Contacts of the helix formed by residues 208 - 220 (chain A) in PDB entry 1ZQB
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 PRO 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A LYS* 4.2 9.2 - - + -
207A GLN* 1.4 92.0 - - + +
209A LYS* 1.3 69.2 - - + +
211A LEU* 2.8 25.5 + - - +
212A HIS* 3.0 27.1 - - + +
232A GLU* 3.7 44.6 - - + +
259A LEU* 5.7 0.4 - - + -
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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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207A GLN* 2.9 9.8 + - + +
208A PRO* 1.3 92.6 - - + +
210A LEU* 1.3 53.2 - - - +
212A HIS* 2.7 26.7 + - + +
213A GLN* 2.5 46.9 + - + +
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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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173A TYR* 2.6 41.1 + - + +
195A LEU* 5.0 0.3 - - - +
197A HIS* 3.0 37.9 - - + +
199A SER* 4.4 0.7 - - - +
200A PHE* 3.6 31.9 - - + -
207A GLN* 2.4 68.7 + - + +
209A LYS* 1.3 71.0 - - - +
211A LEU* 1.3 64.7 + - - +
213A GLN* 3.7 9.6 + - - +
214A VAL* 3.7 5.5 - - - +
259A LEU* 3.3 15.5 - - + -
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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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195A LEU* 5.0 5.4 - - + -
208A PRO 2.8 12.2 + - - +
210A LEU* 1.3 85.1 - - - +
212A HIS* 1.4 60.3 - - + +
214A VAL* 3.1 29.3 + - + +
215A VAL* 3.4 23.3 + - + -
230A LYS* 4.8 1.8 - - + -
231A GLY 3.4 23.6 - - - +
232A GLU 4.4 7.9 - - - +
233A THR 4.0 2.5 - - - -
234A LYS* 3.5 21.1 - - - +
235A PHE* 3.6 20.6 - - + +
257A ILE* 4.3 16.8 - - + +
259A LEU* 3.8 20.3 - - + +
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Residues in contact with HIS 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 PRO* 3.0 29.7 + - + +
209A LYS* 2.7 40.4 + - + +
211A LEU* 1.4 80.9 - - + +
213A GLN* 1.3 61.9 - - - +
215A VAL* 3.6 5.5 + - - +
216A GLU* 3.4 27.0 + - - +
230A LYS* 4.4 18.7 - - + +
231A GLY 3.4 19.6 + - - -
232A GLU* 3.7 10.2 - - + -
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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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169A VAL* 3.8 26.9 - - + +
170A ASP* 5.3 2.4 + - - +
173A TYR* 2.7 38.1 + - - +
207A GLN* 5.4 4.8 + - - +
209A LYS* 2.5 25.2 + - + +
210A LEU* 3.7 17.2 - - - +
211A LEU 3.1 0.2 - - - -
212A HIS* 1.3 75.3 - - - +
214A VAL* 1.3 58.0 + - + +
216A GLU* 3.5 9.5 - - - +
217A GLN* 3.2 21.7 + - - +
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Residues in contact with VAL 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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166A VAL* 4.8 12.3 - - + -
169A VAL* 4.7 7.6 - - + -
173A TYR* 4.1 17.5 - - + -
195A LEU* 3.9 20.4 - - + -
210A LEU 3.7 11.0 - - - +
211A LEU* 3.1 16.8 + - + +
213A GLN* 1.3 70.8 - - - +
215A VAL* 1.3 80.8 + - + +
216A GLU 3.1 1.8 - - - -
217A GLN* 3.0 7.3 + - + +
218A LEU* 2.8 50.3 + - + +
257A ILE* 4.3 11.2 - - + -
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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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211A LEU* 3.4 23.0 + - + +
212A HIS* 3.6 7.1 + - - +
213A GLN 3.4 0.8 - - - -
214A VAL* 1.3 86.5 - - + +
216A GLU* 1.3 58.2 + - - +
218A LEU* 3.2 3.6 + - - +
219A GLN* 2.9 44.6 + - - +
224A ILE* 4.1 10.0 - - + +
227A THR* 4.9 0.9 - - - +
230A LYS* 4.4 15.3 - - + +
235A PHE* 3.8 53.4 - - + -
257A ILE* 4.2 8.3 - - + -
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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 HIS 3.4 18.3 + - - +
213A GLN* 3.5 9.0 - - - +
215A VAL* 1.3 74.5 - - - +
217A GLN* 1.3 56.5 + - - +
219A GLN* 3.0 16.8 + - + +
220A LYS* 2.7 38.8 + - + +
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Residues in contact with GLN 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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165A GLU* 2.8 54.4 - - + +
168A LYS* 3.7 9.3 + - + -
169A VAL* 4.8 10.0 - - + +
213A GLN 3.2 11.4 + - - +
214A VAL* 3.0 12.1 + - - +
216A GLU* 1.3 82.9 - - - +
218A LEU* 1.4 62.8 + - + +
219A GLN 3.0 0.2 + - - -
220A LYS* 3.0 36.8 + - - +
221A VAL* 3.0 29.9 + - - +
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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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162A VAL* 4.7 23.8 - - + +
165A GLU* 4.1 20.9 - - + -
166A VAL* 5.0 2.9 - - + +
214A VAL* 2.8 46.3 + - + +
215A VAL 3.7 0.2 - - - +
217A GLN* 1.4 71.9 - - + +
219A GLN* 1.3 54.6 + - - +
221A VAL* 3.3 10.1 - - - +
223A PHE* 2.6 48.9 + - + +
224A ILE* 3.0 26.5 + - + -
255A ILE* 4.7 4.9 - - + -
257A ILE* 3.0 37.5 - - + -
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Residues in contact with GLN 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* 2.9 36.7 + - - +
216A GLU* 3.0 17.8 + - + +
218A LEU* 1.3 72.3 - - - +
220A LYS* 1.3 59.0 + - - +
221A VAL 3.0 1.8 - - - -
222A HIS* 2.5 34.8 + - - -
224A ILE* 4.0 28.8 - - + +
227A THR* 5.4 4.5 + - - -
230A LYS* 4.6 6.2 + - - -
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Residues in contact with LYS 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 GLU* 2.7 17.5 + - + +
217A GLN* 3.0 33.5 + - - +
219A GLN* 1.3 74.1 - - - +
221A VAL* 1.3 64.2 + - + +
222A HIS* 3.6 16.1 + - - -
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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