Contacts of the helix formed by residues 196 - 214 (chain A) in PDB entry 4WLQ
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 TRP 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.3 35.7 + - + +
51A GLY* 4.0 17.0 - - - -
52A LEU* 3.9 26.2 - - + -
168A TYR* 4.5 3.4 - - + -
170A PRO* 3.3 36.5 - - + +
175A LEU* 4.2 18.4 - - + -
191A CYS* 3.6 24.2 - - + -
192A ASN 3.0 13.8 + - - +
193A GLN 3.5 18.4 + - - -
194A ASP 4.4 4.7 + - - -
195A ASP* 1.3 71.3 - - - +
197A ILE* 1.3 75.9 + - + +
198A THR 3.3 2.2 - - - -
199A ALA* 3.3 6.9 + - - +
200A VAL* 3.2 41.0 + - + -
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.7 1.8 - - + +
43A PHE* 3.9 44.9 - - + -
47A LYS* 3.8 31.6 - - + -
49A VAL* 4.4 19.7 - - + +
52A LEU* 5.4 2.9 - - + -
194A ASP 5.1 1.1 - - - +
195A ASP* 3.4 16.7 - - - +
196A TRP* 1.3 101.4 - - + +
198A THR* 1.3 61.7 + - + +
200A VAL* 3.1 14.3 - - + +
201A ARG* 2.8 33.3 + - + +
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Residues in contact with THR 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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40A PRO* 5.4 14.6 - - + -
195A ASP* 3.7 25.6 + - - +
197A ILE* 1.3 79.5 - - + +
199A ALA* 1.3 61.8 + - - +
201A ARG* 3.5 11.7 - - - +
202A PRO* 3.1 20.8 - - - +
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Residues in contact with ALA 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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175A LEU* 4.1 7.7 - - + +
190A ALA 4.0 8.3 - - - +
191A CYS* 3.4 32.5 - - + -
192A ASN 5.2 0.2 - - - +
195A ASP 5.6 0.2 - - - +
196A TRP* 3.3 12.3 + - - +
197A ILE 3.2 0.2 - - - -
198A THR* 1.3 82.7 + - - +
200A VAL* 1.3 62.3 + - - +
202A PRO* 3.3 15.1 - - - +
203A VAL* 3.9 10.0 - - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 6.3 0.9 - - + -
52A LEU* 4.0 25.4 - - + -
168A TYR* 4.5 16.2 - - + -
175A LEU* 3.5 23.7 - - + +
196A TRP* 3.2 22.5 + - + -
197A ILE* 3.1 31.6 - - + +
199A ALA* 1.3 78.3 - - - +
201A ARG* 1.3 66.6 - - - +
203A VAL* 3.1 6.8 + - + +
204A ILE* 3.0 37.2 + - + +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.1 36.6 + - + +
39A GLU* 3.6 31.0 + - - +
40A PRO* 5.0 8.9 - - - +
197A ILE* 2.8 20.1 + - + +
198A THR* 3.5 12.1 - - - +
199A ALA 3.1 0.8 - - - -
200A VAL* 1.3 79.1 - - - +
202A PRO* 1.3 71.2 - - + +
204A ILE* 3.4 7.0 - - - +
205A GLU* 2.8 52.8 + - + +
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Residues in contact with PRO 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 THR 3.1 26.0 - - - +
199A ALA* 3.3 9.9 - - - +
201A ARG* 1.3 87.8 - - + +
203A VAL* 1.3 65.7 + - + +
205A GLU* 3.2 6.4 + - + +
206A LYS* 3.1 33.2 + - + +
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Residues in contact with VAL 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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65A ALA* 4.5 11.8 - - + +
168A TYR* 4.6 11.6 + - + +
175A LEU* 4.7 1.6 - - + -
177A GLU* 5.4 0.2 - - - +
188A LEU* 3.6 52.5 - - + +
199A ALA 3.9 16.6 - - - +
200A VAL* 3.1 9.8 + - + +
202A PRO* 1.3 81.9 - - + +
204A ILE* 1.3 63.5 - - - +
206A LYS* 3.6 8.7 + - - +
207A ARG* 3.4 18.0 + - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.1 28.7 - - + -
52A LEU* 4.1 15.0 - - + -
54A PHE* 4.6 11.4 - - + -
168A TYR* 4.0 27.6 - - + +
200A VAL* 3.0 19.1 + - + +
201A ARG* 3.4 13.7 - - - +
203A VAL* 1.3 77.4 - - - +
205A GLU* 1.3 58.4 + - - +
207A ARG* 3.4 5.7 + - + +
208A ILE* 2.7 37.6 + - + +
220A LEU* 3.5 39.7 - - + -
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Residues in contact with GLU 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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38A LEU* 3.4 34.7 - - + +
201A ARG* 2.8 56.1 + - + +
202A PRO* 3.2 6.9 + - + +
204A ILE* 1.3 76.7 - - - +
206A LYS* 1.3 59.5 + - - +
208A ILE* 3.1 15.8 - - + +
209A GLN* 2.8 34.5 + - - +
