Contacts of the strand formed by residues 262 - 266 (chain A) in PDB entry 1UWY
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ASN* 6.0 1.3 + - - +
171A ASN* 3.6 9.1 + - - +
173A HIS* 3.1 39.0 - - + +
179A ALA* 3.3 4.2 - - - -
180A SER* 2.7 50.1 + - - -
184A ASP* 4.3 1.0 + - - -
241A TRP* 6.0 1.3 - - + -
249A GLN* 2.6 34.1 + - - +
261A ILE* 1.3 71.4 - - - +
263A LEU* 1.3 64.9 + - - +
264A GLU* 3.6 12.2 + - + +
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Residues in contact with LEU 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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61A TYR* 4.5 6.1 - - + -
170A ALA* 4.3 12.3 - - + -
171A ASN 3.4 7.7 + - - -
172A LEU* 3.3 30.9 - - + -
173A HIS* 2.7 35.1 + - - +
178A VAL 4.0 0.4 - - - -
179A ALA* 3.9 8.5 - - + -
212A TYR* 3.2 53.8 - - + +
219A MET* 5.3 0.2 - - - -
261A ILE* 3.6 33.7 - - + -
262A THR* 1.3 74.7 - - - +
264A GLU* 1.3 58.4 + - - +
265A LEU* 3.4 13.3 + - + +
287A LEU* 4.9 0.2 - - + -
290A TYR* 5.3 0.9 - - + -
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Residues in contact with GLU 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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173A HIS* 3.2 30.9 - - - +
174A GLY 3.4 21.5 - - - +
175A GLY* 4.4 0.3 - - - -
176A ALA* 3.3 20.5 + - + +
177A LEU* 2.9 7.1 - - - -
178A VAL* 2.6 43.4 + - + +
180A SER* 5.6 0.7 - - - -
219A MET* 2.9 19.1 - - - +
241A TRP* 3.8 28.4 - - + -
262A THR* 4.4 10.8 - - + +
263A LEU* 1.3 70.3 - - - +
265A LEU* 1.3 58.3 + - - +
1405A ZN 4.1 4.5 - - - -
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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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71A VAL* 4.6 7.2 - - + -
72A GLY* 4.8 3.1 - - - +
75A LEU* 3.5 31.0 - - + -
172A LEU* 3.7 31.4 - - + -
173A HIS 2.7 14.6 + - - +
177A LEU* 3.2 18.4 - - - +
212A TYR* 3.3 13.5 - - + +
216A ASN* 5.1 0.2 + - - -
219A MET* 3.6 20.4 - - + -
263A LEU* 3.6 21.1 - - + +
264A GLU* 1.3 70.7 - - - +
266A SER* 1.3 59.1 + - - +
279A PHE* 4.0 13.7 - - - -
283A ASN* 3.3 28.2 + - - +
287A LEU* 5.3 0.2 - - + -
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Residues in contact with SER 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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71A VAL* 3.2 30.1 - - - +
173A HIS 4.1 1.6 + - - -
174A GLY* 3.5 12.6 - - - -
175A GLY 2.4 35.5 + - - -
176A ALA 2.7 12.5 + - - +
177A LEU* 4.1 3.1 - - - -
265A LEU* 1.3 80.0 - - - +
267A CYS* 1.3 54.7 + - - +
268A CYS 3.0 19.6 + - - -
269A LYS* 4.2 1.2 - - - -
279A PHE* 3.8 15.9 - - - -
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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