Contacts of the helix formed by residues 186 - 201 (chain A) in PDB entry 3P8Z
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.7 39.3 - - - +
154A PRO* 4.1 12.6 - - + +
155A THR* 4.1 18.2 - - + -
158A GLU* 3.7 39.7 - - + +
183A ASN* 3.3 25.9 + - - +
184A PRO 3.6 0.6 - - - -
185A TYR* 1.3 84.7 - - - +
187A PRO* 1.4 70.0 - - + +
188A THR 3.3 0.2 - - - -
189A VAL* 2.9 32.5 + - + +
190A ILE* 3.1 8.9 + - - +
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Residues in contact with PRO 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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6A GLY* 6.0 4.9 - - - -
8A THR* 4.1 17.9 - - + -
11A GLU* 4.5 4.5 - - - +
158A GLU* 5.5 0.7 - - - +
185A TYR 3.5 6.5 - - - +
186A MET* 1.4 92.8 - - + +
188A THR* 1.3 64.0 + - + +
190A ILE* 3.2 13.6 + - + +
191A GLU* 3.1 27.9 + - - +
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Residues in contact with THR 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* 2.2 41.2 + - - +
162A ILE* 3.5 11.7 - - - +
187A PRO* 1.3 80.0 - - + +
189A VAL* 1.3 63.9 + - - +
191A GLU* 3.4 19.2 + - - +
192A HIS* 3.2 31.9 + - - -
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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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158A GLU* 4.1 17.7 - - + -
161A THR* 3.9 22.2 - - + -
162A ILE* 4.1 19.3 - - + -
165A LEU* 4.2 4.7 - - + -
181A VAL* 4.2 0.2 - - + -
183A ASN 3.4 28.9 - - - +
184A PRO* 4.0 5.2 - - + -
186A MET* 2.9 15.2 + - + +
188A THR* 1.3 78.4 + - - +
190A ILE* 1.3 56.8 + - - +
192A HIS* 3.2 8.8 + - - +
193A LEU* 2.9 48.5 + - + +
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Residues in contact with ILE 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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8A THR* 5.8 2.2 - - + -
184A PRO 3.4 20.2 - - - +
185A TYR* 3.9 22.0 - - - +
186A MET 3.1 7.2 + - - +
187A PRO* 3.2 13.4 + - + +
189A VAL* 1.3 76.0 - - - +
191A GLU* 1.3 58.5 + - + +
193A LEU* 3.2 7.5 + - - +
194A GLU* 2.9 55.3 + - + +
227A ILE* 5.0 9.9 - - + -
228A VAL* 3.7 24.2 - - + -
231A VAL* 4.9 9.2 - - + -
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Residues in contact with GLU 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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187A PRO* 3.1 17.8 + - + +
188A THR* 3.5 18.8 - - - +
190A ILE* 1.3 77.0 - - + +
192A HIS* 1.3 65.2 + - + +
194A GLU* 3.3 12.5 + - - +
195A ARG* 3.0 23.6 + - - +
198A ARG* 4.8 1.9 + - - -
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Residues in contact with HIS 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 ILE* 3.7 42.7 - - + +
165A LEU* 4.0 18.5 - - + +
166A LYS* 4.8 16.6 - - + +
188A THR* 3.2 23.1 + - - -
189A VAL 3.2 7.3 + - - +
191A GLU* 1.3 79.1 - - + +
193A LEU* 1.3 58.2 + - - +
195A ARG* 3.1 35.4 + - - +
196A LEU* 2.9 35.9 + - + +
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Residues in contact with LEU 193 (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 LEU* 3.9 28.5 - - + -
181A VAL* 4.1 19.5 - - + -
184A PRO 4.4 8.5 - - - +
189A VAL* 2.9 38.2 + - + +
190A ILE* 3.6 4.9 - - - +
192A HIS* 1.3 76.4 - - - +
194A GLU* 1.3 58.2 + - - +
196A LEU* 3.3 7.4 + - + +
