Contacts of the helix formed by residues 206 - 224 (chain A) in PDB entry 5VO8
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 THR 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 5.5 6.1 - - + -
17A GLY 5.6 1.8 - - - +
18A ARG* 3.6 38.4 + - - +
201A THR* 4.1 1.6 - - - -
205A VAL* 1.3 74.6 - - - +
207A PRO* 1.3 77.3 - - + +
208A LEU* 3.2 25.6 - - + +
209A GLU* 2.9 32.4 + - + +
210A ALA* 2.9 12.5 + - - +
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Residues in contact with PRO 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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15A THR* 5.7 1.8 - - + -
17A GLY 5.1 0.7 - - - +
18A ARG* 3.0 22.0 - - - +
19A GLU 3.6 3.8 - - - +
20A TYR 3.3 32.3 - - - +
21A GLY* 3.7 12.6 - - - +
23A PHE* 3.8 6.8 - - + -
199A ILE* 3.5 40.1 - - + +
201A THR* 3.6 7.8 - - - +
206A THR* 1.3 87.0 - - + +
208A LEU* 1.3 61.2 + - - +
210A ALA* 3.4 3.8 + - + +
211A LEU* 3.1 22.7 + - - +
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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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11A PHE* 4.8 10.1 - - + -
13A VAL* 4.9 12.3 - - + -
15A THR* 4.9 7.4 - - + +
23A PHE* 3.6 31.4 - - + -
206A THR* 3.1 13.6 - - + +
207A PRO* 1.3 76.0 - - - +
209A GLU* 1.3 67.6 + - + +
211A LEU* 3.1 9.1 + - + +
212A ASN* 3.0 43.6 + - - +
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Residues in contact with GLU 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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18A ARG* 4.0 11.4 + - - -
88A ARG* 5.0 4.5 + - - -
204A SER 5.0 0.7 - - - +
205A VAL* 3.5 17.8 - - + +
206A THR* 2.9 36.0 + - + +
208A LEU* 1.3 76.9 - - + +
210A ALA* 1.3 65.3 + - - +
212A ASN* 3.2 10.2 + - - +
213A GLN* 2.9 38.8 + - + +
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Residues in contact with ALA 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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44A LEU* 3.6 17.6 - - + +
48A ILE* 4.0 7.0 - - + +
174A VAL* 4.4 16.4 - - + -
199A ILE* 4.5 4.3 - - + -
201A THR* 5.0 1.3 - - - +
205A VAL* 4.2 11.6 - - + +
206A THR 2.9 10.6 + - - +
207A PRO* 3.4 13.0 - - + +
209A GLU* 1.3 75.8 - - - +
211A LEU* 1.3 52.2 + - - +
213A GLN* 3.0 14.2 + - - +
214A ALA* 2.8 35.2 + - - +
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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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11A PHE* 4.3 6.1 - - + -
23A PHE* 3.4 43.7 - - + -
40A LEU* 3.9 19.5 - - + -
44A LEU* 3.7 12.9 - - + +
197A LEU* 3.8 25.1 - - + -
199A ILE* 5.1 5.2 - - + -
207A PRO 3.1 10.8 + - - +
208A LEU* 3.1 9.8 + - + +
210A ALA* 1.3 77.8 - - - +
212A ASN* 1.3 60.8 + - - +
214A ALA* 3.3 0.3 + - - +
215A VAL* 2.9 40.7 + - + +
225B PHE* 4.2 22.2 - - + -
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Residues in contact with ASN 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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11A PHE* 5.7 1.2 - - - -
208A LEU* 3.0 45.8 + - - +
209A GLU* 3.6 9.2 - - - +
211A LEU* 1.3 78.0 - - - +
213A GLN* 1.3 60.4 + - + +
215A VAL* 3.3 6.5 + - - +
216A GLU* 2.8 30.8 + - - +
225B PHE* 4.3 19.9 - - - +
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Residues in contact with GLN 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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48A ILE* 4.1 15.6 - - + +
49A PRO* 3.7 26.0 - - + +
205A VAL* 4.4 13.9 - - - +
209A GLU* 2.9 37.0 + - + +
210A ALA* 3.4 9.6 - - - +
212A ASN* 1.3 74.6 - - + +
214A ALA* 1.3 58.0 + - - +
216A GLU* 3.2 7.5 + - - +
217A ILE* 2.8 39.3 + - + +
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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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40A LEU* 4.0 14.4 - - + -
43A ILE* 3.6 27.7 - - + +
44A LEU* 3.7 25.1 - - + -
48A ILE* 3.9 3.5 - - + +
210A ALA 2.8 19.2 + - - +
211A LEU* 3.6 5.8 - - - +
213A GLN* 1.3 72.5 - - - +
215A VAL* 1.3 61.6 + - - +
217A ILE* 3.1 4.7 + - - +
218A LEU* 2.9 23.9 + - - +
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Residues in contact with VAL 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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40A LEU* 3.7 20.9 - - + -
