Contacts of the strand formed by residues 63 - 67 (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 VAL 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG* 1.3 75.9 - - - +
64A ILE* 1.3 64.0 + - - +
177A LEU* 4.5 8.3 - - + -
181A THR* 5.2 7.9 - - - +
184A LEU* 4.5 14.1 - - + +
191A ALA* 3.4 8.3 - - + +
193A PHE* 3.5 35.2 - - + -
217A LEU* 4.0 11.0 - - + -
220A TYR* 2.9 37.0 - - + +
221A ALA* 3.3 8.6 - - - -
222A SER* 3.1 20.8 + - - +
223A VAL 3.7 3.3 + - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.2 48.7 - - + -
59A PRO* 4.0 13.2 - - + -
62A ARG 4.7 0.7 - - - +
63A VAL* 1.3 82.5 - - - +
65A GLU* 1.3 65.1 + - - +
66A ILE* 3.9 25.8 - - + -
190A THR* 3.7 18.6 - - - +
191A ALA 2.5 15.9 + - - +
192A ILE* 3.4 7.5 - - + +
193A PHE* 2.9 30.1 + - - +
217A LEU* 5.1 0.2 - - - -
223A VAL* 3.6 13.5 - - + +
225A LEU* 4.0 14.6 - - + -
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Residues in contact with GLU 65 (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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64A ILE* 1.3 73.4 - - - +
66A ILE* 1.3 62.3 + - - +
67A TYR* 3.2 20.8 - - + -
193A PHE* 3.8 6.7 - - - +
195A ASN* 3.9 16.9 + - + +
214A GLY* 6.1 0.3 - - - -
217A LEU* 2.7 53.8 - - + +
218A LYS* 3.9 0.9 + - - +
221A ALA* 4.3 2.0 - - + +
223A VAL 3.0 11.6 + - - +
224A ARG* 2.5 39.7 + - + +
225A LEU* 2.6 34.0 + - - +
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Residues in contact with ILE 66 (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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58A LEU* 5.5 3.4 - - + -
64A ILE* 3.9 16.6 - - + -
65A GLU* 1.3 78.9 - - - +
67A TYR* 1.3 60.2 + - - +
74A LYS* 3.4 41.8 - - + +
77A VAL* 4.6 17.9 - - + -
78A ALA* 5.1 2.5 - - + +
192A ILE* 4.0 28.5 - - + -
193A PHE 3.2 10.7 + - - +
194A ILE* 3.8 3.3 - - + -
195A ASN 3.4 17.0 + - - -
225A LEU* 3.3 23.3 - - + +
227A VAL* 3.8 21.3 - - + -
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Residues in contact with TYR 67 (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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65A GLU* 3.2 21.8 - - + +
66A ILE* 1.3 75.5 - - - +
68A GLY* 1.3 56.6 + - - +
74A LYS* 4.1 4.9 - - - -
195A ASN* 3.6 27.8 - - + -
196A GLN 4.0 11.0 - - - +
224A ARG* 3.5 29.3 + - + -
225A LEU 2.8 15.7 + - - -
226A ASP* 3.3 41.0 + - + +
227A VAL* 2.7 33.1 + - - +
228A ARG* 5.0 6.3 - - - -
249A VAL* 3.6 22.0 - - + +
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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