Contacts of the helix formed by residues 203 - 220 (chain A) in PDB entry 5ZX2
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 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASP 4.9 5.2 - - - -
198A THR* 4.0 1.3 - - - -
202A ILE* 1.3 78.7 - - - +
204A PRO* 1.3 74.8 - - - +
205A ARG* 3.8 22.0 + - - +
206A ASP* 3.0 42.3 + - - +
207A ALA* 3.2 10.0 + - - +
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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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11A GLU* 5.6 0.4 - - - +
16A ASP 3.8 15.5 - - - +
17A ASN 3.3 27.1 - - - +
18A ARG 3.8 3.6 - - - +
19A SER* 3.8 29.8 - - - +
21A PHE* 4.0 6.3 - - + -
196A VAL* 4.1 20.5 - - + +
198A THR* 3.7 19.5 - - + +
203A SER* 1.3 86.5 - - - +
205A ARG* 1.3 61.8 + - - +
207A ALA* 3.3 2.1 + - - +
208A LEU* 2.9 25.6 + - - +
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Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 2.6 49.5 + - - +
13A VAL* 4.4 9.3 - - - +
21A PHE* 3.9 12.2 - - - -
203A SER* 3.2 19.9 + - - +
204A PRO* 1.3 81.0 - - - +
206A ASP* 1.3 65.0 + - - +
208A LEU* 3.5 2.8 + - - +
209A ALA* 2.9 26.7 + - - +
225B LEU* 4.1 34.3 - - + +
226B ASN* 5.8 0.4 - - + -
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Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 4.7 12.9 - - + +
203A SER* 3.0 28.5 + - - +
205A ARG* 1.3 79.4 + - - +
207A ALA* 1.3 62.0 + - - +
209A ALA* 3.1 7.0 + - - +
210A SER* 2.9 29.5 + - - -
226B ASN* 3.3 32.0 + - - +
229B ALA* 4.0 4.4 - - + +
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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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42A LEU* 3.7 16.6 - - + -
46A ILE* 3.5 5.7 - - + +
171A VAL* 4.0 16.6 - - + -
196A VAL* 4.9 1.1 - - + -
198A THR* 4.1 8.5 - - + -
202A ILE* 3.9 22.3 - - + +
203A SER 3.2 9.4 + - - +
204A PRO 3.7 6.7 - - - +
206A ASP* 1.3 77.4 - - - +
208A LEU* 1.3 58.5 + - - +
210A SER* 3.1 9.9 + - - -
211A ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 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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9A LEU* 4.6 7.9 - - + -
21A PHE* 3.5 47.8 - - + -
23A ILE* 6.2 1.1 - - + -
38A LEU* 3.9 29.2 - - + -
42A LEU* 4.0 10.8 - - + +
194A LEU* 4.1 17.9 - - + -
196A VAL* 5.3 3.1 - - + -
204A PRO 2.9 16.7 + - - +
205A ARG 3.8 4.3 - - - +
207A ALA* 1.3 77.2 - - - +
209A ALA* 1.3 58.4 + - - +
211A ALA* 3.5 4.0 + - + -
212A GLY* 2.9 23.6 + - - -
222B ALA* 3.7 10.8 - - + +
225B LEU* 3.8 13.7 - - + -
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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 ARG 2.9 15.8 + - - +
206A ASP 3.1 8.5 + - - +
208A LEU* 1.3 76.8 - - - +
210A SER* 1.3 57.9 + - - +
212A GLY* 3.0 4.0 + - - -
213A LYS* 2.9 24.9 + - - +
222B ALA 3.4 13.2 + - - +
223B ARG* 3.8 6.6 - - - +
225B LEU* 4.2 0.6 - - + +
226B ASN* 3.6 32.1 - - + +
229B ALA* 3.6 18.5 - - + +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.2 18.4 - - - +
47A PRO* 3.8 9.5 - - - +
206A ASP 2.9 12.6 + - - -
207A ALA* 3.1 9.9 + - - -
209A ALA* 1.3 73.2 - - - +
211A ALA* 1.3 69.9 + - - +
213A LYS* 3.2 7.5 + - - +
214A THR* 2.9 28.3 + - - -
229B ALA* 3.7 9.5 - - - +
230B GLU 3.0 30.3 - - - -
231B GLY* 4.3 1.3 - - - -
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Residues in contact with ALA 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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38A LEU* 4.7 6.7 - - + -
41A THR* 3.9 22.7 - - + -
42A LEU* 4.0 16.8 - - + -
46A ILE* 3.7 11.8 - - + +
207A ALA 2.9 16.6 + - - +
208A LEU* 3.5 12.1 - - + +
210A SER* 1.3 77.9 + - - +
212A GLY* 1.3 56.1 + - - +
214A THR* 3.3 2.1 + - - -
215A LEU* 2.9 35.9 + - - +
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Residues in contact with GLY 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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38A LEU* 5.2 2.0 - - - +
208A LEU 2.9 15.9 + - - -
209A ALA 3.0 5.1 + - - -
