Contacts of the helix formed by residues 259 - 266 (chain A) in PDB entry 3VVK
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 PHE 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A THR* 5.3 3.1 - - + -
74A VAL* 5.8 1.3 - - + -
134A ILE* 3.6 38.4 - - + -
137A ALA* 5.6 0.2 - - + -
138A LEU* 3.7 24.0 - - + -
214A LEU* 4.1 18.7 - - + +
217A LEU* 4.0 21.1 - - + -
218A THR* 3.2 28.0 - - - -
222A TRP* 6.3 0.4 - - - -
254A VAL 3.0 7.3 + - - +
255A ALA* 3.1 30.5 - - - +
256A LYS 4.1 2.9 - - - -
257A TYR 3.2 0.4 - - - -
258A ILE* 1.3 82.1 - - - +
260A ALA* 1.3 69.3 + - + +
262A LEU* 3.2 3.5 + - - +
263A LEU* 3.0 46.0 + - + +
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Residues in contact with ALA 260 (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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52A PHE* 3.5 24.0 - - + -
71A THR* 3.4 31.4 - - + +
74A VAL* 5.4 2.5 - - + -
75A PRO* 5.2 2.7 - - + -
256A LYS 3.0 20.3 + - - +
257A TYR 3.7 0.4 - - - +
259A PHE* 1.3 81.3 - - + +
261A PHE* 1.3 55.0 + - - +
263A LEU* 3.1 3.1 + - - +
264A LEU* 2.8 38.1 + - - +
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Residues in contact with PHE 261 (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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51A LEU* 3.5 24.0 - - + -
52A PHE* 3.6 18.3 - + + -
55A MET* 3.3 35.7 - - + -
257A TYR 3.0 17.7 + - - +
258A ILE* 3.5 9.0 - - - +
260A ALA* 1.3 74.9 - - - +
262A LEU* 1.3 66.5 - - + +
264A LEU* 3.7 0.8 - - - -
265A ASN* 2.8 35.7 + - + +
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Residues in contact with LEU 262 (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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210A ILE* 4.4 6.5 - - + +
213A THR* 5.5 7.9 - - + -
214A LEU* 4.0 14.8 - - + -
217A LEU* 3.7 29.4 - - + -
258A ILE* 2.9 33.4 + - + +
259A PHE 3.5 5.2 - - - +
261A PHE* 1.3 84.5 - - + +
263A LEU* 1.3 62.8 + - - +
265A ASN* 3.4 9.7 + - + +
266A TYR* 3.3 20.8 + - - +
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Residues in contact with LEU 263 (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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67A ILE* 4.3 17.3 - - + -
71A THR* 3.8 24.0 - - + +
137A ALA* 3.9 16.6 - - + -
138A LEU* 4.6 4.9 - - + -
141A LEU* 4.1 19.1 - - + -
214A LEU* 3.7 25.5 - - + +
259A PHE* 3.0 41.7 + - + +
260A ALA* 3.1 8.3 + - - +
262A LEU* 1.3 76.2 - - - +
264A LEU* 1.3 58.6 + - + +
266A TYR* 3.3 7.5 + - + +
267A LEU* 3.1 25.7 + - + +
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Residues in contact with LEU 264 (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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52A PHE* 3.6 39.3 - - + -
55A MET* 3.7 15.0 - - + -
56A THR* 3.7 17.7 - - + +
67A ILE 4.6 0.2 - - - +
68A ALA* 4.2 8.3 - - - -
71A THR* 3.7 40.8 - - + +
72A ILE* 4.2 8.5 - - + -
260A ALA 2.8 15.5 + - - +
261A PHE* 4.0 1.3 - - - +
263A LEU* 1.3 70.7 - - + +
265A ASN* 1.3 64.6 + - - +
266A TYR 3.1 2.0 - - - -
267A LEU* 4.2 23.3 - - + -
268A THR* 2.9 29.8 + - - -
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Residues in contact with ASN 265 (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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55A MET* 3.6 14.5 - - + +
261A PHE* 2.8 22.7 + - + +
262A LEU* 3.5 12.8 - - + +
263A LEU 3.3 0.2 - - - -
264A LEU* 1.3 76.6 - - - +
266A TYR* 1.3 63.8 + - - +
268A THR* 3.2 20.2 - - - +
269A SER* 3.7 10.9 + - - -
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Residues in contact with TYR 266 (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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141A LEU* 3.9 26.9 - - + -
206A GLY 4.5 2.4 + - - -
207A THR* 3.6 17.0 - - - +
210A ILE* 3.5 52.2 - - + +
262A LEU 3.3 3.6 + - - +
263A LEU* 3.5 9.6 - - + +
264A LEU 3.1 0.6 - - - -
265A ASN* 1.3 78.1 - - - +
267A LEU* 1.3 66.3 + - + +
268A THR 3.1 1.6 - - - -
269A SER* 2.8 18.9 + - - -
270A ASN* 2.9 60.6 + - + +
273A VAL* 3.6 13.2 - - - +
274A VAL* 4.4 9.2 - - + -
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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