Contacts of the helix formed by residues 216 - 223 (chain A) in PDB entry 1W31
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 TYR 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A LYS* 3.6 16.8 - - + +
211A PHE 2.7 30.4 + - - -
213A GLY* 4.0 20.1 + - - +
214A ASN 3.6 1.4 - - - -
215A LEU* 1.3 82.9 - - - +
217A GLY* 1.3 67.7 + - - +
219A PHE* 3.5 13.6 + - + +
220A ARG* 3.5 33.4 + - - +
236A GLN* 3.7 23.1 - - - -
263A LYS* 3.5 42.2 + - - +
264A PRO* 3.5 10.0 - - + +
289A VAL* 3.8 10.1 - - + -
290A SER* 3.6 6.1 - - - -
363A SHO 4.1 16.4 - - + -
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Residues in contact with GLY 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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59A SER* 4.7 0.9 - - - -
214A ASN* 4.8 3.6 + - - +
215A LEU* 3.3 5.3 - - - +
216A TYR* 1.3 75.5 - - - +
218A PRO* 1.3 61.1 - - - +
220A ARG* 2.7 40.1 + - - +
221A ASP* 3.8 4.3 - - - +
291A GLY* 4.9 0.2 - - - -
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Residues in contact with PRO 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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57A ILE* 4.0 1.6 - - - +
59A SER* 2.8 56.2 + - - +
60A LEU* 3.7 7.2 - - + -
217A GLY* 1.3 84.4 - - - +
219A PHE* 1.3 57.2 + - - +
221A ASP* 2.8 17.7 + - - +
222A ALA* 3.1 12.0 + - - +
290A SER* 3.1 36.1 - - - +
291A GLY* 3.9 9.6 - - - +
294A ALA* 3.9 8.3 - - + -
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Residues in contact with PHE 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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46A PHE* 3.3 35.2 - + - -
60A LEU* 5.4 1.8 - - - -
89A PHE* 3.8 26.2 - + - -
135A CYS* 5.6 4.9 - - - -
136A GLU* 4.4 6.1 - - + -
216A TYR* 3.6 9.6 - - + +
217A GLY 2.9 0.4 + - - -
218A PRO* 1.3 78.6 - - - +
220A ARG* 1.3 60.0 + - - +
222A ALA* 4.4 4.9 - - - +
223A ALA* 2.7 54.5 + - + +
225A SER* 3.7 13.7 - - - -
290A SER* 3.1 5.5 + - - -
329A TYR* 4.0 0.7 - - - -
363A SHO 3.1 62.8 - - + +
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Residues in contact with ARG 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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216A TYR* 3.5 35.6 + - - +
217A GLY* 2.7 22.2 + - - +
219A PHE* 1.3 76.8 - - - +
221A ASP* 1.3 61.2 + - - +
224A CYS* 3.0 24.8 + - - -
225A SER* 2.9 39.8 + - - +
226A ALA* 3.8 11.4 - - + +
227A PRO* 3.8 21.7 - - - +
232A ARG* 4.9 12.8 - - - +
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Residues in contact with ASP 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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57A ILE* 4.0 8.9 - - + +
58A ASP* 3.5 27.2 - - + +
59A SER* 2.8 32.3 + - - +
65A ARG* 5.5 1.6 + - - -
217A GLY 3.8 8.5 - - - +
218A PRO 2.8 1.8 + - - +
220A ARG* 1.3 82.8 - - - +
222A ALA* 1.3 64.2 + - - +
224A CYS* 3.3 21.2 - - - -
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Residues in contact with ALA 222 (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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46A PHE* 4.1 18.8 - - + +
57A ILE* 3.2 42.4 - - + +
60A LEU* 3.9 15.5 - - + -
65A ARG* 4.2 8.8 + - - +
91A VAL* 3.7 22.3 - - - +
218A PRO 3.1 6.2 + - - +
219A PHE* 4.0 2.7 - - - +
221A ASP* 1.3 80.0 - - - +
223A ALA* 1.3 59.6 + - - +
224A CYS* 4.4 0.3 - - - -
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Residues in contact with ALA 223 (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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46A PHE* 4.6 2.9 - - + -
91A VAL* 4.4 13.1 - - - +
92A PRO* 5.9 0.3 - - - +
98A LYS* 5.1 1.2 + - - -
136A GLU* 3.4 32.5 - - - +
219A PHE* 2.7 52.9 + - + +
222A ALA* 1.3 73.6 - - - +
224A CYS* 1.3 72.0 + - - +
225A SER* 3.8 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