Contacts of the strand formed by residues 259 - 264 (chain A) in PDB entry 3DVA
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 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ALA 3.2 3.8 + - - -
196A ILE* 3.8 3.0 - - - +
197A PHE* 3.0 28.1 + - - +
228A ILE* 4.4 5.2 - - - -
229A PRO* 3.6 16.3 - - - +
231A ILE* 4.1 19.3 - - + -
244A ALA 5.7 0.4 - - - +
248A ALA* 3.7 32.4 + - + +
251A ARG* 3.7 20.3 - - - -
257A GLY 4.8 0.2 + - - -
258A PRO* 1.3 79.7 + - - +
260A LEU* 1.3 71.8 + - - +
261A ILE* 4.1 4.9 + - + -
9C PHE* 4.4 9.5 - - + -
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Residues in contact with LEU 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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181A PHE* 4.2 18.6 - - + -
185A ILE* 4.6 4.9 - - + -
197A PHE* 3.4 26.9 - - + +
199A VAL* 3.6 27.4 - - + -
219A LEU 3.7 14.6 - - - +
220A ALA* 3.7 14.0 - - - +
222A LYS 4.3 1.8 - - - -
223A ALA* 3.6 41.1 - - + +
228A ILE* 4.4 7.6 - - + +
229A PRO 3.0 6.7 + - - -
230A GLY* 3.3 0.2 - - - -
231A ILE* 2.8 27.5 + - - +
259A THR* 1.3 73.7 - - - +
261A ILE* 1.3 63.7 + - - +
262A GLU* 4.1 0.4 + - + -
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Residues in contact with ILE 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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196A ILE* 4.1 17.3 - - + -
197A PHE 2.8 14.2 + - - +
198A VAL* 3.4 9.5 - - + +
199A VAL* 2.6 35.6 + - - +
231A ILE* 3.4 11.9 - - + +
233A VAL* 3.7 27.1 - - + -
241A VAL* 6.3 1.1 - - + -
244A ALA* 3.6 37.9 - - + +
245A VAL* 4.0 20.0 - - + +
248A ALA* 4.2 4.7 - - + -
259A THR* 4.3 11.2 - - + -
260A LEU* 1.3 79.0 - - - +
262A GLU* 1.3 55.8 + - - +
263A THR* 3.8 9.4 + - + -
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Residues in contact with GLU 262 (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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199A VAL* 3.4 9.6 - - + +
201A ASN* 3.0 34.0 + - + -
218A THR* 3.8 1.2 - - - -
219A LEU* 2.9 31.9 + - + +
220A ALA* 2.8 38.5 + - + +
231A ILE 2.8 9.4 + - - +
232A GLN* 3.2 25.8 + - - +
233A VAL* 2.8 30.2 + - - +
260A LEU* 4.1 0.8 + - + -
261A ILE* 1.3 70.3 - - - +
263A THR* 1.3 62.2 + - - +
264A LEU* 3.4 13.0 + - + +
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Residues in contact with THR 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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84A SER* 2.9 32.1 + - - +
198A VAL* 4.1 19.3 - - + -
199A VAL 2.7 9.1 + - - -
200A GLN* 3.3 14.9 - - - +
201A ASN* 2.9 24.6 + - - +
233A VAL* 3.6 18.4 - - + -
235A GLY* 3.8 13.9 - - - -
241A VAL* 4.8 9.9 - - + -
261A ILE* 4.1 6.3 - - + -
262A GLU* 1.3 75.2 - - - +
264A LEU* 1.3 62.5 + - - +
265A CYS* 3.5 2.1 + - - -
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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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22A THR* 4.1 18.6 - - + +
201A ASN* 3.7 17.9 - - - +
203A ARG* 5.9 4.0 - - - +
232A GLN* 3.7 33.2 - - + +
233A VAL 2.9 17.7 + - - +
234A ASP* 3.7 6.2 - - - +
235A GLY* 2.7 21.6 + - - +
236A MET* 3.5 8.3 + - - +
262A GLU* 3.4 28.3 - - + +
263A THR* 1.3 69.8 - - - +
265A CYS* 1.3 60.3 + - - +
290A TRP* 5.3 5.6 - - + -
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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