Contacts of the helix formed by residues 192 - 207 (chain A) in PDB entry 1W7L
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 SER 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A VAL 3.4 3.4 + - - -
191A PHE* 1.3 76.3 - - - +
193A ARG* 1.3 65.0 + - - +
194A GLU* 3.7 7.8 + - - +
195A GLU* 2.8 39.1 + - - +
196A LEU* 3.1 22.4 + - - +
227A ILE* 4.7 1.6 - - - -
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Residues in contact with ARG 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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192A SER* 1.3 73.6 - - - +
194A GLU* 1.3 58.4 - - - +
196A LEU* 3.3 8.6 + - - +
197A GLU* 2.9 54.2 + - + +
227A ILE* 3.7 44.9 - - + +
231A SER* 5.5 1.6 + - - -
232A LEU* 4.1 22.8 - - + +
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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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192A SER* 3.3 7.2 + - - +
193A ARG* 1.3 77.6 - - - +
195A GLU* 1.3 58.9 + - + +
197A GLU* 3.3 16.3 + - - +
198A LEU* 3.0 27.0 + - - +
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Residues in contact with GLU 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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158A SER 4.7 1.3 - - - +
160A TRP 4.2 0.5 - - - +
161A GLN* 3.9 19.2 + - - +
162A LEU* 4.7 13.2 + - + +
189A LYS* 2.9 38.2 + - - -
190A VAL 4.2 1.0 - - - +
191A PHE* 3.4 16.5 - - + -
192A SER* 2.8 40.7 + - - +
194A GLU* 1.3 78.2 - - + +
196A LEU* 1.3 61.9 + - - +
198A LEU* 3.2 13.9 + - + +
199A VAL* 3.0 26.6 + - - +
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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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180A LEU* 3.6 31.0 - - + -
182A THR* 4.7 2.2 - - + -
191A PHE* 3.8 25.6 - - + +
192A SER 3.1 17.0 + - - +
193A ARG* 3.6 7.0 - - - +
195A GLU* 1.3 74.6 - - - +
197A GLU* 1.3 53.1 + - - +
199A VAL* 3.2 6.0 + - + +
200A ALA* 2.7 36.4 + - - +
227A ILE* 3.5 51.1 - - + +
229A ILE* 3.5 16.5 - - + +
232A LEU* 3.8 13.5 - - + -
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Residues in contact with GLU 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 ARG* 2.9 41.6 + - + +
194A GLU* 3.5 18.4 - - + +
195A GLU 3.3 0.2 - - - -
196A LEU* 1.3 73.7 - - - +
198A LEU* 1.3 59.9 + - - +
200A ALA* 3.7 2.2 - - - +
201A SER* 2.8 33.3 + - - -
232A LEU* 3.9 20.7 - - + +
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Residues in contact with LEU 198 (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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162A LEU* 3.9 28.3 - - + +
164A PRO* 4.0 32.8 - - + +
167A LEU* 3.8 20.4 - - + -
194A GLU 3.0 13.1 + - - +
195A GLU* 3.2 15.5 + - + +
197A GLU* 1.3 76.1 - - - +
199A VAL* 1.3 61.0 + - - +
201A SER* 3.2 19.4 + - - +
202A LEU* 3.3 29.0 + - + +
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Residues in contact with VAL 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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121A ILE* 5.3 0.9 - - + -
162A LEU* 4.2 24.5 - - + -
167A LEU* 4.2 10.8 - - + -
171A PHE* 5.1 0.6 - - - -
178A LEU* 4.0 31.2 - - + -
180A LEU* 4.9 6.7 - - + -
191A PHE* 5.0 8.3 - - + -
195A GLU 3.0 14.9 + - - +
196A LEU* 3.2 7.4 + - - +
198A LEU* 1.3 76.8 - - - +
200A ALA* 1.3 63.5 + - - +
202A LEU* 3.4 2.8 + - - +
203A CYS* 3.0 33.3 + - - +
210A CYS* 4.4 2.9 - - - -
229A ILE* 3.5 20.4 - - + -
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Residues in contact with ALA 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 LEU 2.7 22.1 + - - +
197A GLU* 3.7 4.7 - - - +
199A VAL* 1.3 73.3 - - - +
201A SER* 1.3 56.6 - - - +
203A CYS* 3.2 1.6 + - - +
204A GLN* 2.9 40.3 + - - +
229A ILE* 4.2 2.0 - - + -
232A LEU* 3.8 14.8 - - + -
233A PRO 5.8 0.2 - - - +
235A MET* 3.7 37.2 - - + -
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Residues in contact with SER 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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197A GLU 2.8 18.8 + - - -
198A LEU* 3.2 14.9 + - - +
200A ALA* 1.3 72.8 - - - +
202A LEU* 1.3 63.1 + - - +
204A GLN* 3.8 10.4 + - - +
205A GLN* 2.9 30.7 + - - +
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Residues in contact with LEU 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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167A LEU* 3.8 33.0 - - + -
168A ALA* 3.8 35.2 - - + +
171A PHE* 3.7 18.8 - - + -
198A LEU* 3.3 28.9 + - + +
199A VAL 3.9 1.8 - - - +
201A SER* 1.3 82.3 + - - +
203A CYS* 1.3 58.6 + - - +
205A GLN* 3.2 12.5 + - - +
206A HIS* 2.9 54.5 + - + +
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Residues in contact with CYS 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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171A PHE* 4.5 6.3 - - - -
178A LEU* 4.4 10.1 - - - -
199A VAL* 3.0 34.4 + - - +
200A ALA 3.7 4.0 - - - +
202A LEU* 1.3 77.1 - - - +
204A GLN* 1.3 56.6 - - - +
207A ASP* 2.9 9.7 + - - -
208A VAL* 2.8 61.9 + - - +
210A CYS* 4.2 16.2 - - - -
235A MET* 4.1 14.1 - - + -
238A ARG* 3.8 3.8 + - - -
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Residues in contact with GLN 204 (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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200A ALA* 2.9 30.4 + - - +
201A SER* 3.9 8.2 + - - +
203A CYS* 1.3 73.4 - - - +
205A GLN* 1.3 64.7 + - - +
207A ASP* 3.6 8.5 + - - +
233A PRO 3.2 24.4 + - - +
234A GLY* 3.6 19.0 + - - -
235A MET* 3.8 7.9 - - - -
238A ARG* 3.6 35.0 + - - +
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Residues in contact with GLN 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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201A SER 2.9 19.3 + - - +
202A LEU* 3.7 14.4 - - - +
204A GLN* 1.3 78.8 - - - +
206A HIS* 1.3 85.0 + - + +
207A ASP* 3.7 0.9 + - - +
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Residues in contact with HIS 206 (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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168A ALA 4.8 3.1 + - - -
171A PHE* 3.6 41.2 - + + +
172A THR* 4.8 13.6 + - - +
175A THR 5.2 1.6 - - - +
202A LEU* 2.9 41.5 + - + +
205A GLN* 1.3 100.3 + - + +
207A ASP* 1.3 70.9 + - - +
208A VAL* 3.8 18.1 - - + +
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Residues in contact with ASP 207 (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 THR 4.7 4.0 - - - +
176A LYS* 5.0 1.0 - - - +
203A CYS 2.9 9.3 + - - -
204A GLN 3.6 3.4 + - - +
205A GLN 3.4 4.0 - - - +
206A HIS* 1.3 81.9 - - - +
208A VAL* 1.3 58.9 + - - +
209A VAL* 5.8 0.5 - - - +
238A ARG* 3.0 26.0 + - - +
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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