Contacts of the helix formed by residues 210 - 218 (chain A) in PDB entry 1QWN
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A SER* 1.4 84.9 - - - +
211A THR* 1.3 63.7 + - - +
212A MET 3.1 0.4 - - - -
213A PRO* 3.2 6.9 - - + +
214A TYR* 3.1 6.8 + - - +
247A TRP* 3.5 18.6 - - + +
248A ARG 5.2 2.0 - - - +
249A GLN* 2.9 39.2 + - - +
250A ILE* 5.7 3.1 - - + +
402A GLY* 3.6 22.4 - - - +
403A ASP* 3.5 23.1 - - + -
808A LEU* 3.7 20.9 - - + -
812A GLN* 4.1 10.3 - - - +
814A ILE* 5.5 0.9 - - + -
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Residues in contact with THR 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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175A TRP* 3.7 30.7 - - + -
178A VAL* 5.3 1.6 - - + -
209A SER* 3.0 4.8 + - - -
210A PRO* 1.3 80.0 - - - +
212A MET* 1.3 66.4 + - - +
214A TYR* 3.4 7.5 - - - +
215A ILE* 3.0 33.1 + - + +
808A LEU* 3.7 6.1 + - - +
809A ASN* 2.8 36.2 + - + +
811A LEU* 3.7 17.7 - - + +
812A GLN* 3.8 6.8 + - - +
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Residues in contact with MET 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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162A THR* 6.2 3.4 - - + -
168A PRO* 4.0 20.4 - - + -
170A GLU* 3.3 46.0 - - + +
178A VAL* 3.6 38.1 - - + -
181A GLN* 5.3 1.6 - - - +
209A SER* 3.1 5.4 + - - +
210A PRO 3.1 0.6 - - - -
211A THR* 1.3 77.9 - - - +
213A PRO* 1.3 75.0 - - + +
214A TYR 3.2 0.3 + - - -
215A ILE* 3.2 4.3 + - + +
216A LEU* 2.8 42.3 + - + +
224A MET* 4.2 12.6 - - + -
809A ASN* 6.0 0.9 - - - -
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Residues in contact with PRO 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 SER 3.5 8.1 - - - +
210A PRO* 3.2 17.9 - - + +
212A MET* 1.3 94.3 - - + +
214A TYR* 1.4 60.6 + - - +
217A GLN* 2.8 29.3 + - - +
224A MET* 3.7 22.7 - - + -
247A TRP* 3.7 36.3 - - + +
249A GLN* 4.1 5.6 - - - +
257A THR 4.5 2.0 - - - +
259A LEU* 3.8 28.0 - - + -
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Residues in contact with TYR 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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175A TRP* 5.6 2.9 - + - -
210A PRO 3.1 14.6 + - - +
211A THR* 3.4 11.0 - - - +
212A MET 3.1 0.6 - - - -
213A PRO* 1.4 79.6 - - - +
215A ILE* 1.3 73.7 + - + +
217A GLN* 4.2 2.3 - - - +
218A LYS* 3.5 52.8 + - + +
249A GLN* 3.6 28.8 - - + +
251A TRP* 4.1 12.8 - + - -
257A THR* 4.9 6.1 - - + -
811A LEU* 3.6 28.5 - - + -
980A HIS* 4.0 2.9 + - - -
1014A LEU* 5.5 1.6 - - + -
1034A MET 2.6 29.6 + - - -
1035A GLU* 3.4 2.1 - - - -
1036A THR* 2.7 36.3 + - + -
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Residues in contact with ILE 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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175A TRP* 3.6 35.2 - - + +
178A VAL* 3.7 25.8 - - + -
179A LEU* 4.2 20.4 - - + +
182A LEU* 4.0 23.3 - - + -
211A THR* 3.0 27.6 + - + +
212A MET* 3.9 2.9 - - - +
214A TYR* 1.3 86.2 - - + +
216A LEU* 1.3 66.7 + - + +
218A LYS* 3.1 4.7 + - - +
219A SER* 2.9 30.6 + - - +
1014A LEU* 4.5 10.8 - - + -
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Residues in contact with LEU 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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162A THR* 4.7 4.0 - - + -
182A LEU* 4.2 17.9 - - + -
200A SER* 3.7 29.2 - - - +
212A MET* 2.8 40.6 + - + +
215A ILE* 1.3 78.3 - - + +
217A GLN* 1.3 58.0 + - - +
219A SER* 2.9 17.7 + - - -
221A PHE* 3.0 64.0 + - + +
224A MET* 4.2 22.4 - - + -
259A LEU* 3.9 5.6 - - + -
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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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213A PRO 2.8 22.4 + - - +
214A TYR* 4.2 2.3 - - - +
216A LEU* 1.3 72.7 - - - +
218A LYS* 1.3 76.9 + - - +
219A SER 3.2 1.1 + - - -
220A GLY* 3.8 8.1 + - - -
221A PHE 4.2 12.7 + - - +
256A ASP 3.5 22.9 + - - +
257A THR* 3.7 23.9 - - - +
258A ALA 3.7 13.2 + - - +
259A LEU* 4.3 13.2 - - + +
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Residues in contact with LYS 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 TYR* 3.5 50.0 + - + +
215A ILE 3.1 1.5 + - - +
216A LEU 3.1 0.8 - - - -
217A GLN* 1.3 90.4 + - - +
219A SER* 1.3 58.5 + - - +
220A GLY 3.6 1.1 - - - -
257A THR* 4.2 10.1 - - - +
1013A THR* 3.6 8.7 - - - +
1014A LEU* 3.1 44.2 + - + +
1020A LEU* 5.6 1.4 - - - +
1035A GLU* 2.8 34.5 + - - -
1036A THR* 3.5 27.1 - - - +
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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