Contacts of the strand formed by residues 259 - 264 (chain B) in PDB entry 2XXL
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ILE* 3.2 17.1 - - - +
258B SER* 1.3 90.0 + - - +
260B TYR* 1.3 62.1 + - - +
281B ASN* 3.6 35.0 - - + +
282B VAL 3.6 11.0 - - - +
283B PRO* 4.9 3.6 - - - +
324B ALA* 4.6 4.2 - - - +
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Residues in contact with TYR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ALA* 2.6 42.3 + - - +
257B ILE* 3.8 23.4 - - + +
259B THR* 1.3 73.8 - - - +
261B PHE* 1.3 60.9 + - - +
262B VAL* 3.7 0.8 + - + -
280B ALA 3.4 1.6 - - - +
281B ASN* 3.4 4.1 - - - -
282B VAL* 2.8 37.8 + - - +
284B LEU* 4.1 25.8 - - + -
303B LEU* 4.7 1.8 - - + +
305B VAL* 5.1 1.6 - - + -
322B LEU* 3.5 46.7 - - + -
323B GLN 3.6 16.6 - - - +
324B ALA* 3.7 10.8 - - + -
339B PHE* 3.6 34.7 - + + +
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Residues in contact with PHE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 5.2 5.8 - + - -
130B ARG* 3.7 9.6 - - - -
260B TYR* 1.3 72.0 - - - +
262B VAL* 1.3 60.8 + - - +
263B THR* 3.7 14.6 + - - +
279B GLN* 3.4 29.6 - - + +
280B ALA 3.4 1.8 - - - -
281B ASN* 3.4 25.4 - - - -
321B PRO 4.5 0.3 - - - +
322B LEU* 4.0 4.5 - - - +
323B GLN* 2.8 47.3 + - + +
324B ALA* 5.4 0.2 - - + -
325B PRO* 4.0 20.9 - - + -
336B MET* 3.7 32.1 - - + -
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B TYR 4.6 0.4 - - - +
261B PHE* 1.3 73.0 - - - +
263B THR* 1.3 59.5 + - - +
279B GLN* 3.2 1.9 - - - -
280B ALA 2.8 33.6 + - - -
282B VAL* 3.7 37.2 - - + -
305B VAL* 4.6 1.1 - - + -
312B ASP 3.9 7.6 - - - +
313B SER* 3.6 17.7 - - - +
315B LYS* 3.8 4.0 - - - +
316B GLY* 3.3 29.6 - - - +
321B PRO 4.9 3.8 - - - +
322B LEU* 3.8 15.3 - - + -
342B VAL* 6.0 0.2 - - + -
358B TYR* 3.7 21.5 - - - +
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Residues in contact with THR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.6 0.7 - - + -
130B ARG* 4.0 17.3 - - + -
133B MET* 3.2 20.7 - - + +
261B PHE* 3.7 5.8 + - - +
262B VAL* 1.3 77.8 - - - +
264B GLY* 1.3 62.0 + - - +
277B LEU* 3.9 17.0 - - + -
278B LEU 3.3 12.1 - - - +
279B GLN* 2.7 33.9 + - + +
315B LYS 3.9 4.9 - - - -
316B GLY* 3.5 10.9 - - - -
317B ASP 4.1 2.3 + - - -
321B PRO* 4.6 9.6 + - - +
323B GLN* 3.5 19.5 + - - -
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Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 4.1 1.8 - - - -
263B THR* 1.3 77.9 - - - +
265B TRP* 1.3 59.7 + - - -
277B LEU* 3.5 16.4 - - - +
278B LEU* 2.9 35.5 + - - +
315B LYS 3.3 12.4 + - - +
317B ASP* 3.3 15.5 - - - -
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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