Contacts of the helix formed by residues 196 - 211 (chain A) in PDB entry 4WTM
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A TYR* 1.3 74.0 - - - +
197A PRO* 1.3 71.5 - - - +
198A ALA* 3.5 7.2 + - - +
199A GLN* 2.8 38.7 + - - +
200A ARG* 2.8 27.6 + - - +
466A LEU* 4.3 15.7 + - - +
551A PHE* 3.7 22.6 + - - +
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Residues in contact with PRO 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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195A TYR 4.6 0.4 - - - +
196A SER* 1.3 87.1 - - - +
198A ALA* 1.3 61.6 + - - +
200A ARG* 3.3 5.7 + - + +
201A VAL* 3.0 29.2 + - - +
384A LEU* 4.1 31.4 - - + +
414A GLN* 3.8 31.6 - - + +
415A TYR* 6.1 0.4 - - + -
466A LEU* 5.4 1.8 - - + -
467A HIS* 4.2 13.5 - - + +
551A PHE* 3.8 31.0 - - + -
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Residues in contact with ALA 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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196A SER* 3.2 4.9 + - - +
197A PRO* 1.3 79.3 - - - +
199A GLN* 1.3 59.8 + - + +
201A VAL* 3.5 8.7 + - - +
202A GLU* 3.0 26.9 + - - +
383A TYR* 6.3 0.9 - - - +
466A LEU 3.8 21.3 + - - +
467A HIS* 4.9 13.7 + - - +
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Residues in contact with GLN 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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194A GLN 4.0 5.7 - - - +
195A TYR* 3.5 23.6 - - + -
196A SER* 2.8 43.8 + - - +
198A ALA* 1.3 78.1 - - + +
200A ARG* 1.3 59.9 + - - +
202A GLU* 3.4 18.0 + - - +
203A TYR* 2.9 30.8 + - - +
551A PHE* 5.1 0.7 - - - +
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Residues in contact with ARG 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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192A GLY 4.6 6.1 + - - -
195A TYR* 3.7 15.3 - - + +
196A SER 2.8 15.6 + - - +
197A PRO* 3.6 10.8 - - + +
199A GLN* 1.3 71.2 - - - +
201A VAL* 1.3 64.2 + - + +
203A TYR* 3.3 5.6 + - - +
204A LEU* 3.0 38.3 + - + +
314A LEU* 3.4 39.4 + - + +
316A CYS* 3.2 28.9 - - - -
319A ASP 5.8 0.8 + - - -
320A LEU* 6.2 0.2 - - - +
321A ILE* 4.3 6.3 - - - +
365A SER* 3.8 24.0 + - - -
366A CYS* 3.7 24.1 - - - -
368A SER* 4.6 7.9 + - - -
384A LEU* 4.4 23.8 - - + +
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Residues in contact with VAL 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 PRO 3.0 18.8 + - - +
198A ALA* 3.6 11.0 - - - +
199A GLN 3.2 0.2 - - - -
200A ARG* 1.3 77.3 - - - +
202A GLU* 1.3 56.8 + - - +
204A LEU* 3.3 3.5 + - - +
205A LEU* 3.0 35.3 + - + +
370A VAL* 4.2 20.8 - - + +
382A TYR* 3.8 37.2 - - + +
383A TYR* 3.7 5.4 - - - +
384A LEU* 3.6 35.2 - - + +
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Residues in contact with GLU 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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198A ALA 3.0 17.2 + - - +
199A GLN* 3.4 20.5 + - - +
201A VAL* 1.3 77.3 - - - +
203A TYR* 1.3 58.0 + - - +
205A LEU* 3.4 8.5 + - - +
206A LYS* 3.0 30.5 + - + +
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Residues in contact with TYR 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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189A ALA* 3.6 27.8 + - + +
190A SER* 4.0 2.3 + - - -
195A TYR* 3.5 32.1 - + + -
199A GLN 2.9 18.2 + - - +
200A ARG* 3.5 6.3 - - - +
202A GLU* 1.3 78.9 - - - +
204A LEU* 1.3 73.4 + - + +
206A LYS* 3.4 6.5 + - + +
207A ALA* 3.0 24.3 + - + +
312A THR* 3.3 26.2 - - + +
313A MET 2.7 25.0 + - - -
314A LEU* 3.5 29.2 - - + -
