Contacts of the helix formed by residues 201 - 213 (chain A) in PDB entry 3HYW
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 ALA 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ILE 3.3 1.0 + - - -
200A GLY* 1.3 70.5 - - - -
202A SER* 1.3 56.6 + - - +
203A LYS* 3.3 3.4 - - - -
204A ARG* 3.4 11.3 + - + +
205A LEU* 2.9 29.1 + - - +
372A THR* 4.1 12.9 + - - +
208E ASP* 3.7 33.9 - - + +
211E ALA* 4.3 3.3 - - - +
212E GLU* 4.9 6.4 - - + +
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Residues in contact with SER 202 (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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192A GLY 2.6 28.2 + - - -
194A PHE* 3.8 7.4 - - - -
198A GLY* 3.4 2.8 - - - -
199A ILE 2.9 33.6 + - - -
200A GLY 3.2 2.1 + - - -
201A ALA* 1.3 73.8 - - - +
203A LYS* 1.3 60.2 + - - +
205A LEU* 4.1 6.5 - - - -
206A VAL* 2.9 37.2 + - - +
358A PHE* 3.7 23.8 - - - -
372A THR* 5.0 0.7 - - - -
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Residues in contact with LYS 203 (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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190A TYR* 3.7 43.1 - - + -
191A LEU 3.1 24.1 - - - +
200A GLY 4.9 0.6 + - - -
201A ALA* 3.3 1.0 - - - -
202A SER* 1.3 80.4 + - - +
204A ARG* 1.3 57.2 + - - +
206A VAL* 3.9 0.7 - - - +
207A GLU* 2.9 62.7 + - + +
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Residues in contact with ARG 204 (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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201A ALA* 3.4 16.0 + - + +
203A LYS* 1.3 80.1 - - - +
205A LEU* 1.3 56.3 + - - +
207A GLU* 4.2 3.8 - - - -
208A ASP* 3.1 39.9 + - - +
204C ARG* 3.1 42.3 + - - +
203E LYS* 6.3 0.2 - - - +
204E ARG* 3.2 49.8 + - - +
207E GLU* 2.7 32.7 + - - +
208E ASP* 2.5 42.8 + - - +
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Residues in contact with LEU 205 (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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201A ALA 2.9 17.7 + - - +
202A SER* 3.6 4.7 - - - +
203A LYS 3.2 0.2 - - - -
204A ARG* 1.3 76.7 - - - +
206A VAL* 1.3 66.3 + - + +
208A ASP* 3.5 4.8 + - - +
209A LEU* 3.1 39.8 + - + +
351A PHE* 5.2 4.0 - - + -
356A GLY* 5.5 0.9 - - - -
358A PHE* 4.1 25.4 - - + -
372A THR* 4.5 22.7 - - - +
373A LYS* 4.5 18.6 - - - +
374A MET* 4.6 23.3 - - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.5 34.5 - - + -
191A LEU* 4.0 17.3 - - + -
192A GLY* 4.2 12.6 - - - +
194A PHE* 4.2 14.1 - - + -
202A SER 2.9 23.7 + - - +
203A LYS 4.1 1.8 - - - +
205A LEU* 1.3 81.3 - - + +
207A GLU* 1.3 61.5 + - - +
209A LEU* 3.5 11.0 - - + +
210A PHE* 2.8 39.4 + - + +
351A PHE* 6.1 2.0 - - + -
358A PHE* 4.8 2.7 - - + -
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Residues in contact with GLU 207 (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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190A TYR* 5.3 0.9 - - - +
191A LEU* 3.8 26.6 + - + +
203A LYS* 2.9 50.3 + - - +
204A ARG* 3.8 5.7 - - - +
206A VAL* 1.3 77.3 - - - +
208A ASP* 1.3 57.9 + - - +
210A PHE* 3.4 2.6 + - - +
211A ALA* 3.0 28.8 + - - +
217A TRP* 4.0 29.8 + - + +
204C ARG* 3.7 24.2 + - - +
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Residues in contact with ASP 208 (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 ARG* 3.1 19.7 + - - +
205A LEU* 3.9 4.7 - - - +
207A GLU* 1.3 75.8 - - - +
209A LEU* 1.3 57.0 + - - +
211A ALA* 3.4 6.7 + - - +
212A GLU* 2.8 50.8 + - - +
201C ALA* 4.6 9.3 - - + +
204C ARG* 2.6 50.7 + - - +
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Residues in contact with LEU 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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165A LEU* 3.3 33.4 - - + -
205A LEU* 3.1 23.1 + - + +
206A VAL* 3.5 14.1 - - + +
208A ASP* 1.3 75.7 - - - +
210A PHE* 1.3 66.3 + - + +
212A GLU* 3.4 9.5 + - - +
213A ARG* 3.1 64.8 + - - +
351A PHE* 3.5 23.3 - - + -
374A MET* 3.7 27.1 - - + -
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Residues in contact with PHE 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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161A TYR* 3.6 27.8 - + - -
164A ALA* 4.9 4.9 - - + -
165A LEU* 4.0 31.2 - - + -
184A PHE* 3.5 40.8 - + + -
191A LEU* 3.8 19.3 - - + -
206A VAL* 2.8 27.6 + - + +
207A GLU 3.8 3.4 - - - +
209A LEU* 1.3 75.1 - - + +
211A ALA* 1.3 58.2 + - - +
213A ARG 3.4 0.9 + - - -
214A ASN 2.9 9.0 + - - -
215A ILE* 2.7 62.7 + - + +
217A TRP* 3.9 17.3 - + + -
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Residues in contact with ALA 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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207A GLU 3.0 19.4 + - - +
208A ASP* 3.6 6.3 - - - +
210A PHE* 1.3 77.9 - - - +
212A GLU* 1.3 62.1 + - - +
213A ARG 3.3 0.5 + - - -
214A ASN* 3.3 11.9 + - - +
215A ILE 5.3 0.4 - - - -
217A TRP* 5.6 0.8 - - - +
200C GLY* 3.3 34.0 + - - +
201C ALA* 4.2 6.5 - - - -
370C VAL* 5.0 0.3 - - - +
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Residues in contact with GLU 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 ASP* 2.8 40.9 + - - +
209A LEU* 3.8 15.3 + - - +
210A PHE 3.4 0.4 - - - -
211A ALA* 1.3 72.6 - - - +
213A ARG* 1.3 77.9 + - - +
214A ASN* 3.5 0.6 + - - +
374A MET* 5.8 2.1 - - - +
200C GLY* 4.0 8.1 - - - -
201C ALA* 4.0 20.4 - - + +
370C VAL* 3.4 23.3 + - + +
372C THR* 5.6 3.6 - - - +
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Residues in contact with ARG 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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165A LEU* 3.6 23.9 - - - +
168A HIS* 3.4 36.2 + - + +
172A LYS* 6.1 0.7 - - - +
177A ARG* 2.9 24.6 + - - -
209A LEU* 3.1 37.6 + - - +
211A ALA 3.2 0.2 - - - -
212A GLU* 1.3 99.6 + - - +
214A ASN* 1.3 63.8 + - - +
215A ILE* 3.4 11.3 + - + +
351A PHE* 5.5 3.2 - - - +
354A ASP* 3.2 30.9 + - - -
374A MET* 3.8 11.1 - - - +
367C ARG 5.2 0.6 - - - +
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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