Contacts of the helix formed by residues 190 - 205 (chain A) in PDB entry 3ROT
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A VAL 4.8 0.2 + - - -
188A GLY* 3.8 0.4 - - - -
189A THR* 1.3 77.6 + - - +
191A PRO* 1.3 70.5 - - - +
192A ASN* 3.3 14.2 + - - +
193A GLN* 2.9 62.3 + - + +
194A VAL* 3.0 13.7 + - - +
32B SER* 3.6 14.7 + - - +
33B GLN* 3.2 20.9 - - - +
61B PRO* 5.6 2.3 - - - +
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Residues in contact with PRO 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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189A THR 3.1 10.5 - - - +
190A ASP* 1.3 83.1 - - - +
192A ASN* 1.3 62.7 + - - +
194A VAL 3.4 0.3 + - - -
195A GLN* 3.2 28.6 + - - +
221A PRO* 3.6 28.1 - - + +
32B SER 3.9 6.1 - - - +
33B GLN* 3.5 46.9 - - - +
35B PRO* 6.3 0.2 - - + -
38B THR* 3.3 24.2 - - + +
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Residues in contact with ASN 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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190A ASP* 3.2 12.6 + - - +
191A PRO* 1.3 79.3 - - - +
193A GLN* 1.3 62.4 + - - +
195A GLN* 3.5 7.0 + - - +
196A SER* 2.9 36.4 + - - -
32B SER 5.2 0.8 + - - +
38B THR* 3.9 6.8 - - + +
41B PHE* 4.0 35.9 - - + +
45B LYS* 2.8 33.9 + - - +
57B ILE* 4.8 14.1 - - - +
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Residues in contact with GLN 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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187A VAL 4.3 7.3 - - - +
188A GLY* 5.6 2.1 - - - -
189A THR 5.8 0.2 + - - -
190A ASP* 2.9 33.4 + - + +
192A ASN* 1.3 78.8 - - - +
194A VAL* 1.3 66.4 + - - +
196A SER* 3.2 5.5 + - - -
197A ARG* 2.9 65.3 + - - +
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Residues in contact with VAL 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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155A LEU* 5.0 2.5 - - + -
187A VAL* 3.4 40.5 + - + +
188A GLY 3.7 14.1 - - - +
189A THR* 4.3 3.4 - - - -
190A ASP 3.0 21.2 + - - +
191A PRO 3.7 2.0 - - - +
193A GLN* 1.3 74.8 - - - +
195A GLN* 1.3 62.2 + - - +
197A ARG* 4.0 0.7 - - - +
198A VAL* 2.9 41.2 + - + +
217A GLN 4.6 3.8 - - - +
218A ALA* 3.9 11.9 - - - +
221A PRO* 3.7 31.6 - - + -
222A LEU* 4.9 3.8 - - + +
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Residues in contact with GLN 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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191A PRO 3.2 17.1 + - - +
192A ASN* 3.8 7.0 - - - +
194A VAL* 1.3 78.4 - - - +
196A SER* 1.3 63.6 + - - +
198A VAL* 3.3 1.4 + - - +
199A LYS* 2.9 33.2 + - + +
221A PRO* 3.0 35.3 + - + +
224A GLN* 3.3 23.8 + - - +
225A MSE 3.6 25.7 - - - +
232A TYR* 3.5 26.9 - - + -
38B THR* 4.1 14.8 - - - +
42B GLN* 5.5 0.2 - - - +
45B LYS* 4.6 10.7 + - - +
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Residues in contact with SER 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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192A ASN* 2.9 27.7 + - - -
193A GLN* 3.5 7.8 - - - -
195A GLN* 1.3 77.3 - - - +
197A ARG* 1.3 60.3 + - - +
199A LYS* 3.3 8.3 + - - +
200A SER* 3.0 34.6 + - - -
203A LYS* 5.0 0.9 + - - -
45B LYS* 4.2 14.4 + - - +
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Residues in contact with ARG 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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185A LEU* 3.7 28.8 - - + +
186A ASP* 2.9 35.8 + - - -
187A VAL* 3.5 25.6 + - + +
188A GLY* 3.9 4.0 - - - +
193A GLN* 2.9 53.6 + - - +
194A VAL 4.1 2.0 - - - +
196A SER* 1.3 76.4 - - - +
198A VAL* 1.3 62.0 + - - +
200A SER* 3.6 7.9 + - - -
201A TYR* 3.2 16.6 + - - +