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Residues in contact with LEU 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 ARG* 3.0 34.8 + - + +
201A VAL 3.8 4.3 - - - +
203A TYR* 1.3 82.9 - - + +
205A LEU* 1.3 57.7 + - - +
207A ALA* 3.5 2.7 + - + +
208A TRP* 3.0 29.2 + - - +
314A LEU* 4.2 21.3 - - + -
321A ILE* 4.1 31.6 - - + -
323A ILE* 3.7 26.0 - - + +
360A LEU* 4.5 17.7 - - + +
370A VAL* 4.0 21.8 - - + -
384A LEU* 5.8 1.3 - - + -
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Residues in contact with LEU 205 (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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201A VAL* 3.0 28.6 + - + +
202A GLU* 3.8 7.0 - - - +
204A LEU* 1.3 75.0 - - - +
206A LYS* 1.3 59.6 + - - +
208A TRP* 3.4 8.0 + - + +
209A ALA* 3.0 31.4 + - - +
360A LEU* 3.8 20.9 - - + -
370A VAL* 5.3 0.7 - - + -
382A TYR* 3.8 55.0 - - + -
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Residues in contact with LYS 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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202A GLU* 3.0 19.2 + - + +
203A TYR* 3.7 7.2 - - + +
205A LEU* 1.3 75.5 - - - +
207A ALA* 1.3 57.5 + - - +
209A ALA* 3.2 6.5 + - - +
210A GLU* 3.0 44.0 + - - +
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Residues in contact with ALA 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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203A TYR* 3.0 16.8 + - + +
204A LEU* 3.6 5.8 - - + +
206A LYS* 1.3 79.4 - - - +
208A TRP* 1.3 60.8 + - - +
210A GLU* 3.4 18.7 + - - +
211A LYS* 3.4 23.3 - - - +
312A THR* 3.8 31.4 - - + -
323A ILE* 3.9 17.0 - - + -
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Residues in contact with TRP 208 (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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204A LEU 3.0 16.4 + - - +
205A LEU* 3.6 10.3 - - + +
207A ALA* 1.3 76.8 - - - +
209A ALA* 1.3 62.5 + - - +
210A GLU 3.3 0.3 + - - -
211A LYS 3.4 11.3 + - - +
214A PRO* 3.4 39.3 - - + +
215A MET 4.3 2.2 - - - -
216A GLY* 4.0 18.4 - - - -
323A ILE* 3.9 29.0 - - + +
357A GLU 4.0 11.4 - - - -
358A TYR* 3.5 26.9 + - - -
359A ASP* 3.7 20.4 - - - -
360A LEU* 4.0 27.8 - - + +
363A ILE* 4.1 15.5 - - + -
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Residues in contact with ALA 209 (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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205A LEU 3.0 17.7 + - - +
206A LYS* 3.8 5.4 - - - +
208A TRP* 1.3 78.5 - - - +
210A GLU* 1.3 61.9 + - - +
211A LYS 3.4 6.4 + - - +
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Residues in contact with GLU 210 (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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206A LYS* 3.0 28.1 + - - +
207A ALA* 3.5 11.8 - - - +
208A TRP 3.2 0.6 - - - -
209A ALA* 1.3 77.9 - - - +
211A LYS* 1.3 70.0 + - + +
212A LYS 3.7 1.0 + - - -
312A THR* 4.8 7.6 + - - +
325A GLU* 4.5 1.0 - - - +
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Residues in contact with LYS 211 (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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207A ALA* 3.4 20.6 - - - +
208A TRP 3.8 5.2 - - - +
209A ALA 3.4 7.9 - - - +
210A GLU* 1.3 86.4 + - + +
212A LYS* 1.3 64.3 + - - +
214A PRO* 3.8 25.8 - - + +
310A ALA* 2.6 34.8 + - + +
311A PRO 4.7 0.2 + - - -
312A THR* 3.0 22.3 + - - -
323A ILE* 3.6 23.6 - - + -
324A SER 3.6 19.5 - - - +
325A GLU* 3.3 21.1 - - + +
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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