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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 PRO* 3.1 21.6 + - - +
203A VAL* 3.7 10.1 - - - +
204A ILE 3.4 0.2 - - - -
205A GLU* 1.3 77.4 - - - +
207A ARG* 1.3 61.9 + - - +
209A GLN* 3.3 6.3 + - - +
210A LYS* 3.1 24.9 + - - +
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Residues in contact with ARG 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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54A PHE* 3.7 15.9 - - + -
56A PHE* 3.4 24.7 - - - -
62A GLU* 3.1 22.8 + - - +
166A VAL* 3.7 12.7 - - - +
168A TYR* 2.9 24.6 + - - -
177A GLU* 2.6 32.1 + - - -
179A ASP* 4.7 7.5 + - - -
182A ARG* 5.0 5.5 - - - +
203A VAL* 3.4 10.2 + - - +
204A ILE* 3.4 10.2 + - + +
205A GLU 3.2 0.4 - - - -
206A LYS* 1.3 77.4 - - - +
208A ILE* 1.3 64.6 + - - +
209A GLN 3.1 0.3 + - - -
210A LYS* 3.2 4.6 + - + -
211A TYR* 2.7 63.6 + - + +
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Residues in contact with ILE 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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38A LEU* 5.1 10.3 - - + -
54A PHE* 3.5 25.1 - - + -
204A ILE* 2.7 25.9 + - + +
205A GLU* 3.1 27.6 + - + +
207A ARG* 1.3 72.4 - - - +
209A GLN* 1.3 57.0 + - + +
211A TYR* 3.8 2.4 + - - -
212A SER* 2.6 32.8 + - - +
218A PHE* 3.5 37.9 - - + -
220A LEU* 5.0 11.7 - - + -
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Residues in contact with GLN 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 GLU* 2.8 19.4 + - - +
206A LYS* 3.8 6.4 - - - +
208A ILE* 1.3 79.2 - - + +
210A LYS* 1.3 65.2 + - - +
211A TYR 3.1 1.3 - - - -
212A SER* 2.6 19.6 + - - +
213A GLU* 3.1 39.2 + - + +
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Residues in contact with LYS 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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59A GLN* 4.0 17.0 + - - -
62A GLU* 4.3 19.5 + - - +
206A LYS 3.1 16.6 + - - +
207A ARG* 3.2 4.7 + - + +
209A GLN* 1.3 76.8 - - - +
211A TYR* 1.3 73.1 + - + +
213A GLU* 4.0 11.7 - - - +
214A GLY* 3.0 23.0 + - - -
216A ILE* 5.3 0.7 - - - +
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Residues in contact with TYR 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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54A PHE* 3.4 39.9 - + - -
56A PHE* 4.1 17.1 - + + -
59A GLN* 3.1 30.3 + - - -
62A GLU* 2.3 30.5 + - - -
207A ARG* 2.7 48.3 + - + +
210A LYS* 1.3 95.2 - - + +
212A SER* 1.3 62.8 + - - +
214A GLY 3.8 0.9 - - - +
215A GLU 3.4 1.4 + - - -
216A ILE* 2.8 47.4 + - + +
218A PHE* 3.8 17.9 - - + -
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Residues in contact with SER 212 (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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208A ILE* 2.6 19.4 + - - +
209A GLN* 2.6 27.0 + - - +
211A TYR* 1.3 77.5 - - - +
213A GLU* 1.3 59.5 + - - +
215A GLU* 3.1 21.1 + - - +
216A ILE 4.9 0.9 - - - +
218A PHE* 4.1 14.6 - - - -
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Residues in contact with GLU 213 (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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209A GLN* 3.1 41.2 + - + +
210A LYS* 4.2 9.9 - - - +
212A SER* 1.3 74.0 - - - +
214A GLY* 1.3 58.8 + - - +
215A GLU* 2.9 18.7 + - - +
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Residues in contact with GLY 214 (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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210A LYS 3.0 18.6 + - - -
211A TYR 3.7 1.1 + - - -
212A SER 3.3 0.6 - - - -
213A GLU* 1.3 75.2 - - - +
215A GLU* 1.3 71.0 + - - +
216A ILE* 3.2 19.8 + - - +
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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
------------------------------------------------------------
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