Contacts of the helix formed by residues 209 - 220 (chain A) in PDB entry 4ZGA
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 LYS 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A PRO* 2.7 17.7 + - + +
208A THR* 1.3 75.3 - - - +
210A THR* 1.3 67.1 + - - +
211A PHE 3.5 0.4 - - - -
212A PRO* 3.3 16.9 - - + +
213A ASN* 2.9 18.6 + - - -
230A GLY* 6.1 0.2 - - - -
231A ASN* 3.6 34.9 - - + +
360A HIS* 4.0 3.4 - - - -
388A GLY* 6.0 1.2 - - - -
389A THR* 4.2 10.4 + - - +
390A LEU* 4.4 14.6 - - + -
474A ASP* 3.5 19.0 + - - -
475A HIS* 3.3 37.7 + - + +
476A GLY* 4.3 4.7 - - - -
905A EDO 4.2 5.8 + - - +
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Residues in contact with THR 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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172A ASP* 2.5 37.2 + - - +
209A LYS* 1.3 73.9 - - - +
211A PHE* 1.3 75.4 + - + +
213A ASN* 3.2 2.8 + - - +
214A LEU* 2.9 57.4 + - + +
231A ASN* 3.9 0.4 + - - -
244A LEU* 5.7 0.7 - - + -
307A TYR* 4.1 6.7 - - - +
359A ASP* 3.7 8.7 - - - +
360A HIS* 3.1 3.7 + - - -
905A EDO 3.1 24.3 + - - -
910A 4O3 4.7 2.0 - - + +
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Residues in contact with PHE 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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210A THR* 1.3 85.7 - - + +
212A PRO* 1.3 71.1 - - + +
215A TYR* 3.4 16.5 + - - +
228A ILE* 3.8 14.6 - - + +
231A ASN* 3.2 18.1 + - - +
242A PHE* 3.9 30.1 - + - -
244A LEU* 3.1 35.9 - - + -
249A LYS* 4.7 19.5 - - + -
255A TRP* 4.2 9.6 - + - -
909A ACD 5.4 12.8 - - + -
910A 4O3 3.6 59.7 - + + -
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Residues in contact with PRO 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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205A VAL* 4.5 1.3 - - + -
207A PRO* 3.9 27.1 - - + +
209A LYS* 3.3 13.0 - - + +
211A PHE* 1.3 95.1 - - + +
213A ASN* 1.3 57.0 + - - +
216A THR* 3.0 31.5 + - - -
223A PRO* 3.9 13.7 - - + -
226A HIS* 3.3 5.2 + - + -
228A ILE* 3.4 25.8 - - + +
230A GLY* 3.8 20.6 - - - +
231A ASN* 3.3 15.0 - - - +
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Residues in contact with ASN 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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204A PRO* 3.2 2.7 - - - +
205A VAL* 2.6 47.5 + - - +
207A PRO 3.4 3.0 + - - -
208A THR* 3.6 4.9 - - - +
209A LYS 2.9 33.3 + - - +
210A THR 3.2 3.0 + - - +
212A PRO* 1.3 73.8 - - - +
214A LEU* 1.3 63.3 + - - +
216A THR* 3.3 5.3 + - - -
217A LEU* 2.8 35.9 + - + +
359A ASP* 3.2 31.1 + - + +
506A ASN* 3.0 13.5 + - - +
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Residues in contact with LEU 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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170A SER* 4.5 16.2 - - - +
210A THR* 2.9 41.5 + - + +
213A ASN* 1.3 76.5 - - - +
215A TYR* 1.3 57.5 + - - +
217A LEU* 3.3 17.7 - - + +
218A ALA* 2.9 22.0 + - - +
307A TYR* 4.0 9.4 - - + -
358A GLY 5.8 0.2 - - - -
359A ASP* 3.6 27.4 - - + +
910A 4O3 3.4 69.3 - - + +
