Contacts of the strand formed by residues 263 - 266 (chain A) in PDB entry 1UA4
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 VAL 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ALA* 3.3 13.7 - - + +
231A LEU* 3.8 23.3 - - + -
253A LEU* 4.0 8.7 - - + -
256A LEU* 3.5 29.6 - - + -
257A ASN* 4.8 6.7 - - - +
261A ILE 3.2 16.6 - - - +
262A PRO* 1.3 74.8 - - - +
264A HIS* 1.3 63.2 + - - +
285A MET 4.9 0.9 + - - +
286A PHE* 3.6 33.6 - - + +
287A TYR* 2.8 31.9 + - - +
288A SER 3.1 6.6 + - - +
447A PHE* 4.2 1.8 - - - -
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Residues in contact with HIS 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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229A ALA 2.8 8.2 + - - +
230A ILE* 3.3 16.8 - - + +
231A LEU* 2.9 26.0 + - - +
263A VAL* 1.3 73.7 - - - +
265A LEU* 1.3 71.0 + - - +
266A GLU* 2.8 31.4 - - + -
286A PHE* 3.8 2.9 - - - -
288A SER* 2.7 33.7 - - - -
289A VAL 3.4 5.2 - - - -
290A GLY* 3.1 17.3 + - - -
338A ARG* 3.8 10.7 + - - -
340A HIS* 5.1 0.6 - - - +
443A SER* 4.0 15.9 + - - -
447A PHE* 3.5 36.1 - + + -
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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
----------------------------------------------------------
231A LEU* 3.4 18.8 - - + +
232A SER* 4.5 4.3 - - - -
234A LEU* 4.6 19.1 - - + -
264A HIS* 1.3 75.5 - - - +
266A GLU* 1.3 68.9 + - - +
267A PHE* 4.0 15.5 - - + -
279A ILE* 3.6 30.5 - - + -
283A LEU* 3.7 20.4 - - + -
286A PHE* 3.5 35.4 - - + -
288A SER 2.8 10.6 + - - +
289A VAL* 3.2 6.6 - - + +
290A GLY 2.9 24.1 + - - -
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Residues in contact with GLU 266 (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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113A GLN* 3.9 20.9 - - + +
117A MET* 4.0 14.1 - - + +
230A ILE* 4.8 1.8 - - + -
231A LEU 3.0 8.6 + - - +
232A SER* 2.8 38.0 + - - +
235A GLN* 4.7 1.6 - - - +
264A HIS* 2.8 30.4 + - + +
265A LEU* 1.3 76.4 - - - +
267A PHE* 1.3 71.9 + - - +
268A ALA* 3.8 0.7 + - - +
290A GLY* 3.6 11.0 - - - +
291A LEU* 4.9 0.2 - - - -
295A GLU* 5.5 0.2 - - - +
342A HIS* 3.9 14.4 - - - -
439A GLY 3.9 6.1 - - - +
440A ASP* 4.1 4.4 - - - +
443A SER* 2.7 30.5 + - - -
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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
------------------------------------------------------------
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