Contacts of the strand formed by residues 168 - 175 (chain A) in PDB entry 1UMZ
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 LYS 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLN* 3.8 22.0 + - - +
47A SER* 3.5 25.7 + - - +
48A LYS 4.0 10.9 + - - -
49A GLY 3.4 10.5 - - - +
50A SER* 3.4 25.4 - - - +
76A LEU* 3.2 5.5 - - - -
77A SER 3.0 29.7 + - - -
79A GLN* 6.0 5.5 - - + +
167A MET* 1.3 74.4 - - - +
169A ILE* 1.3 63.6 + - - +
170A TYR* 3.5 29.1 - - + +
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Residues in contact with ILE 169 (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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15A TYR* 3.3 28.1 - - + +
46A GLN* 3.1 5.4 - - - +
47A SER* 2.7 45.0 + - - +
51A TYR* 3.7 16.4 - - + -
56A PHE* 3.6 35.0 - - + -
58A MET* 5.2 0.4 - - + -
74A PHE* 3.5 28.5 - - + -
75A TYR 3.4 7.2 - - - +
76A LEU* 3.9 14.1 - - + -
168A LYS* 1.3 73.9 - - - +
170A TYR* 1.3 63.8 + - - +
204A ILE* 3.6 18.6 - - + -
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Residues in contact with TYR 170 (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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18A THR* 6.1 0.2 - - - -
45A PHE* 3.5 8.1 - - - +
46A GLN* 3.3 41.3 + - + -
74A PHE* 3.4 5.0 - - - -
75A TYR* 2.8 73.2 + + + +
77A SER* 3.8 22.5 + - - -
79A GLN* 3.4 25.8 + - - +
168A LYS* 3.5 44.6 - - + +
169A ILE* 1.3 74.7 - - - +
171A SER* 1.3 64.5 + - - +
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Residues in contact with SER 171 (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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35A LEU* 4.6 2.0 - - - -
44A GLY* 3.1 2.3 - - - -
45A PHE* 2.9 63.0 + - - +
73A ALA 2.4 27.3 + - - -
74A PHE* 3.9 8.8 - - - -
75A TYR* 4.8 0.4 - - - -
170A TYR* 1.3 77.9 - - - +
172A SER* 1.3 60.3 + - - +
199A TYR* 2.5 29.6 + - - -
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Residues in contact with SER 172 (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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35A LEU* 4.1 6.5 - - - -
43A THR 3.2 14.8 - - - -
44A GLY* 4.0 4.0 - - - -
71A VAL 3.8 1.2 + - - +
72A THR* 3.4 2.8 - - - -
73A ALA* 2.8 44.4 + - - +
75A TYR* 4.3 10.6 + - - -
171A SER* 1.3 77.8 + - - +
173A LEU* 1.3 63.5 + - - +
174A TRP* 5.4 7.6 + - - +
199A TYR* 3.9 2.6 + - - -
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Residues in contact with LEU 173 (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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35A LEU* 3.4 31.1 - - + +
36A HIS 4.1 0.2 - - - -
37A LEU* 3.6 28.0 - - + +
42A GLY* 3.3 6.6 - - - -
43A THR* 3.0 28.9 + - + +
63A VAL* 4.3 7.4 - - + -
70A THR* 4.3 10.3 - - - -
71A VAL 3.4 10.3 - - - +
72A THR* 3.4 24.5 - - + +
172A SER* 1.3 74.2 - - - +
174A TRP* 1.3 63.7 + - - +
195A PHE* 3.3 30.5 - - + +
196A ILE 4.7 0.2 - - - -
197A ALA* 4.1 11.2 - - + +
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Residues in contact with TRP 174 (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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19A TRP* 3.7 21.1 - + + -
37A LEU* 3.8 12.7 - - + +
40A TYR 5.4 1.8 - - - -
41A THR* 3.7 14.6 - - - -
42A GLY* 3.3 38.4 - - - -
43A THR* 3.6 6.7 - - - -
70A THR* 3.6 1.9 - - - -
71A VAL* 2.9 35.7 + - + +
172A SER* 4.2 7.2 - - - +
173A LEU* 1.3 87.7 - - - +
175A ASN* 1.3 90.8 + - + +
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Residues in contact with ASN 175 (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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37A LEU* 4.0 8.2 - - + +
69A GLY 3.6 5.7 + - - -
70A THR* 4.5 0.6 - - - +
174A TRP* 1.3 94.8 - - + +
176A ALA* 1.3 61.7 + - - +
177A ASP* 3.0 32.4 + - - +
188A THR* 2.6 35.6 + - - -
190A TRP* 3.5 29.3 - - + -
4D XYS 5.4 0.9 + - - -
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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