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Residues in contact with TYR 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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211A PHE 3.4 12.7 + - - +
213A ASN 3.4 0.4 - - - -
214A LEU* 1.3 75.2 - - - +
216A THR* 1.3 60.8 + - - +
218A ALA* 3.0 6.9 + - + -
219A THR* 2.4 49.1 + - + +
226A HIS* 3.3 48.5 - + + -
228A ILE* 3.8 6.1 - - + -
255A TRP* 3.5 46.2 + + + +
256A GLY 2.5 31.4 + - - -
259A PRO* 3.9 28.5 - - + +
261A TRP* 4.5 7.2 - + - -
275A PHE* 6.2 0.2 - + - -
909A ACD 4.7 4.9 - - + +
910A 4O3 3.7 18.5 - + + -
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Residues in contact with THR 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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205A VAL* 3.4 17.9 - - + +
212A PRO 3.0 15.6 + - - -
213A ASN 3.4 4.5 - - - -
214A LEU 3.2 0.2 - - - -
215A TYR* 1.3 73.9 - - - +
217A LEU* 1.3 55.7 + - - +
219A THR* 2.6 35.6 + - - -
220A GLY* 2.8 9.9 + - - -
221A LEU 2.7 22.2 + - - +
223A PRO* 3.5 1.6 - - - +
226A HIS* 3.0 14.2 + - - -
506A ASN* 3.4 30.7 - - - +
507A ILE* 3.6 18.8 - - + -
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Residues in contact with LEU 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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170A SER* 5.7 0.9 - - - -
202A MET* 4.7 1.6 - - + -
213A ASN 2.8 19.4 + - - +
214A LEU* 3.3 28.9 - - + +
216A THR* 1.3 74.0 - - - +
218A ALA* 1.3 60.3 + - - +
219A THR 3.4 0.7 + - - -
220A GLY 4.4 1.9 + - - -
357A VAL* 4.1 25.6 - - + -
358A GLY 4.1 18.2 - - - +
359A ASP* 4.8 2.7 - - - -
506A ASN* 4.0 30.5 - - + +
509A LEU* 4.2 19.0 - - + +
510A TYR* 4.5 8.8 + - - +
513A MET* 3.6 25.8 - - + +
910A 4O3 4.1 19.7 - - - -
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Residues in contact with ALA 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 LEU 2.9 17.2 + - - +
215A TYR* 3.0 10.5 + - + +
216A THR 2.9 1.8 + - - -
217A LEU* 1.3 75.2 - - - +
219A THR* 1.3 57.5 + - + +
259A PRO* 3.3 8.7 - - + +
260A LEU* 3.1 28.6 + - + +
261A TRP* 3.8 32.5 - - + -
274A PHE* 5.8 0.9 - - + -
510A TYR* 3.6 9.7 - - - -
513A MET* 5.4 1.6 - - - -
910A 4O3 4.2 8.7 - - + -
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Residues in contact with THR 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 TYR* 2.4 65.2 + - + +
216A THR* 2.6 21.9 + - - -
217A LEU 3.3 0.2 - - - -
218A ALA* 1.3 76.2 - - - +
220A GLY* 1.3 58.6 + - - +
221A LEU* 3.2 29.5 + - + +
226A HIS* 3.6 7.7 - - + -
256A GLY 4.8 0.2 - - - +
258A GLN 4.3 10.7 + - - +
259A PRO* 4.3 9.6 - - + -
510A TYR* 3.5 18.1 - - - -
523A PRO 5.1 0.3 - - - +
524A ASN* 3.4 13.7 - - - +
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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 THR 2.8 8.8 + - - -
219A THR* 1.3 77.3 - - - +
221A LEU* 1.3 54.9 + - - +
506A ASN 5.4 0.2 - - - -
507A ILE* 3.6 22.7 - - - +
510A TYR* 3.6 20.8 - - - +
524A ASN* 3.4 5.3 - - - +
525A ASN* 2.7 35.3 + - - +
526A GLY 3.4 4.3 + - - -
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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