Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 1UBE
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 GLN 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ALA* 4.2 6.6 - - - +
245A ARG* 3.0 43.2 + - - +
246A VAL 3.0 17.7 - - - +
247A LYS* 4.0 26.4 - - + +
257A PHE 4.3 7.0 + - - +
258A LYS* 1.3 78.3 - - - +
260A ALA* 1.3 60.6 + - - +
261A GLU* 5.0 2.5 - - + +
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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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46A SER* 5.5 0.2 - - - +
48A SER* 3.1 41.7 - - - +
49A LEU* 3.6 17.0 - - + +
52A ALA* 3.7 5.3 - - + +
245A ARG* 3.5 1.7 - - - +
246A VAL* 2.6 41.8 + - - +
259A GLN* 1.3 75.0 - - - +
261A GLU* 1.3 61.9 + - - +
262A PHE* 5.2 1.3 - - + -
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Residues in contact with GLU 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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48A SER* 3.0 20.3 + - - -
230A ILE* 4.0 11.8 - - - +
243A ARG* 3.4 41.8 + - - +
244A THR 3.0 14.1 - - - +
245A ARG* 3.6 37.9 + - + -
259A GLN* 5.0 2.5 - - + +
260A ALA* 1.3 80.3 - - - +
262A PHE* 1.3 66.2 + - - +
275A SER* 6.0 0.5 - - - -
278A ASP* 6.0 1.2 - - - +
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Residues in contact with PHE 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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46A SER* 3.2 28.0 - - - +
49A LEU* 4.1 18.6 - - + -
77A VAL* 3.8 16.8 - - + -
243A ARG* 3.5 12.1 + - - +
244A THR* 2.8 49.7 + - + -
246A VAL* 3.9 21.1 - - + -
260A ALA 5.2 0.2 - - - -
261A GLU* 1.3 82.0 - - - +
263A ASP* 1.3 73.6 + - - +
264A ILE* 3.7 22.9 - - + -
270A ILE* 3.7 36.3 - - + -
275A SER* 4.9 11.2 - - - +
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Residues in contact with ASP 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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233A LEU* 3.5 31.9 - - + +
242A ASN 3.4 3.8 - - - +
243A ARG* 3.2 33.4 + - - +
262A PHE* 1.3 77.6 - - - +
264A ILE* 1.3 64.4 + - - +
265A LEU* 4.1 14.8 - - + -
270A ILE* 3.1 25.1 - - - +
271A SER* 3.1 14.2 + - - +
274A GLY* 4.7 12.0 - - - -
275A SER 6.1 1.2 - - - +
278A ASP* 4.2 6.2 - - - +
304A LYS* 4.8 10.0 + - - +
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Residues in contact with ILE 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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72A SER 4.9 0.7 - - - -
73A GLY* 3.8 25.4 - - - +
76A THR* 4.1 13.7 - - + +
105A TYR* 4.1 19.7 - - - +
241A GLY* 2.9 22.6 - - - -
242A ASN* 2.8 22.5 + - + +
244A THR* 3.8 20.2 - - - +
262A PHE* 3.7 22.2 - - + -
263A ASP* 1.3 80.1 - - - +
265A LEU* 1.3 66.1 + - - +
266A TYR 3.5 0.3 + - - -
269A GLY 3.5 9.9 - - - -
270A ILE* 4.2 5.8 - - + -
503A ADP 4.2 18.8 + - - +
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Residues in contact with LEU 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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233A LEU* 6.0 1.1 - - + -
240A VAL* 3.0 41.7 - - + +
241A GLY* 4.0 0.9 - - - -
263A ASP* 4.3 10.8 - - + -
264A ILE* 1.3 76.4 - - - +
266A TYR* 1.3 67.0 + - - +
267A GLY 2.8 4.5 + - - -
268A GLN* 3.0 47.9 + - + +
269A GLY* 3.0 13.9 + - - +
271A SER* 3.5 31.9 - - - +
305A GLU* 4.9 12.3 - - - +
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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