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Residues in contact with VAL 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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153A LEU* 4.7 4.3 - - + -
155A LEU* 4.0 31.0 - - + -
185A LEU* 4.4 4.7 - - - -
187A VAL* 4.4 4.3 - - + -
194A VAL* 2.9 31.7 + - + +
195A GLN* 3.7 3.8 - - - +
197A ARG* 1.3 73.0 - - - +
199A LYS* 1.3 68.3 + - - +
201A TYR* 3.2 3.7 + - - +
202A PHE* 3.1 33.6 + - + -
211A ILE* 4.7 3.4 - - + -
222A LEU* 4.6 8.7 - - + -
225A MSE 4.0 10.8 - - + -
234A PHE* 3.8 26.9 - - + -
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Residues in contact with LYS 199 (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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195A GLN* 2.9 27.1 + - + +
196A SER* 3.7 6.3 - - - +
198A VAL* 1.3 75.8 - - - +
200A SER* 1.3 63.0 + - - +
202A PHE* 3.3 3.3 + - - +
203A LYS* 2.9 48.6 + - - +
225A MSE 3.7 26.0 - - - -
232A TYR* 3.0 28.2 + - + +
233A ASP* 4.3 11.2 + - - +
234A PHE* 4.0 17.9 - - + -
236A TYR* 5.0 1.6 + - + -
42B GLN* 3.7 27.9 + - - +
45B LYS* 5.2 4.9 - - - +
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Residues in contact with SER 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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196A SER* 3.0 19.7 + - - -
197A ARG* 3.8 8.8 - - - -
199A LYS* 1.3 75.7 - - - +
201A TYR* 1.3 62.3 + - - +
203A LYS* 3.3 28.3 + - - +
204A ILE* 3.3 23.7 + - - +
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Residues in contact with TYR 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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151A ARG* 3.1 26.3 + - + +
152A ALA 4.9 0.9 + - - -
153A LEU* 3.7 44.0 - - + -
183A GLU* 3.4 43.4 + - + +
185A LEU* 4.5 11.0 - - + -
197A ARG 3.2 11.1 + - - +
198A VAL 3.2 9.7 + - - +
200A SER* 1.3 79.8 - - - +
202A PHE* 1.3 55.0 + + - +
204A ILE* 3.0 9.6 + - + +
205A HIS* 2.7 52.9 + + + -
208A THR* 3.4 27.6 - - + -
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Residues in contact with PHE 202 (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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153A LEU* 3.9 18.8 - - + -
198A VAL* 3.1 22.8 + - + +
199A LYS 3.3 2.9 + - - +
201A TYR* 1.3 76.5 - + - +
203A LYS* 1.3 62.5 + - - +
205A HIS 3.9 7.9 - - - -
206A PRO* 2.9 31.5 - - - +
208A THR* 3.2 42.6 - - + -
211A ILE* 3.5 34.5 - - + -
234A PHE* 3.9 14.8 - + + -
236A TYR* 3.3 57.5 + + + -
238A PRO* 4.0 7.4 - - + -
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Residues in contact with LYS 203 (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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196A SER 5.0 0.8 + - - -
199A LYS* 2.9 44.7 + - - +
200A SER* 3.4 26.5 + - - +
201A TYR 3.2 0.2 - - - -
202A PHE* 1.3 77.9 - - - +
204A ILE* 1.3 62.4 + - + +
206A PRO* 4.1 5.7 - - - +
236A TYR* 4.1 13.0 - - - +
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Residues in contact with ILE 204 (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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200A SER* 3.4 18.4 - - - +
201A TYR* 3.0 10.4 + - + +
203A LYS* 1.3 81.8 - - + +
205A HIS* 1.3 84.4 + - + +
206A PRO* 3.4 8.8 - - - +
207A GLU* 4.7 0.7 - - - +
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Residues in contact with HIS 205 (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 ARG* 3.2 43.8 + - - +
183A GLU* 4.9 4.3 - - - -
201A TYR* 2.7 37.7 + + + +
202A PHE* 3.3 8.5 - - - +
204A ILE* 1.3 104.0 - - + +
206A PRO* 1.3 62.8 - - - +
207A GLU* 3.1 16.2 - - - +
208A THR* 2.6 39.5 + - - +
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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