Contacts of the helix formed by residues 211 - 219 (chain A) in PDB entry 2HU2
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A TYR* 3.7 12.1 - - - -
209A VAL* 3.9 2.9 - - - +
210A SER* 1.3 87.2 + - - +
212A LEU* 1.3 63.9 + - - +
213A GLN* 4.0 8.7 + - - +
214A ASP* 2.7 46.5 + - - +
215A LEU 3.3 9.0 + - - -
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Residues in contact with LEU 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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169A ILE* 3.9 20.4 - - + -
192A TYR* 3.6 34.6 + - + +
211A THR* 1.3 73.2 - - - +
213A GLN* 1.3 57.8 + - - +
215A LEU* 3.3 3.9 + - + +
216A LEU* 3.0 49.4 + - + +
235A LEU* 4.1 33.9 - - + +
236A ILE* 5.0 2.0 - - + -
240A THR* 4.0 24.7 - - + -
243A GLN* 5.2 0.4 - - - +
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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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211A THR* 3.2 7.9 + - - +
212A LEU* 1.3 77.4 - - - +
214A ASP* 1.3 58.2 + - - +
216A LEU* 3.6 3.5 - - - +
217A PHE* 2.8 39.6 + - + +
239A PHE* 5.4 0.5 - - - -
243A GLN* 3.0 49.0 + - + +
9B LEU* 4.6 19.1 + - - +
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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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209A VAL* 3.8 20.3 - - + +
210A SER* 4.3 9.0 + - - -
211A THR* 2.7 35.6 + - - +
213A GLN* 1.3 81.6 + - - +
215A LEU* 1.3 61.1 + - - +
217A PHE* 3.6 5.4 + - - +
218A HIS* 3.0 42.0 + - - +
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Residues in contact with LEU 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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167A GLY* 4.1 7.4 - - - -
168A ILE 3.3 34.3 - - - +
169A ILE* 3.7 23.1 - - + -
190A LEU* 3.9 12.6 - - + -
191A PHE 3.7 5.6 - - - -
192A TYR* 3.5 26.5 - - + +
209A VAL* 3.7 12.7 - - + +
211A THR 3.3 2.8 + - - +
212A LEU* 3.3 8.4 + - - +
213A GLN 3.3 0.4 - - - -
214A ASP* 1.3 77.7 - - - +
216A LEU* 1.3 76.8 + - + +
218A HIS* 3.2 1.6 + - - +
219A SER* 2.7 42.8 + - - +
222A VAL* 4.1 8.3 - - + -
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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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169A ILE* 4.3 6.7 - - + -
212A LEU* 3.0 48.2 + - + +
213A GLN 3.3 4.2 + - - +
215A LEU* 1.3 92.8 - - + +
217A PHE* 1.3 60.9 + - - +
218A HIS 3.5 0.5 + - - -
219A SER 4.0 3.8 + - - +
222A VAL* 4.5 12.1 - - + +
236A ILE* 4.8 6.7 - - + -
240A THR* 3.4 29.6 - - - +
243A GLN* 3.3 38.8 - - + +
244A MET* 3.6 24.0 - - + +
245A ARG* 3.6 14.2 + - - +
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Residues in contact with PHE 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 GLN* 2.8 24.2 + - + +
214A ASP* 3.9 7.4 - - - +
215A LEU 3.2 0.2 - - - -
216A LEU* 1.3 78.5 - - - +
218A HIS* 1.3 90.2 + + - +
243A GLN 3.6 6.9 + - - +
245A ARG* 2.9 31.0 + - - +
1B ARG* 4.3 1.4 + - - -
5B ALA* 5.5 2.5 - - + -
6B PRO* 3.8 21.3 - - + -
9B LEU* 3.9 31.6 - - + -
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Residues in contact with HIS 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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165A THR* 3.5 8.4 - - + -
190A LEU* 4.1 22.0 - - + +
209A VAL* 5.0 7.8 - - + +
214A ASP* 3.0 33.3 + - + +
215A LEU 3.2 3.3 + - - +
217A PHE* 1.3 107.7 - + - +
219A SER* 1.3 58.6 + - - +
245A ARG* 3.9 0.4 - - - -
1B ARG* 3.0 37.9 + - - +
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Residues in contact with SER 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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165A THR* 3.7 6.7 - - - -
167A GLY* 3.2 37.5 - - - -
190A LEU* 3.4 10.2 - - - +
215A LEU* 2.7 23.2 + - - +
216A LEU 4.0 3.0 + - - +
217A PHE 3.7 0.4 - - - -
218A HIS* 1.3 75.9 - - - +
220A ASP* 1.3 60.8 + - - +
221A CYS 3.9 0.9 - - - -
222A VAL* 3.9 19.6 - - - +
245A ARG* 3.3 22.1 + - - +
248A ALA* 4.3 4.9 - - - +
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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