Contacts of the helix formed by residues 203 - 221 (chain A) in PDB entry 5WIU
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 LEU 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL* 2.9 37.5 + - + +
199A CYS* 4.7 6.5 - - - +
202A PHE* 1.3 78.3 - - - +
204A PRO* 1.3 67.0 - - + +
205A CYS 3.3 0.2 - - - -
206A PRO* 3.3 11.7 - - + +
207A LEU* 3.3 36.5 - - + +
1208A OLA 4.8 16.8 - - + -
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Residues in contact with PRO 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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123A ILE* 4.1 7.9 - - + -
124A PHE* 4.2 4.7 - - + -
127A CYS* 3.3 25.4 - - - -
198A VAL 3.6 2.0 - - - +
199A CYS 3.3 20.9 - - - +
200A SER 3.3 26.0 - - - +
201A PHE* 3.4 7.9 - - - +
203A LEU* 1.3 92.4 - - + +
205A CYS* 1.3 56.3 + - - +
207A LEU* 3.2 6.8 + - + +
208A MET* 2.8 34.5 + - - +
1208A OLA 4.2 17.0 - - + -
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Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 4.6 4.7 - - - -
201A PHE* 3.0 49.1 + - - +
204A PRO* 1.3 77.4 - - - +
206A PRO* 1.3 69.0 - - + +
208A MET* 3.4 17.0 + - - +
209A LEU* 3.0 33.4 + - + +
403A PHE* 5.6 1.3 - - - -
404A LEU* 3.6 29.8 - - + -
1213A OLA 3.9 15.7 - - + -
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Residues in contact with PRO 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE 3.0 29.8 - - - +
203A LEU* 3.3 16.6 - - + +
205A CYS* 1.3 88.8 - - + +
207A LEU* 1.3 66.2 + - + +
209A LEU* 3.3 9.8 + - + +
210A LEU* 3.0 23.9 + - - +
1213A OLA 4.8 7.2 - - + -
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Residues in contact with LEU 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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127A CYS* 5.8 1.6 - - - -
203A LEU* 3.3 32.3 - - + +
204A PRO* 3.2 7.7 + - + +
206A PRO* 1.3 79.9 - - + +
208A MET* 1.3 63.9 + - - +
210A LEU* 3.3 15.4 + - + +
211A LEU* 3.1 32.6 + - + +
1208A OLA 4.7 17.9 - - + -
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Residues in contact with MET 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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123A ILE* 4.0 19.7 - - + +
126A LEU* 3.7 30.1 - - + -
127A CYS* 3.5 30.0 - - - -
130A SER* 3.9 16.4 - - - +
204A PRO 2.8 19.3 + - - +
205A CYS* 3.7 21.1 - - - +
207A LEU* 1.3 74.2 - - - +
209A LEU* 1.3 59.9 + - + +
211A LEU* 3.3 1.8 + - - +
212A TYR* 2.9 52.8 + - + -
400A VAL* 4.3 17.7 - - + -
403A PHE* 6.3 0.9 - - + -
404A LEU* 5.8 1.6 - - + -
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Residues in contact with LEU 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 CYS* 3.0 27.7 + - + +
206A PRO* 3.8 8.5 - - + +
208A MET* 1.3 76.4 - - + +
210A LEU* 1.3 62.6 + - - +
212A TYR* 3.6 3.9 + - + +
213A TRP* 3.1 23.6 + - - +
400A VAL* 4.0 14.6 - - + -
404A LEU* 4.2 18.2 - - + -
1210A OLA 3.6 46.5 - - + +
1213A OLA 5.8 4.5 - - + -
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Residues in contact with LEU 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 PRO 3.0 17.3 + - - +
207A LEU* 3.3 15.7 + - + +
209A LEU* 1.3 75.5 - - - +
211A LEU* 1.3 66.2 + - + +
213A TRP* 3.4 25.3 + - + +
214A ALA* 3.0 27.5 + - + +
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Residues in contact with LEU 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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130A SER* 3.7 24.9 - - - +
131A VAL* 3.6 34.3 - - + -
134A PHE* 4.1 33.4 - - + -
207A LEU* 3.1 22.2 + - + +
208A MET 3.8 0.2 - - - +
210A LEU* 1.3 83.6 - - + +
212A TYR* 1.3 65.2 + - - +
214A ALA* 3.4 4.6 + - + +
215A THR* 2.9 29.2 + - - -
1211A OLA 4.0 21.3 - - + -
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Residues in contact with TYR 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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126A LEU* 2.8 23.3 + - - +
129A ILE* 3.3 26.0 - - + +
130A SER* 3.5 28.5 - - - -
133A ARG* 5.7 1.8 - - + -
208A MET* 2.9 41.3 + - + +
209A LEU* 4.0 2.9 - - - +
211A LEU* 1.3 75.4 - - - +
213A TRP* 1.3 62.5 + - - +
215A THR* 3.3 6.2 + - - -
216A PHE* 3.0 44.9 + + + -
