Contacts of the helix formed by residues 223 - 233 (chain A) in PDB entry 3VS5
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 4.3 11.0 - - - +
221A PHE* 3.7 7.1 - - - +
222A SER* 1.3 88.5 - - - +
224A LEU* 1.3 63.0 + - - +
225A GLN* 3.1 19.9 + - - +
226A GLU* 3.1 23.7 + - + +
227A LEU* 3.3 17.8 + - - +
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Residues in contact with LEU 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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144A LEU* 3.9 35.2 - - + -
149A TRP* 3.7 17.5 - - + -
150A PHE* 5.3 0.2 - - + -
175A ILE* 3.6 33.2 - - + +
185A TYR* 4.0 23.1 - - + -
205A ILE* 4.2 17.5 - - + -
213A PHE* 4.2 27.4 - - + -
223A THR* 1.3 71.4 - - - +
225A GLN* 1.3 61.3 + - - +
227A LEU* 3.4 9.5 - - + +
228A VAL* 3.0 31.7 + - - +
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Residues in contact with GLN 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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147A GLU* 3.8 18.0 + - - +
149A TRP* 3.6 37.4 - - + +
223A THR* 3.1 9.7 + - - +
224A LEU* 1.3 78.1 - - - +
226A GLU* 1.3 55.1 + - + +
228A VAL* 4.3 5.6 - - - +
229A ASP* 2.6 66.9 + - - +
232A LYS* 5.8 2.3 + - - +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 3.6 16.4 - - + +
222A SER* 2.7 46.4 + - - -
223A THR* 3.1 26.0 + - + +
225A GLN* 1.3 74.4 - - + +
227A LEU* 1.3 65.4 + - - +
229A ASP* 3.3 6.4 + - - +
230A HIS* 2.9 25.6 + - - +
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Residues in contact with LEU 227 (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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175A ILE* 4.5 11.0 - - + -
187A LEU* 4.7 7.6 - - + -
205A ILE* 4.4 13.0 - - + -
213A PHE* 4.9 3.6 - - + +
214A TYR* 4.6 2.9 - - - +
215A ILE* 3.8 38.6 - - + +
221A PHE* 3.6 33.4 - - + -
223A THR 3.3 10.1 + - - +
224A LEU* 3.4 23.8 - - + +
226A GLU* 1.3 79.5 - - - +
228A VAL* 1.3 69.3 + - + +
230A HIS* 3.1 9.7 + - - +
231A TYR* 3.2 29.7 + - + -
242A LEU* 5.2 1.1 - - + -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 4.3 17.0 - - + -
173A PHE* 3.8 37.9 - - + -
175A ILE* 3.5 25.6 - - + -
224A LEU 3.0 18.5 + - - +
225A GLN* 3.7 13.7 - - - +
227A LEU* 1.3 81.1 - - + +
229A ASP* 1.3 59.4 + - - +
231A TYR 3.5 0.2 + - - -
232A LYS* 2.9 44.9 + - + +
242A LEU* 3.6 13.6 - - + +
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Residues in contact with ASP 229 (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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225A GLN* 2.6 47.5 + - - +
226A GLU* 3.8 6.5 + - - +
227A LEU 3.3 0.2 - - - -
228A VAL* 1.3 72.9 - - - +
230A HIS* 1.3 63.2 + - - +
232A LYS* 3.5 29.3 + - - +
233A LYS* 3.7 6.9 + - - +
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Residues in contact with HIS 230 (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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219A SER* 4.8 4.3 + - - -
221A PHE* 3.4 39.9 - + + -
226A GLU 2.9 7.5 + - - +
227A LEU 3.3 8.5 - - - +
229A ASP* 1.3 72.8 - - - +
231A TYR* 1.3 81.3 + + - +
232A LYS 2.9 3.4 - - - -
233A LYS* 2.8 42.0 + - - +
234A GLY 5.7 0.2 - - - -
236A ASP* 3.4 28.7 + - + +
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Residues in contact with TYR 231 (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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187A LEU* 5.2 0.4 - - + -
215A ILE* 4.1 15.9 - - + +
216A SER* 3.8 30.7 + - - -
219A SER* 4.6 4.9 - - - -
221A PHE* 4.1 20.1 - + - -
227A LEU* 3.2 39.6 + - + -
230A HIS* 1.3 87.0 - + - +
232A LYS* 1.3 58.5 + - - +
233A LYS 3.3 0.4 - - - -
234A GLY 3.0 16.4 - - - +
235A ASN 4.5 0.2 - - - -
236A ASP* 3.4 42.7 + - + -
238A LEU* 3.5 38.1 - - + -
241A LYS* 3.7 2.4 - - - -
242A LEU* 2.9 35.2 + - + -
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Residues in contact with LYS 232 (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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149A TRP* 6.3 1.2 - - - -
173A PHE* 4.7 6.3 - - - -
225A GLN* 5.8 2.0 + - - +
228A VAL* 2.9 34.2 + - + +
229A ASP* 3.5 23.9 + - - +
230A HIS 2.8 0.4 + - - -
231A TYR* 1.3 79.1 - - - +
233A LYS* 1.3 56.3 + - - +
234A GLY 3.7 0.2 - - - -
241A LYS* 3.3 17.8 + - - +
242A LEU* 3.3 36.5 - - + +
243A SER 3.7 17.9 - - - +
245A PRO* 5.5 5.7 - - - +
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Residues in contact with LYS 233 (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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229A ASP 3.7 5.8 + - - +
230A HIS* 2.8 17.9 + - - +
232A LYS* 1.3 76.5 - - + +
234A GLY* 1.3 66.4 + - - +
241A LYS* 3.9 19.8 - - - +
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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