Contacts of the helix formed by residues 201 - 213 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ASP* 4.6 15.0 - - - +
211A ALA* 4.2 8.9 - - + +
212A GLU* 4.0 27.2 - - + +
199C ILE 3.4 0.4 + - - -
200C GLY* 1.3 69.4 - - - -
202C SER* 1.3 57.3 + - - +
203C LYS* 3.2 3.5 + - - +
204C ARG* 3.3 15.6 + - + +
205C LEU* 3.0 27.4 + - - +
372C THR* 4.4 10.8 + - - +
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Residues in contact with SER 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLY 2.7 27.6 + - - -
194C PHE* 4.0 7.1 - - - -
198C GLY* 3.5 1.6 - - - -
199C ILE 2.9 33.0 + - - -
200C GLY 3.1 2.1 + - - -
201C ALA* 1.3 76.9 - - - +
203C LYS* 1.3 57.7 + - - +
205C LEU* 3.6 9.1 - - - +
206C VAL* 2.9 36.2 + - - +
358C PHE* 3.7 24.2 - - - -
372C THR* 4.7 0.4 - - - +
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C TYR* 3.5 44.9 - - + +
191C LEU 3.2 24.6 - - - +
200C GLY 4.9 0.6 + - - -
201C ALA* 3.2 1.3 - - - -
202C SER* 1.3 79.9 + - - +
204C ARG* 1.3 59.4 + - - +
206C VAL 4.0 0.2 - - - -
207C GLU* 3.0 65.3 + - - +
217C TRP* 5.8 1.0 - - - -
204E ARG* 6.1 0.7 - - - +
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Residues in contact with ARG 204 (chain C).
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 43.2 + - - +
207A GLU* 3.7 24.9 + - - +
208A ASP* 2.6 50.8 + - - +
201C ALA* 3.3 14.1 + - + +
203C LYS* 1.3 79.0 - - - +
205C LEU* 1.3 62.6 + - - +
207C GLU* 3.5 3.5 + - - -
208C ASP* 3.1 38.3 + - - +
204E ARG* 3.2 45.0 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ALA 3.0 16.8 + - - +
202C SER* 3.6 4.9 - - - +
204C ARG* 1.3 76.5 - - - +
206C VAL* 1.3 70.4 + - + +
208C ASP* 3.7 5.4 - - - +
209C LEU* 3.0 40.8 + - + +
351C PHE* 5.5 2.2 - - + -
356C GLY* 5.8 1.3 - - - -
358C PHE* 4.2 27.8 - - + -
372C THR* 4.2 25.8 - - - +
373C LYS 4.7 11.0 - - - +
374C MET* 4.4 17.3 - - + -
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C TYR* 3.6 33.9 - - + -
165C LEU* 5.9 0.4 - - + -
191C LEU* 4.0 17.3 - - + -
192C GLY* 4.0 14.6 - - - -
194C PHE* 4.3 13.5 - - + -
202C SER 2.9 24.3 + - - +
203C LYS 4.3 1.8 - - - +
205C LEU* 1.3 79.8 - - + +
207C GLU* 1.3 61.5 + - - +
209C LEU* 3.3 11.3 + - + +
210C PHE* 2.9 40.3 + - + +
351C PHE* 6.5 0.7 - - + -
358C PHE* 4.9 4.0 - - + -
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Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C TYR* 5.1 0.7 - - - +
191C LEU* 4.0 18.2 - - + +
203C LYS* 3.0 57.6 + - - +
204C ARG* 3.8 5.1 - - - +
206C VAL* 1.3 76.3 - - - +
208C ASP* 1.3 58.6 - - - +
210C PHE* 3.6 2.5 + - - +
211C ALA* 3.0 28.6 + - - +
217C TRP* 3.9 38.4 + - + +
204E ARG* 3.2 28.5 + - - +
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Residues in contact with ASP 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ARG* 3.1 29.9 + - - +
205C LEU* 3.7 5.2 - - - +
207C GLU* 1.3 75.9 - - - +
209C LEU* 1.3 59.4 + - - +
211C ALA* 3.4 6.0 + - - +
212C GLU* 2.9 43.7 + - - +
201E ALA* 4.3 15.6 - - + +
204E ARG* 2.6 36.9 + - - +
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 3.8 22.0 - - + -
205C LEU* 3.0 30.9 + - + +
206C VAL* 3.5 13.0 - - + +
208C ASP* 1.3 76.7 - - - +
210C PHE* 1.3 59.2 + - + +
212C GLU* 3.4 9.9 + - - +
213C ARG* 3.1 66.6 + - - +
351C PHE* 3.5 33.7 - - + -
374C MET* 3.5 24.5 - - + -
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Residues in contact with PHE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C TYR* 3.5 23.8 - + - -
164C ALA* 5.0 3.4 - - + -
165C LEU* 4.0 29.6 - - + -
184C PHE* 3.6 40.8 - + + -
191C LEU* 3.6 22.2 - - + -
206C VAL* 2.9 25.1 + - + +
207C GLU 3.9 3.4 - - - +
209C LEU* 1.3 76.9 - - + +
211C ALA* 1.3 60.9 + - - +
213C ARG* 3.2 1.1 + - - -
214C ASN* 2.9 10.7 + - - -
215C ILE* 2.9 64.1 + - + +
217C TRP* 3.8 15.7 - + + -
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C GLU 3.0 18.7 + - - +
208C ASP* 3.4 8.9 + - - +
210C PHE* 1.3 77.0 - - - +
212C GLU* 1.3 61.6 + - - +
213C ARG 3.4 0.2 + - - -
214C ASN* 3.4 9.6 + - - +
215C ILE 5.4 0.4 - - - -
217C TRP* 5.6 2.3 - - - +
200E GLY* 3.4 39.2 + - - +
201E ALA* 4.2 5.8 - - + +
370E VAL* 4.4 2.4 - - - +
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Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ASP* 2.9 29.7 + - - +
209C LEU* 3.7 14.7 - - - +
211C ALA* 1.3 75.5 - - - +
213C ARG* 1.3 68.8 + - + +
214C ASN* 3.4 1.2 + - - +
374C MET* 5.5 4.2 - - - +
200E GLY* 4.5 1.3 - - - -
201E ALA* 5.1 14.6 - - + +
369E ARG* 5.3 2.3 - - - -
370E VAL* 3.6 30.6 + - + +
372E THR* 5.7 3.9 + - - +
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Residues in contact with ARG 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 3.6 20.1 + - - +
168C HIS* 3.3 41.4 + - + +
169C TYR* 6.3 0.6 - - - +
177C ARG* 3.0 19.9 + - - -
209C LEU* 3.1 39.6 + - - +
210C PHE 3.2 0.4 + - - -
212C GLU* 1.3 85.0 + - + +
214C ASN* 1.3 67.1 + - - +
215C ILE* 3.2 13.8 + - + +
351C PHE* 3.9 19.8 + - - +
354C ASP* 3.0 39.0 + - - -
374C MET* 4.8 5.1 - - - +
367E ARG 5.0 0.4 - - - +
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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