Contacts of the helix formed by residues 197 - 217 (chain A) in PDB entry 2Z4U
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 ASN 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A TYR* 3.1 21.7 + - - -
185A GLN* 3.4 21.8 + - - +
195A ASN 3.2 6.2 + - - +
196A PRO* 1.3 76.3 - - - +
198A PRO* 1.4 75.7 - - + +
199A LYS* 2.9 19.1 + - - +
200A VAL* 3.0 24.7 + - - +
201A LEU* 3.2 12.8 + - - +
231A ALA* 3.7 16.9 - - - +
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Residues in contact with PRO 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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197A ASN* 1.4 90.3 - - + +
199A LYS* 1.3 55.3 + - - +
201A LEU* 3.5 11.0 + - + +
202A SER* 2.9 28.9 + - - -
229A LYS* 3.8 7.9 - - + +
230A ASN 3.7 11.4 - - - +
231A ALA 3.3 17.3 - - - +
233A ASP* 3.5 35.9 - - + +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A TYR* 3.6 38.2 - - + +
197A ASN* 2.9 9.0 + - - +
198A PRO* 1.3 77.0 - - - +
200A VAL* 1.3 66.7 + - - +
202A SER* 3.7 0.8 - - - -
203A LEU* 2.9 33.4 + - + +
229A LYS 3.4 24.9 - - - +
230A ASN* 3.8 7.5 + - - +
231A ALA* 3.6 19.3 - - + +
236A TRP* 3.6 25.1 - - + -
247A ASP* 2.7 33.6 + - - -
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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
----------------------------------------------------------
139A LEU* 5.5 3.6 - - + -
171A GLN* 4.5 0.2 - - - +
181A TYR* 3.8 17.9 - - + -
182A ILE* 3.8 25.9 - - + +
185A GLN* 4.0 18.6 - - + +
194A PHE* 5.5 2.2 - - + -
196A PRO* 3.8 20.4 - - + -
197A ASN* 3.0 34.2 + - - +
199A LYS* 1.3 77.3 - - - +
201A LEU* 1.4 63.1 + - - +
203A LEU* 3.8 2.6 - - - +
204A GLU* 3.0 48.4 + - - +
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Residues in contact with LEU 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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133A SER* 4.3 9.2 - - - +
134A ARG* 3.6 40.6 - - + +
135A SER* 4.3 23.3 - - - +
196A PRO* 4.2 18.4 - - + +
197A ASN 3.2 13.9 + - - +
198A PRO* 3.8 11.9 - - + +
200A VAL* 1.4 75.1 - - - +
202A SER* 1.3 58.3 + - - +
204A GLU* 3.4 9.3 + - - +
205A GLU* 3.0 47.6 + - - +
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Residues in contact with SER 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 PRO 2.9 18.7 + - - -
199A LYS 3.3 3.8 + - - -
201A LEU* 1.3 73.6 - - - +
203A LEU* 1.3 66.4 + - - +
205A GLU* 3.3 6.1 + - - -
206A ASN* 2.9 35.8 + - - +
228A LEU* 3.4 17.3 - - - +
229A LYS* 3.1 39.2 + - - +
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Residues in contact with LEU 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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179A PHE* 3.1 40.8 - - + -
181A TYR* 3.7 43.3 - - + -
182A ILE* 4.7 2.9 - - + -
199A LYS* 2.9 27.9 + - + +
200A VAL 3.8 3.4 - - - +
202A SER* 1.3 76.5 - - - +
204A GLU* 1.3 64.2 + - - +
206A ASN 3.1 11.1 + - - -
207A TRP 3.1 11.1 + - - -
210A ILE* 3.9 22.4 - - + -
228A LEU* 4.4 4.9 - - + -
236A TRP* 4.3 20.6 - - + -
244A ILE* 4.4 5.8 - - + -
247A ASP* 4.5 5.2 - - + -
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Residues in contact with GLU 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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122A TYR* 3.9 11.2 - - + -
134A ARG* 2.9 36.1 + - - +
171A GLN* 2.6 32.1 - - - +
175A GLU* 3.5 39.2 - - + +
179A PHE* 4.0 2.4 - - - -
182A ILE* 3.8 8.6 - - + +
200A VAL* 3.0 33.8 + - - +
201A LEU* 3.6 8.3 - - - +
203A LEU* 1.3 76.8 - - - +
205A GLU* 1.3 61.6 + - - +
206A ASN 3.4 0.3 + - - -
207A TRP* 3.9 10.6 + - - +
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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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122A TYR* 5.6 2.9 - - + -
134A ARG* 2.9 30.7 + - - +
201A LEU* 3.0 27.6 + - - +
202A SER* 3.9 7.3 - - - +
203A LEU 3.2 0.2 - - - -
204A GLU* 1.3 75.5 - - - +
206A ASN* 1.3 69.1 + - - +
207A TRP 3.7 0.4 - - - -
208A GLY 5.5 0.3 + - - -
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Residues in contact with ASN 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 SER* 2.9 26.5 + - - +
203A LEU 3.1 4.4 + - - -
205A GLU* 1.3 90.4 + - - +
207A TRP* 1.3 58.9 + - - +
208A GLY 3.2 2.9 - - - -
209A LYS* 3.1 37.3 + - + +
210A ILE* 2.8 33.9 + - + +
226A LEU* 5.1 2.0 - - - +
227A GLU 5.2 3.4 + - - +
228A LEU* 3.6 28.2 - - + +
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Residues in contact with TRP 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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40A LEU* 3.5 22.4 - - + -
70A ASN* 3.5 25.1 - - + -
72A TYR* 4.7 8.1 - + - -
178A ARG* 3.4 40.3 - - + +
179A PHE* 3.4 33.4 - + + -