211A ALA* 1.3 76.3 - - - +
213A LYS* 1.3 56.9 + - - +
215A LEU* 4.0 1.1 - - - +
216A VAL* 2.9 35.0 + - - +
219B PHE* 3.8 10.9 - - - +
222B ALA* 3.9 5.6 - - - -
223B ARG* 3.7 20.4 - - - -
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Residues in contact with LYS 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 ALA 2.9 10.1 + - - +
210A SER* 3.2 8.9 + - - +
212A GLY* 1.3 75.0 - - - +
214A THR* 1.3 65.2 + - - +
216A VAL* 3.2 4.7 + - + +
217A GLU* 3.0 38.0 + - + +
223B ARG* 3.7 37.1 - - - +
229B ALA 3.8 12.7 + - - +
230B GLU* 4.5 6.9 - - - +
231B GLY* 3.4 38.9 + - - +
232B ILE 4.4 0.2 - - - -
233B GLU* 3.0 30.2 + - - +
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Residues in contact with THR 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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41A THR* 4.0 20.8 - - + +
45A SER* 4.6 4.3 + - - -
46A ILE* 5.9 0.7 - - - +
210A SER 2.9 17.1 + - - -
211A ALA 3.6 4.0 - - - -
213A LYS* 1.3 77.6 - - - +
215A LEU* 1.3 58.9 - - - +
217A GLU* 3.9 1.7 - - - +
218A LEU* 2.9 33.9 + - + +
30B PHE* 4.2 21.1 - - + -
231B GLY* 3.8 1.4 - - - -
232B ILE* 3.1 51.5 + - + +
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Residues in contact with LEU 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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37A SER* 4.1 11.9 - - - +
38A LEU* 3.7 18.4 - - + -
41A THR* 3.2 29.2 - - + +
211A ALA 2.9 18.7 + - - +
214A THR* 1.3 73.8 - - - +
216A VAL* 1.3 61.1 + - - +
218A LEU* 4.2 8.5 - - + -
219A PHE* 2.9 52.5 + - + +
30B PHE* 4.9 2.9 - - + -
33B THR* 5.0 3.4 - - - +
34B LEU* 4.8 9.9 - - + -
219B PHE* 3.6 48.2 - - + -
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Residues in contact with VAL 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 GLY 2.9 23.0 + - - +
213A LYS* 3.7 5.6 - - + +
215A LEU* 1.3 76.9 - - - +
217A GLU* 1.3 64.0 + - + +
219A PHE* 5.2 0.2 - - - -
220A GLY* 3.2 17.7 + - - -
216B VAL* 3.5 34.9 - - + +
219B PHE* 3.5 6.3 - - + +
220B GLY* 3.3 35.2 - - - +
223B ARG* 4.3 18.4 - - + +
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Residues in contact with GLU 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 LYS* 3.0 23.6 + - + +
214A THR 4.1 2.2 - - - +
216A VAL* 1.3 80.0 - - + +
218A LEU* 1.3 63.4 + - - +
220A GLY* 3.4 11.9 + - - -
221A LEU* 4.2 5.2 + - - +
232B ILE 3.1 21.3 - - - +
233B GLU* 3.1 43.3 - - - +
234B ILE 3.5 18.0 + - - +
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Residues in contact with LEU 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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214A THR* 2.9 22.7 + - + +
215A LEU* 3.8 8.1 - - + +
216A VAL 3.2 0.2 - - - -
217A GLU* 1.3 76.8 - - - +
219A PHE* 1.3 62.8 + - - +
220A GLY 3.1 0.2 - - - -
221A LEU* 3.1 43.1 + - + +
7B PRO* 5.0 6.7 - - + -
26B LEU* 4.6 10.5 - - + -
30B PHE* 3.5 47.6 - - + -
34B LEU* 3.8 29.6 - - + +
232B ILE* 6.4 1.8 - - + -
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Residues in contact with PHE 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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37A SER* 4.9 0.9 - - - -
215A LEU* 2.9 40.6 + - + +
216A VAL* 5.2 0.2 - - - -
218A LEU* 1.3 68.2 - - - +
220A GLY* 1.3 57.3 + - - +
221A LEU* 3.0 5.8 - - - -
222A ALA* 2.8 30.2 + - + +
33B THR 4.0 7.0 - - - -
34B LEU* 3.5 53.8 - - + -
37B SER* 4.3 7.6 - - - -
38B LEU* 4.0 12.6 - - + -
212B GLY* 4.3 2.2 - - - +
215B LEU* 3.6 34.1 - - + -
216B VAL* 4.0 16.7 - - + +
219B PHE* 3.2 37.2 - + - -
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Residues in contact with GLY 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 VAL 3.2 13.8 + - - -
217A GLU* 3.4 8.5 + - - -
218A LEU 3.1 3.0 - - - -
219A PHE* 1.3 76.9 - - - +
221A LEU* 1.3 59.3 + - - +
222A ALA 3.2 4.9 - - - -
223A ARG* 3.0 29.0 + - - -
216B VAL* 4.1 9.6 - - - -
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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