - - - +
232A TYR* 3.5 23.8 - - + -
233A ARG* 3.5 30.4 - - + +
236A TYR* 3.7 36.3 - + + -
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Residues in contact with LYS 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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187A MET* 3.6 30.9 + - + +
189A TRP* 1.3 77.0 - - - +
191A LYS* 1.3 56.5 + - + +
193A ILE* 3.0 1.5 + - - +
194A GLU* 2.8 63.1 + - + +
215A TYR 3.3 15.2 + - - -
216A LEU* 4.2 2.2 - - - +
217A PHE* 4.8 4.4 - - - +
227A PRO* 6.0 1.6 - - - +
229A ASN* 4.6 0.4 - - - +
232A TYR* 2.9 61.8 + - + +
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Residues in contact with LYS 191 (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 GLU* 3.2 31.0 + - + +
162A SER* 5.4 14.8 - - - -
186A GLY* 3.4 23.0 + - - +
187A MET* 2.8 21.6 + - + +
188A LEU* 4.2 12.1 - - + -
190A LYS* 1.3 76.0 - - + +
192A LEU* 1.3 61.0 + - - +
194A GLU* 3.7 12.8 + - - +
195A ARG* 3.3 22.2 + - - +
198A ARG* 5.9 0.5 + - - -
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Residues in contact with LEU 192 (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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162A SER* 4.6 4.0 - - - +
164A LEU 3.3 23.8 - - - +
165A ASP* 4.8 2.2 - - - -
166A ALA* 4.0 23.6 - - + +
169A LEU* 4.4 11.2 - - + -
188A LEU* 3.2 21.4 + - + +
189A TRP* 2.8 10.9 + - + +
191A LYS* 1.3 71.4 - - - +
193A ILE* 1.3 61.5 + - - +
195A ARG* 3.4 32.4 + - - +
196A MET* 3.3 28.5 + - + +
236A TYR* 3.6 32.8 - - + +
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TRP* 2.6 25.5 + - + +
190A LYS* 3.8 4.3 - - - +
192A LEU* 1.3 71.7 - - - +
194A GLU* 1.3 59.1 + - - +
195A ARG 3.2 0.4 - - - -
196A MET* 3.3 6.3 + - - +
197A VAL* 3.2 25.6 + - + +
203A TRP* 4.1 16.4 - - + -
212A TRP* 4.2 24.0 - - + -
216A LEU* 4.6 11.7 - - + -
232A TYR* 3.8 35.9 - - + +
235A LEU* 4.8 5.4 - - + -
236A TYR* 3.8 31.2 - - + +
239A ILE* 4.3 14.4 - - + -
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Residues in contact with GLU 194 (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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190A LYS* 2.8 52.3 + - - +
191A LYS* 4.0 12.9 - - - +
193A ILE* 1.3 69.3 - - - +
195A ARG* 1.3 57.5 + - - +
197A VAL* 4.6 1.1 - - - -
198A ARG* 3.4 44.0 + - - +
216A LEU* 3.7 18.0 - - + -
217A PHE* 2.8 58.1 + - + -
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Residues in contact with ARG 195 (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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162A SER* 2.4 35.0 + - - -
163A TYR* 4.2 11.6 + - - -
164A LEU 4.2 6.5 + - - -
165A ASP* 5.5 1.4 - - - +
191A LYS 3.3 17.5 + - - +
192A LEU* 3.4 36.6 + - - +
193A ILE 3.2 0.8 - - - -
194A GLU* 1.3 76.1 - - - +
196A MET* 1.3 68.8 + - - +
198A ARG* 3.6 14.9 + - + +
199A THR* 2.7 33.4 + - - +
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Residues in contact with MET 196 (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 ASP* 6.4 1.8 - - + -
192A LEU* 3.3 24.4 + - + +
193A ILE* 3.3 11.0 - - - +
195A ARG* 1.3 82.9 - - - +
197A VAL* 1.3 60.7 + - - +
199A THR* 2.9 19.2 + - - -
200A ASP* 3.0 22.2 + - - -
203A TRP* 3.4 53.4 - - + +
236A TYR* 3.7 25.1 - - + +
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Residues in contact with VAL 197 (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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193A ILE* 3.2 15.1 + - + +
194A GLU* 4.5 3.6 - - - +
196A MET* 1.3 73.8 - - - +
198A ARG* 1.3 54.4 + - - +
199A THR 2.7 16.7 + - - -
203A TRP* 3.5 22.4 - - + +
204A ARG* 3.3 46.4 + - + +
207A ALA* 3.9 16.4 - - + -
212A TRP* 4.3 13.2 - - + -
216A LEU* 5.1 5.8 - - + -
217A PHE* 4.3 21.1 - - + -
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Residues in contact with ARG 198 (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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191A LYS 5.9 0.6 + - - -
194A GLU* 3.4 31.4 + - - +
195A ARG* 3.9 15.4 - - + +
196A MET 3.3 1.4 - - - -
197A VAL* 1.3 75.8 - - - +
199A THR* 1.3 65.7 + - - +
204A ARG* 4.2 8.0 + - - -
217A PHE* 3.3 39.0 - - + -
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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