393A MET* 5.2 4.0 - - + -
396A LEU* 4.3 22.3 - - + +
397A PRO 6.2 0.2 - - - -
400A VAL* 3.6 30.4 - - + +
1210A OLA 3.9 27.6 - - + -
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Residues in contact with TRP 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 LEU 3.1 18.6 + - - +
210A LEU* 3.6 28.5 - - + +
211A LEU 3.2 0.2 - - - -
212A TYR* 1.3 77.6 - - - +
214A ALA* 1.3 81.4 + - + +
216A PHE* 3.5 3.3 + - + +
217A ARG* 3.0 41.3 + - + +
1210A OLA 4.0 19.0 - - + +
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Residues in contact with ALA 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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134A PHE* 3.9 24.6 - - + -
210A LEU* 3.0 20.0 + - + +
211A LEU* 3.8 8.7 - - + +
213A TRP* 1.3 92.1 - - + +
215A THR* 1.3 52.5 + - - +
217A ARG* 3.3 4.5 + - - +
218A GLY* 2.7 32.9 + - - -
221A ARG* 5.3 1.4 + - - -
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Residues in contact with THR 215 (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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130A SER* 4.1 2.6 + - - -
133A ARG* 3.9 11.9 - - + +
134A PHE* 3.2 30.1 + - - +
137A VAL* 3.7 26.8 - - + +
211A LEU 2.9 21.2 + - - -
212A TYR* 3.5 8.0 - - - -
214A ALA* 1.3 73.4 - - - +
216A PHE* 1.3 66.4 + - - +
218A GLY* 3.2 2.9 + - - -
219A LEU* 3.0 24.0 + - + +
393A MET* 3.6 27.4 - - + -
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Residues in contact with PHE 216 (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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212A TYR* 3.0 40.2 + + - +
213A TRP* 4.0 4.7 - - + +
215A THR* 1.3 75.4 - - - +
217A ARG* 1.3 63.4 + - - +
219A LEU* 3.4 3.3 + - - +
220A GLN* 3.1 26.5 + - - +
390A ARG* 3.7 26.2 - - + -
393A MET* 3.4 56.1 - - + -
394A ARG* 4.8 2.7 - - - -
396A LEU* 5.3 0.4 - - + -
397A PRO* 3.8 24.0 - - + -
1210A OLA 3.6 58.6 - - + +
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Residues in contact with ARG 217 (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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213A TRP* 3.0 40.1 + - + +
214A ALA* 3.7 6.1 - - - +
216A PHE* 1.3 78.0 - - - +
218A GLY* 1.3 62.7 + - - +
220A GLN* 3.3 11.4 + - + +
221A ARG* 3.3 43.3 + - - +
1210A OLA 5.5 0.7 - - - -
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Residues in contact with GLY 218 (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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134A PHE* 6.5 0.2 - - - -
137A VAL* 3.8 14.4 - - - -
214A ALA 2.7 21.4 + - - -
215A THR 3.2 2.6 + - - -
217A ARG* 1.3 74.0 - - - +
219A LEU* 1.3 59.8 + - - +
221A ARG* 3.4 28.7 + - - +
222A TRP* 3.1 20.1 + - - -
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Residues in contact with LEU 219 (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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137A VAL* 3.6 29.2 - - + -
215A THR 3.0 19.3 + - - +
216A PHE 3.9 0.2 - - - +
218A GLY* 1.3 73.1 - - - +
220A GLN* 1.3 57.6 + - - +
222A TRP* 2.8 31.6 + - - +
223A GLU* 3.5 10.9 + - + +
384A LYS* 3.5 32.4 - - + +
389A GLU* 3.7 14.8 - - + +
390A ARG* 3.9 38.1 - - + +
393A MET* 3.7 31.4 - - + -
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Residues in contact with GLN 220 (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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216A PHE 3.1 14.8 + - - +
217A ARG* 3.3 14.1 + - + +
219A LEU* 1.3 75.9 - - - +
221A ARG* 1.3 61.7 + - - +
223A GLU* 3.1 29.9 + - - +
390A ARG* 3.0 46.1 - - - +
1046A PRO* 5.1 1.2 - - - +
1203A PO4 3.9 7.5 + - - -
1210A OLA 3.6 11.8 + - - +
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Residues in contact with ARG 221 (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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214A ALA 5.3 0.8 + - - -
217A ARG* 3.3 36.4 + - - +
218A GLY* 3.5 23.6 - - - +
219A LEU 3.1 0.8 - - - -
220A GLN* 1.3 78.5 - - - +
222A TRP* 1.3 60.1 + - + +
1046A PRO* 3.4 18.8 - - + +
1047A LYS* 3.1 39.9 + - + +
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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