Contacts of the helix formed by residues 215 - 222 (chain A) in PDB entry 2VF8
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ILE* 3.9 26.7 - - + -
211A LEU* 4.9 12.1 - - + -
212A PRO* 3.5 32.7 - - + +
213A GLU 2.3 16.4 + - - -
214A GLU* 1.3 79.2 + - - +
216A ARG* 1.3 57.6 + - - +
217A HIS 3.1 2.8 - - - +
218A TRP* 3.5 8.0 - - - +
219A ILE* 2.5 45.1 + - + +
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Residues in contact with ARG 216 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.6 16.4 + - - +
208A TRP* 3.4 56.0 - - + +
209A ARG* 3.7 14.5 + - - +
211A LEU* 2.8 37.8 + - + +
212A PRO* 3.4 8.3 + - - +
213A GLU* 2.8 35.0 + - - +
215A THR* 1.3 79.3 - - - +
217A HIS* 1.3 57.0 + - - +
219A ILE* 4.2 1.8 - - - -
220A LEU* 2.8 33.8 + - - +
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Residues in contact with HIS 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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165A GLU* 5.0 3.9 + - - +
213A GLU* 3.3 23.6 + - - +
214A GLU* 4.0 13.0 - - + +
215A THR 3.1 0.4 - - - -
216A ARG* 1.3 76.2 - - - +
218A TRP* 1.3 62.2 + - - +
221A PHE* 2.7 72.2 + + + +
222A THR* 3.8 2.1 + - - -
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Residues in contact with TRP 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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197A LEU* 4.4 12.8 - - + -
200A LEU* 4.4 15.9 - - + -
202A ILE* 5.1 7.2 - - + -
214A GLU 3.8 9.3 - - - +
215A THR* 3.2 19.5 + - - +
217A HIS* 1.3 84.2 + - - +
219A ILE* 1.3 83.2 + - + +
220A LEU 3.1 0.2 + - - -
222A THR* 3.0 55.9 + - + +
224A GLU* 3.9 18.8 + - - -
226A PRO* 4.0 26.9 - - + -
255A PHE* 3.6 36.8 - + - -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ILE* 4.3 12.1 - - + -
181A VAL* 5.0 3.6 - - + -
184A TRP* 4.4 20.2 - - + -
197A LEU* 4.1 22.9 - - + -
202A ILE* 3.9 35.9 - - + -
208A TRP* 3.6 25.1 - - + -
211A LEU* 4.6 6.1 - - + -
215A THR* 2.5 37.8 + - + +
216A ARG 3.8 3.8 - - - +
218A TRP* 1.3 79.8 - - + +
220A LEU* 1.3 62.0 + - + +
255A PHE* 3.6 12.3 - - + -
257A SER* 3.8 0.5 - - - -
258A ALA* 3.4 15.8 + - - +
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Residues in contact with LEU 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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165A GLU* 3.5 47.6 - - + +
168A MET* 3.7 21.9 - - + +
169A VAL* 4.8 3.1 - - + -
181A VAL* 4.0 15.3 - - + -
208A TRP* 3.5 30.1 - - + -
216A ARG 2.8 16.3 + - - +
218A TRP 3.8 0.2 - - - -
219A ILE* 1.3 74.6 - - - +
221A PHE* 1.3 76.6 + - + +
257A SER* 3.5 1.3 - - - -
258A ALA* 3.2 21.2 + - + -
259A ARG* 2.8 32.1 + - - +
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Residues in contact with PHE 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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163A VAL* 3.8 33.4 - - + -
164A THR* 3.8 4.0 - - - -
165A GLU* 3.6 31.4 - - + -
168A MET* 4.6 1.6 - - - -
217A HIS* 2.7 63.8 + + + +
220A LEU* 1.3 96.5 - - + +
222A THR* 1.3 66.3 + - - +
223A ASP* 3.3 2.6 + - - +
257A SER* 3.3 6.8 + - - -
259A ARG* 3.2 43.9 + - + +
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Residues in contact with THR 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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217A HIS* 3.8 3.3 + - - -
218A TRP* 3.0 62.4 + - + +
221A PHE* 1.3 75.3 - - - +
223A ASP* 1.3 57.3 + - - +
224A GLU* 2.8 37.0 + - + +
255A PHE* 3.9 15.9 - - + -
257A SER* 2.7 28.2 + - - -
260A ARG* 4.7 0.3 + - - -
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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