203A LEU 3.1 7.5 + - - +
204A GLU 3.9 7.6 + - - +
205A GLU 3.7 1.6 - - - -
206A ASN* 1.3 76.9 - - - +
208A GLY* 1.3 59.4 + - - +
210A ILE* 3.8 3.2 - - - +
211A SER* 2.8 40.6 + - - -
248A MET* 4.1 7.0 - - + -
250A LEU* 2.9 24.1 + - + -
251A LEU 3.9 1.3 - - - -
252A ASN* 3.4 50.5 - - + -
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Residues in contact with GLY 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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206A ASN 3.2 0.6 - - - -
207A TRP* 1.3 81.6 - - - +
209A LYS* 1.3 62.9 + - - +
211A SER* 3.4 2.6 + - - -
212A LEU* 3.1 23.9 + - - +
252A ASN* 4.2 20.0 - - - +
254A VAL* 5.6 0.5 - - - +
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Residues in contact with LYS 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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206A ASN* 3.1 32.5 + - - +
208A GLY* 1.3 77.4 - - - +
210A ILE* 1.3 61.6 + - - +
212A LEU* 3.5 9.8 + - + +
213A ALA* 3.0 23.9 + - - +
226A LEU* 3.9 26.6 - - + +
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Residues in contact with ILE 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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179A PHE* 4.2 10.1 - - + -
203A LEU* 3.9 30.3 - - + +
206A ASN* 2.8 33.2 + - + +
207A TRP* 3.8 3.8 - - - +
209A LYS* 1.3 76.3 - - - +
211A SER* 1.3 59.0 + - - +
213A ALA* 3.2 3.1 + - - +
214A ILE* 2.9 39.7 + - + +
226A LEU* 3.4 24.5 - - + -
228A LEU* 3.9 10.8 - - + -
244A ILE* 3.9 14.1 - - + -
248A MET* 3.8 28.5 - - + -
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Residues in contact with SER 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 TRP* 2.8 30.6 + - - -
208A GLY 3.8 1.8 - - - -
210A ILE* 1.3 77.4 - - - +
212A LEU* 1.3 56.2 + - - +
214A ILE* 3.4 2.6 + - - +
215A HIS* 3.0 30.1 + - - +
248A MET* 4.7 0.7 - - - +
251A LEU* 3.6 23.1 - - - +
252A ASN* 2.9 46.5 + - - +
254A VAL* 4.1 5.0 - - - +
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Residues in contact with LEU 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 GLY 3.1 17.3 + - - +
209A LYS* 3.7 8.5 - - + +
211A SER* 1.3 77.2 - - - +
213A ALA* 1.3 57.8 + - - +
215A HIS* 3.3 1.1 + - - +
216A ASN* 2.9 59.6 + - - +
254A VAL* 4.0 27.3 - - + +
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Residues in contact with ALA 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 LYS 3.0 17.9 + - - +
210A ILE* 3.6 7.6 - - - +
212A LEU* 1.3 78.6 - - - +
214A ILE* 1.3 62.8 + - + +
216A ASN* 3.4 4.6 + - - +
217A ALA* 3.1 23.4 + - - +
222A LEU* 3.8 33.3 - - + +
223A THR 5.2 1.8 + - - +
224A SER 5.0 4.9 - - - +
226A LEU* 4.6 7.0 - - + -
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Residues in contact with ILE 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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34A CYS* 4.3 2.2 - - + +
35A TYR* 3.4 34.3 - - + -
37A ILE* 4.1 15.7 - - + -
210A ILE* 2.9 36.3 + - + +
211A SER 3.9 3.1 - - - +
213A ALA* 1.3 75.3 - - + +
215A HIS* 1.3 65.8 + - - +
217A ALA* 3.2 13.6 + - - +
222A LEU* 5.5 2.0 - - + -
241A VAL* 4.3 13.9 - - + -
244A ILE* 4.1 19.5 - - + -
248A MET* 4.0 15.7 - - + -
251A LEU* 3.9 34.1 - - + -
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Residues in contact with HIS 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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34A CYS* 3.6 31.6 - - - +
39A MET* 4.0 5.2 - - + -
211A SER 3.0 18.2 + - - +
212A LEU 3.7 3.8 - - - +
214A ILE* 1.3 78.0 - - - +
216A ASN* 1.3 84.5 + - - +
217A ALA 3.5 3.3 + - - +
218A LYS* 5.4 1.6 - - - -
251A LEU* 5.2 0.2 - - - +
254A VAL* 3.6 33.0 + - + +
255A SER 3.3 20.3 + - - -
256A GLY* 2.9 24.6 + - - -
257A THR 3.3 20.8 + - - +
258A CYS* 3.3 19.0 - - + +
259A GLN 4.8 0.7 + - - -
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Residues in contact with ASN 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 LEU* 2.9 41.1 + - - +
213A ALA* 3.8 5.4 - - - +
215A HIS* 1.3 100.0 + - - +
217A ALA* 1.3 64.0 + - - +
218A LYS* 3.3 21.6 + - - +
223A THR* 3.7 21.6 + - - +
254A VAL* 4.8 0.3 - - - +
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Residues in contact with ALA 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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35A TYR* 2.7 27.2 + - - +
213A ALA 3.1 16.6 + - - +
214A ILE 3.2 10.9 + - - +
215A HIS 3.3 2.5 - - - +
216A ASN* 1.3 78.2 - - - +
218A LYS* 1.3 60.8 + - - +
221A ALA 3.3 21.5 - - - +
222A LEU* 4.2 4.5 - - - +
223A THR 4.8 0.9 - - - +
241A VAL* 3.6 24.9 - - + -
259A GLN* 5.0 4.5 + - - +
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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