Contacts of the strand formed by residues 262 - 267 (chain D) in PDB entry 6ARQ
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 ALA 262 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D TRP* 4.1 28.9 - - + +
259D GLN* 5.3 4.3 - - + -
260D ASN 2.8 12.6 + - - +
261D GLU* 1.3 74.3 - - - +
263D THR* 1.3 57.6 + - - +
298D LEU* 3.6 4.3 - - - +
299D ILE* 2.8 42.4 + - + -
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Residues in contact with THR 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D SER 5.0 0.2 - - - +
250D GLY* 4.7 8.5 - - - -
255D TRP* 6.0 0.3 - - - -
261D GLU 5.3 1.8 - - - +
262D ALA* 1.3 77.9 - - - +
264D LEU* 1.3 65.1 + - - +
265D THR* 4.2 1.6 + - - +
296D GLN* 3.6 27.4 + - - +
297D LEU 3.5 10.7 + - - -
298D LEU* 4.4 14.1 + - + +
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D ILE* 3.9 20.2 - - + -
249D SER 3.9 10.1 - - - +
250D GLY* 3.9 2.9 - - - -
251D TYR* 3.5 37.0 - - + +
255D TRP* 4.1 15.0 - - + -
263D THR* 1.3 76.1 + - - +
265D THR* 1.3 61.0 + - - +
266D CYS 4.2 0.2 + - - -
279D TRP* 4.2 1.2 - - - -
296D GLN* 3.4 3.6 - - - +
297D LEU* 2.8 49.6 + - + +
299D ILE* 3.8 31.2 - - + -
310D LEU* 3.9 19.5 - - + -
325D LEU* 4.3 5.8 - - + -
327D VAL* 4.8 3.8 - - + -
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Residues in contact with THR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D ILE* 3.4 5.8 - - - +
249D SER* 3.4 36.7 + - - +
250D GLY* 5.8 0.2 - - - -
263D THR 4.2 1.5 - - - +
264D LEU* 1.3 73.4 - - - +
266D CYS* 1.3 62.4 + - - +
267D ASP* 3.5 23.8 + - - +
295D ALA* 4.2 4.5 + - - +
296D GLN* 3.9 21.3 + - - +
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Residues in contact with CYS 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D VAL* 3.6 20.6 - - - -
247D SER 3.5 6.5 - - - -
248D ILE* 4.6 1.6 - - - -
264D LEU 4.2 0.4 + - - -
265D THR* 1.3 72.0 + - - +
267D ASP* 1.3 64.3 + - - +
268D ALA 3.2 3.8 + - - -
277D TYR* 3.8 16.7 + - + -
279D TRP* 3.6 8.3 - - + -
295D ALA* 3.1 24.3 + - - +
312D CYS* 2.0 52.5 - - - -
314D VAL* 4.1 7.2 - - - -
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Residues in contact with ASP 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D GLU 3.8 2.6 - - - +
246D VAL* 3.7 0.3 - - - -
247D SER* 2.8 53.7 + - - +
249D SER* 3.8 19.2 - - - -
265D THR* 3.5 31.6 + - - +
266D CYS* 1.3 67.1 - - - +
268D ALA* 1.3 55.7 + - - +
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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