Contacts of the strand formed by residues 259 - 264 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PHE* 4.2 2.9 - - + -
195C ALA 3.2 5.2 + - - +
196C ILE* 3.8 4.0 - - - +
197C PHE* 2.9 27.5 + - - +
228C ILE* 4.5 4.9 - - - -
229C PRO* 3.7 19.9 - - + +
231C ILE* 3.9 26.0 - - + -
248C ALA* 3.8 27.3 + - + +
251C ARG* 3.8 22.2 + - - +
257C GLY 4.6 0.9 + - - -
258C PRO* 1.3 79.3 + - - +
260C LEU* 1.3 71.8 + - - +
261C ILE* 4.0 2.2 + - + -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C TYR* 4.1 1.6 - - - +
181C PHE* 4.3 16.8 - - + -
185C ILE* 4.7 5.2 - - + -
197C PHE* 3.3 29.4 - - + +
199C VAL* 3.8 24.7 - - + -
219C LEU 3.9 13.2 - - - +
220C ALA* 3.8 12.6 - - - +
222C LYS 4.2 2.7 - - - -
223C ALA* 3.6 44.2 - - + +
228C ILE* 4.3 8.0 - - + +
229C PRO 2.9 7.7 + - - -
230C GLY* 3.2 2.0 - - - -
231C ILE 2.8 26.0 + - - -
259C THR* 1.3 75.5 - - - +
261C ILE* 1.3 64.6 + - - +
262C GLU* 6.0 0.2 - - + -
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ILE* 4.4 7.4 - - + -
197C PHE 2.7 13.6 + - - +
198C VAL* 3.4 9.6 - - + +
199C VAL* 2.7 34.8 + - - +
231C ILE* 3.4 19.3 - - + +
233C VAL* 4.0 28.9 - - + -
241C VAL* 6.0 0.9 - - + +
244C ALA* 3.6 36.3 - - + +
245C VAL* 3.9 20.6 - - + +
248C ALA* 4.2 9.4 - - + -
259C THR* 4.3 6.7 - - + +
260C LEU* 1.3 79.0 - - - +
262C GLU* 1.3 55.5 + - - +
263C THR* 3.9 9.5 + - + -
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Residues in contact with GLU 262 (chain C).
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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199C VAL* 3.3 13.7 - - + +
201C ASN* 3.2 33.5 + - + -
218C THR* 3.8 1.0 - - - -
219C LEU* 3.0 32.0 + - + +
220C ALA* 2.8 35.1 + - + +
231C ILE 2.7 8.9 + - - +
232C GLN* 3.2 28.8 + - + +
233C VAL* 2.8 29.3 + - - +
260C LEU 4.2 0.4 - - - -
261C ILE* 1.3 71.0 - - - +
263C THR* 1.3 63.3 + - - +
264C LEU* 3.7 6.3 - - + +
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Residues in contact with THR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C SER* 2.8 30.9 + - - +
198C VAL* 4.2 13.9 - - + -
199C VAL 2.8 9.9 + - - -
200C GLN* 3.5 11.3 - - - -
201C ASN* 2.9 24.6 + - - +
233C VAL* 3.5 21.5 - - + -
235C GLY* 3.8 13.7 - - - -
241C VAL* 4.6 12.8 - - + -
261C ILE* 4.1 11.4 - - + -
262C GLU* 1.3 73.5 - - - +
264C LEU* 1.3 61.2 + - - +
265C CYS* 3.3 5.0 + - - -
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 3.6 32.5 - - + +
201C ASN* 3.9 16.6 - - - +
203C ARG* 5.6 8.1 - - - +
232C GLN* 3.6 22.9 - - + +
233C VAL 2.9 16.1 + - - +
234C ASP* 3.9 4.5 - - - +
235C GLY* 2.9 19.3 + - - +
236C MET* 3.7 7.8 + - - +
262C GLU* 3.7 24.9 - - - +
263C THR* 1.3 69.2 - - - +
265C CYS* 1.3 60.7 + - - +
290C TRP* 4.1 13.9 - - + -
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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