197A GLN* 2.8 30.5 + - - +
204A LEU* 4.0 30.3 - - + -
219A TRP* 5.1 12.2 + - + -
227A ILE* 3.6 23.5 - - + +
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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 ILE* 2.9 39.9 + - + +
191A GLU* 3.7 10.4 - - - +
192A HIS 3.2 0.2 - - - -
193A LEU* 1.3 73.4 - - - +
195A ARG* 1.3 65.3 + - - +
197A GLN* 3.2 6.4 + - - +
198A ARG* 3.1 44.3 + - - +
227A ILE* 4.0 20.4 - - + +
228A VAL* 3.6 15.9 + - - +
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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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165A LEU* 5.8 2.8 + - - +
166A LYS* 5.5 5.7 - - - +
169A GLU* 3.0 30.9 + - - -
191A GLU 3.0 11.8 + - - +
192A HIS* 3.1 40.7 + - - +
194A GLU* 1.3 76.7 - - - +
196A LEU* 1.3 83.0 + - - +
197A GLN 3.3 0.2 + - - -
198A ARG* 3.3 29.0 + - - +
199A LYS* 3.2 22.5 + - + +
198C ARG* 3.7 24.0 - - - +
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Residues in contact with LEU 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 LEU* 3.9 43.5 - - + +
169A GLU* 3.5 42.4 - - + +
192A HIS 2.9 23.3 + - - +
193A LEU* 3.5 7.2 - - + +
195A ARG* 1.3 90.5 - - - +
197A GLN* 1.3 57.5 + - - +
199A LYS* 3.3 1.0 + - - -
200A HIS* 2.8 47.4 + - + +
219A TRP* 3.6 27.0 - - + -
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Residues in contact with GLN 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 LEU 2.8 17.7 + - - +
194A GLU* 3.2 8.4 + - - +
196A LEU* 1.3 74.5 - - - +
198A ARG* 1.3 61.8 + - + +
201A GLY* 2.7 39.9 + - - +
202A GLY 3.2 28.2 + - - +
203A MET* 4.0 9.7 - - - +
219A TRP* 4.4 5.1 - - - +
224A THR* 4.9 2.0 + - - +
225A GLY 2.9 30.8 + - - +
227A ILE* 3.4 23.8 + - + +
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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 GLU 4.8 1.6 + - - -
194A GLU* 3.1 28.0 + - - +
195A ARG* 3.3 38.9 + - - +
197A GLN* 1.3 78.4 - - + +
199A LYS* 1.3 62.6 + - - +
201A GLY 4.7 0.3 + - - -
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Residues in contact with LYS 199 (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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169A GLU* 4.7 7.2 - - - +
195A ARG* 3.2 15.0 + - + +
196A LEU* 4.7 0.9 - - - -
197A GLN 3.2 0.4 - - - -
198A ARG* 1.3 83.1 - - - +
200A HIS* 1.3 91.5 + - + +
201A GLY 3.7 0.2 - - - -
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Residues in contact with HIS 200 (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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169A GLU* 3.0 30.3 + - + +
172A LEU* 3.8 38.7 + - + +
174A ASN 5.5 4.2 + - - -
177A PHE* 3.9 18.5 - - + -
196A LEU* 2.8 37.8 + - + +
199A LYS* 1.3 102.8 + - + +
201A GLY* 1.3 63.7 + - - +
202A GLY 3.9 0.9 + - - -
219A TRP* 3.9 15.9 - + + -
221A SER* 5.2 1.2 - - - +
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Residues in contact with GLY 201 (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 PHE* 4.0 0.8 - - - -
197A GLN* 2.7 32.2 + - - -
198A ARG 4.6 0.4 + - - -
199A LYS 3.7 1.0 - - - -
200A HIS* 1.3 76.4 - - - +
202A GLY* 1.3 63.1 + - - -
219A TRP* 2.9 24.9 + - - -
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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