Contacts of the helix formed by residues 219 - 226 (chain A) in PDB entry 1W88
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 LEU 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ASP* 3.7 26.7 - - + +
176A THR* 3.9 11.2 - - + +
181A PHE* 5.0 0.3 - - - -
199A VAL* 3.6 30.7 - - + -
201A ASN* 3.8 9.4 - - - +
210A VAL* 4.0 19.1 - - + -
214A THR* 4.0 11.9 - - + -
216A ALA 5.1 1.1 - - - +
218A THR* 1.3 74.8 - - - +
220A ALA* 1.3 64.8 + - - +
221A GLN 3.2 1.1 - - - -
222A LYS* 3.0 48.7 + - - +
260A LEU* 3.8 6.4 - - - +
262A GLU* 3.2 28.0 + - + +
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Residues in contact with ALA 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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20A PHE* 4.0 13.9 - - + -
218A THR* 3.3 3.7 - - - +
219A LEU* 1.3 77.9 - - - +
221A GLN* 1.3 56.9 + - - +
223A ALA* 3.0 30.3 + - - +
230A GLY* 3.9 3.1 - - - -
231A ILE 3.8 35.0 - - - +
232A GLN* 3.8 5.6 - - + +
260A LEU* 3.6 9.3 - - - +
262A GLU* 3.2 21.1 + - + +
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Residues in contact with GLN 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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16A VAL* 4.5 8.1 - - + +
17A ALA* 5.4 4.5 - - - -
20A PHE* 3.6 32.1 - - + -
216A ALA* 3.6 16.8 - - + +
217A LYS* 3.7 6.0 + - - +
218A THR* 3.1 46.1 + - - +
220A ALA* 1.3 72.4 - - - +
222A LYS* 1.3 57.4 - - + +
223A ALA 2.9 5.6 - - - -
224A VAL* 2.8 29.0 + - - +
225A ALA 4.3 0.3 + - - -
224C VAL* 2.8 40.5 + - + +
225C ALA 4.4 0.3 + - - -
227C GLY* 4.0 8.7 - - - -
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Residues in contact with LYS 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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176A THR* 3.6 23.8 + - - -
177A SER* 5.9 0.4 + - - -
181A PHE* 3.9 26.5 - - + -
182A TYR* 5.6 0.3 - - - -
185A ILE* 3.6 13.1 - - - +
214A THR* 3.1 24.2 + - - -
216A ALA* 4.3 2.6 - - + +
218A THR 4.9 1.8 - - - +
219A LEU* 3.0 40.2 + - - +
221A GLN* 1.3 77.4 - - + +
223A ALA* 1.3 59.2 + - - +
225A ALA* 3.3 16.6 + - - +
260A LEU* 4.2 2.0 - - + -
182C TYR* 3.1 23.6 + - + +
186C ASN* 3.6 4.9 + - - +
225C ALA* 2.7 46.5 + - + +
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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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20A PHE* 5.2 1.1 - - + -
185A ILE* 4.3 4.3 - - - -
220A ALA 3.0 18.1 + - - +
221A GLN* 5.0 0.4 - - - -
222A LYS* 1.3 75.1 - - - +
224A VAL* 1.3 65.3 + - - +
226A ALA* 2.9 15.2 + - - +
227A GLY 3.2 8.1 + - - -
228A ILE* 3.2 31.9 + - + +
229A PRO 3.6 7.0 - - - +
230A GLY* 3.6 17.0 - - - +
260A LEU* 3.6 15.2 - - + +
12C GLN* 5.3 0.2 - - - +
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Residues in contact with VAL 224 (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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20A PHE* 3.6 27.8 - - + -
221A GLN 2.8 18.7 + - - +
223A ALA* 1.3 77.6 - - + +
225A ALA* 1.3 59.1 + - - +
227A GLY* 3.1 6.0 + - - +
228A ILE 4.0 3.3 + - - +
12C GLN* 5.3 3.1 - - - +
13C LEU* 6.5 0.9 - - + -
16C VAL* 3.3 38.4 - - + -
221C GLN* 2.8 55.2 + - + +
224C VAL* 3.8 17.7 - - + -
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Residues in contact with ALA 225 (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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182A TYR* 3.8 21.6 - - + -
186A ASN* 4.0 0.5 - - - +
221A GLN 4.3 0.4 + - - -
222A LYS 3.3 7.0 + - - +
223A ALA 3.1 1.2 + - - -
224A VAL* 1.3 78.3 - - - +
226A ALA* 1.3 56.4 + - - +
227A GLY 3.4 0.2 - - - -
182C TYR* 5.7 0.2 - - + -
214C THR* 4.0 0.7 + - - -
216C ALA* 4.0 1.6 - - - +
221C GLN 4.4 0.8 + - - -
222C LYS* 2.7 58.6 + - + +
225C ALA* 3.5 30.9 - - + +
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Residues in contact with ALA 226 (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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182A TYR* 5.8 0.4 - - + -
185A ILE* 3.6 45.5 - - + +
186A ASN* 3.9 13.2 - - + +
189A GLY* 4.7 2.8 - - - -
222A LYS 4.2 0.6 + - - -
223A ALA 2.9 10.3 + - - +
225A ALA* 1.3 79.2 - - - +
227A GLY* 1.3 54.5 + - - +
228A ILE* 3.3 14.4 + - + +
214C THR* 3.3 15.8 + - - -
215C VAL* 3.5 17.3 + - - +
216C ALA* 4.1 0.2 - - - -
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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