Contacts of the helix formed by residues 210 - 221 (chain A) in PDB entry 1BQ2
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 3.4 13.3 - - - +
25A GLY* 2.9 30.5 + - - -
26A THR* 4.7 1.8 - - - +
27A LEU* 6.1 1.3 - - - -
208A LEU 3.6 2.1 + - - -
209A TYR* 1.3 70.7 - - - +
211A ASN* 1.3 58.6 + - - +
212A HIS 3.2 4.5 + - - -
213A MET* 3.3 32.4 + - - +
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Residues in contact with ASN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.8 14.4 - - + +
209A TYR* 3.6 17.8 - - - +
210A SER* 1.3 74.7 + - - +
212A HIS* 1.3 65.0 + - - -
213A MET* 3.6 1.1 - - - -
214A ASP* 5.0 2.8 - - - +
215A GLN* 3.6 12.7 + - - +
261A PRO* 3.2 36.1 + - - +
262A VAL* 4.6 4.9 - - - +
263A ALA* 4.8 6.4 + - - +
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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
----------------------------------------------------------
169A ASP* 4.3 3.2 + - - -
171A PHE* 4.0 21.0 - + + +
172A LEU* 3.6 28.9 - - + -
208A LEU* 5.4 0.2 - - + -
209A TYR* 3.0 39.9 + + + +
211A ASN* 1.3 94.4 + - - +
213A MET* 1.3 65.0 + - - +
214A ASP 3.3 2.7 - - - -
215A GLN* 3.1 13.7 + - - +
216A THR* 2.9 32.9 + - + +
260A ALA* 3.6 24.0 - - + +
261A PRO 2.7 28.0 + - - -
262A VAL* 4.5 3.1 - - + -
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Residues in contact with MET 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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12A LEU* 3.5 32.8 - - + -
27A LEU* 4.3 17.5 - - + -
208A LEU* 4.2 15.3 - - + -
209A TYR 3.6 22.7 - - - +
210A SER* 3.3 21.7 + - - +
211A ASN 3.6 0.8 - - - -
212A HIS* 1.3 76.0 - - - +
214A ASP* 1.3 60.8 + - - +
216A THR* 2.7 23.5 + - - -
217A HIS* 2.7 27.9 + - + +
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Residues in contact with ASP 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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211A ASN 5.0 2.4 - - - +
212A HIS 3.2 1.0 + - - -
213A MET* 1.3 76.7 + - - +
215A GLN* 1.3 75.0 + - + +
217A HIS* 3.2 10.1 + - - +
218A LEU* 3.0 27.6 + - - +
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Residues in contact with GLN 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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171A PHE* 3.7 29.2 - - + -
211A ASN 3.6 8.0 + - - +
212A HIS* 3.4 24.4 + - - +
214A ASP* 1.3 98.4 + - + +
216A THR* 1.4 61.5 + - - +
218A LEU* 3.4 9.1 + - - +
219A GLN* 3.0 23.0 + - - +
258A ILE* 3.7 13.1 - - + +
259A LYS 3.4 18.3 - - - +
260A ALA* 4.0 2.3 - - - -
261A PRO* 3.4 28.8 - - - +
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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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8A MET* 4.5 9.6 - - - +
12A LEU* 4.2 10.8 - - - +
171A PHE* 3.9 17.5 - - + -
208A LEU* 3.7 40.2 - - + -
212A HIS* 2.9 23.1 + - + +
213A MET* 2.7 22.6 + - - +
215A GLN* 1.4 76.7 - - - +
217A HIS* 1.4 64.4 + - - +
219A GLN* 2.8 9.1 + - - +
220A LEU* 2.8 38.0 + - - +
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Residues in contact with HIS 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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12A LEU* 4.2 27.6 - - + +
213A MET* 2.7 29.4 + - + +
214A ASP* 3.3 11.1 - - - +
216A THR* 1.4 80.6 + - - +
218A LEU* 1.3 62.3 + - - +
220A LEU* 3.8 10.6 + - + +
221A SER* 3.1 23.4 + - - -
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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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214A ASP 3.0 12.6 + - - +
215A GLN* 3.6 9.4 - - - +
216A THR 3.1 0.2 - - - -
217A HIS* 1.3 74.9 - - - +
219A GLN* 1.3 60.4 + - - +
221A SER* 2.8 36.0 + - - +
222A ARG* 3.5 37.2 - - - +
258A ILE* 4.1 21.5 - - + -
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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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4A TYR* 3.6 16.6 + - - -
5A LEU* 3.9 8.9 - - + +
8A MET* 3.5 24.4 - - + +
45A VAL* 3.8 7.4 - - - +
47A THR* 3.0 47.2 + - - +
48A LYS* 3.5 18.4 - - - +
171A PHE* 3.5 23.2 - - - -
215A GLN 3.0 12.7 + - - +
216A THR* 2.8 13.9 + - - +
218A LEU* 1.3 70.9 - - - +
220A LEU* 1.3 59.8 + - - +
222A ARG* 3.0 23.0 + - - +
258A ILE* 4.0 8.9 - - + +
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Residues in contact with LEU 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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5A LEU* 3.6 41.9 - - + +
8A MET* 4.2 14.1 - - + -
9A GLN* 3.8 26.2 - - + +
12A LEU* 3.6 30.5 - - + -
216A THR* 2.8 23.9 + - - +
217A HIS* 4.0 13.5 - - + +
218A LEU 3.3 0.2 - - - -
219A GLN* 1.3 70.9 - - - +
221A SER* 1.3 60.1 + - - +
222A ARG 3.2 4.3 + - - +
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Residues in contact with SER 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 HIS 3.1 17.1 + - - -
218A LEU* 2.8 30.1 + - - +
220A LEU* 1.3 69.9 - - - +
222A ARG* 1.3 60.2 + - - -
223A GLU* 3.9 2.3 + - - +
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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