211A LEU* 2.9 30.4 + - + +
212A ASN* 3.7 6.5 - - - +
214A ALA* 1.3 74.3 - - - +
216A GLU* 1.3 53.5 + - - +
218A LEU* 3.2 4.0 + - - +
219A ARG* 2.7 36.2 + - + +
222B LEU* 3.6 39.6 - - + +
225B PHE* 3.8 27.4 - - + -
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Residues in contact with GLU 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 ASN 2.8 21.4 + - - +
213A GLN* 3.5 8.1 - - - +
215A VAL* 1.3 75.8 - - - +
217A ILE* 1.3 57.3 + - + +
219A ARG* 2.2 47.4 + - - -
220A GLU* 2.9 41.3 + - - +
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Residues in contact with ILE 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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43A ILE* 3.8 19.3 - - + -
47A SER* 3.8 28.7 - - - +
48A ILE* 4.3 4.3 - - + -
49A PRO* 5.4 2.5 - - + -
213A GLN* 2.8 27.6 + - + +
214A ALA 3.1 6.0 + - - +
216A GLU* 1.3 72.4 - - + +
218A LEU* 1.3 64.3 + - - +
220A GLU* 3.1 10.9 + - - +
221A HIS* 2.8 47.2 + - + +
32B PHE* 3.7 20.4 - - + -
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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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36A LEU* 5.4 2.9 - - + +
39A PRO* 3.8 28.5 - - + -
40A LEU* 4.1 16.2 - - + -
43A ILE* 3.6 21.3 - - + -
214A ALA 2.9 10.9 + - - +
215A VAL* 3.7 4.7 - - - +
217A ILE* 1.3 75.7 - - - +
219A ARG* 1.3 63.9 + - - +
221A HIS* 3.1 15.2 + - + +
222A LEU* 3.2 13.0 + - + +
35B THR* 4.7 5.4 - - + +
36B LEU* 3.7 28.0 - - + -
39B PRO* 6.2 0.2 - - + -
218B LEU* 4.5 21.3 - - + -
222B LEU* 3.7 22.0 - - + -
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Residues in contact with ARG 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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215A VAL* 2.7 22.7 + - + +
216A GLU* 2.2 47.6 + - - +
218A LEU* 1.3 72.3 - - - +
220A GLU* 1.3 81.9 + - - +
222A LEU* 3.1 18.2 + - - +
223A THR* 3.5 28.0 + - + +
219B ARG* 4.6 22.2 - - + +
222B LEU* 3.6 18.9 - - + +
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Residues in contact with GLU 220 (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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216A GLU* 2.9 30.9 + - - +
217A ILE* 3.6 8.0 - - - +
219A ARG* 1.3 89.7 - - - +
221A HIS* 1.3 58.4 + - + +
223A THR* 2.2 39.9 + - + +
224A TYR* 3.4 26.5 + - + +
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Residues in contact with HIS 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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217A ILE* 2.8 39.6 + - + +
218A LEU* 3.3 9.9 - - - +
219A ARG 3.1 0.2 - - - -
220A GLU* 1.3 75.7 - - + +
222A LEU* 1.3 66.7 + - - +
224A TYR* 3.0 52.2 + + - +
225A PHE* 4.1 6.8 - - - -
28B LEU* 4.3 19.5 - - + +
29B GLU* 5.5 5.1 - - + +
32B PHE* 3.3 41.3 - + + -
36B LEU* 4.2 19.7 - - + +
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Residues in contact with LEU 222 (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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218A LEU* 3.2 16.6 + - + +
219A ARG* 3.1 9.0 + - - +
221A HIS* 1.3 76.7 - - - +
223A THR* 1.3 61.7 + - - +
224A TYR 3.1 1.0 + - - -
225A PHE* 3.2 37.2 + - + +
36B LEU* 4.3 13.2 - - + -
40B LEU* 4.6 5.4 - - + -
215B VAL* 3.9 32.8 - - + +
218B LEU* 3.4 47.3 - - + -
219B ARG* 4.1 18.2 - - + +
222B LEU* 4.7 4.7 - - + -
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Residues in contact with THR 223 (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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219A ARG* 3.5 29.6 - - + +
220A GLU* 2.2 37.9 + - + +
222A LEU* 1.3 77.0 - - - +
224A TYR* 1.4 65.2 + - - +
225A PHE 3.0 0.2 - - - -
226A SER* 2.9 33.6 + - - -
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Residues in contact with TYR 224 (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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220A GLU* 3.4 35.2 + - + +
221A HIS* 3.0 55.9 + + - +
223A THR* 1.4 80.1 - - - +
225A PHE* 1.3 57.1 + - - +
226A SER* 3.1 4.9 + - - -
227A ASN 4.6 2.4 + - - +
7B LYS 5.6 0.9 - - - -
8B ALA* 5.0 10.8 - - + -
9B PRO* 3.8 45.1 - - + +
11B PHE* 3.9 16.3 - - - +
25B LEU* 4.2 17.6 - - + +
28B LEU* 5.0 3.4 - - + -
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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