Contacts of the strand formed by residues 70 - 77 (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 THR 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.7 28.0 - - + -
63A VAL* 4.6 4.5 - - - +
67A SER* 2.7 31.4 + - - +
68A ALA 3.8 6.7 - - - +
69A GLY* 1.3 81.5 - - - +
71A VAL* 1.3 65.1 + - - +
72A THR* 5.1 0.9 + - - -
90A PHE 3.6 1.2 - - - +
91A LEU* 3.7 1.0 - - - -
92A GLY* 3.0 25.8 + - - -
99A TYR* 4.3 6.6 + - - -
173A LEU* 4.3 8.5 - - - +
174A TRP 3.6 4.9 - - - -
175A ASN* 4.5 0.7 - - - +
180A ALA* 4.2 1.0 - - - +
188A THR* 4.5 4.5 - - + +
195A PHE* 4.0 24.2 - - + -
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Residues in contact with VAL 71 (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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70A THR* 1.3 79.0 - - - +
72A THR* 1.3 66.0 + - - +
73A ALA* 4.0 5.3 + - + +
89A GLU* 4.0 37.2 - - + +
90A PHE 3.3 5.6 - - - +
91A LEU* 3.7 18.8 - - + -
172A SER 3.8 1.4 - - - +
173A LEU* 3.4 4.1 - - - +
174A TRP* 2.9 37.6 + - + +
176A ALA* 3.6 26.9 - - + -
179A TRP* 4.1 7.2 - - + -
180A ALA* 3.9 6.3 - - + -
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Residues in contact with THR 72 (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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60A MET* 3.7 17.7 - - + -
62A LEU* 3.6 23.1 - - + +
63A VAL* 4.2 5.4 - - - +
70A THR* 5.1 1.0 + - - -
71A VAL* 1.3 71.2 - - - +
73A ALA* 1.3 58.5 + - - +
89A GLU* 3.5 0.2 - - - -
90A PHE* 2.7 43.1 + - - -
99A TYR* 4.3 2.8 + - - -
172A SER 3.4 4.7 - - - +
173A LEU* 3.4 18.0 - - + +
197A ALA* 3.8 20.5 - - + +
199A TYR* 3.3 25.4 - - - +
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Residues in contact with ALA 73 (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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60A MET* 5.1 1.3 - - - -
71A VAL* 3.9 6.0 - - + +
72A THR* 1.3 74.7 - - - +
74A PHE* 1.3 52.4 + - - +
75A TYR* 3.8 20.6 - - + -
88A PHE 3.3 8.5 - - - +
89A GLU* 4.1 14.6 - - + +
171A SER* 2.4 30.9 + - - -
172A SER* 2.8 29.7 + - - +
199A TYR* 3.8 0.6 + - - -
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Residues in contact with PHE 74 (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* 4.6 0.7 - - - -
56A PHE* 4.3 15.5 - - + -
57A SER 4.3 7.0 - - - -
58A MET* 3.9 40.6 - - + -
60A MET* 3.9 20.9 - - + -
72A THR 4.4 0.2 + - - -
73A ALA* 1.3 73.2 - - - +
75A TYR* 1.3 62.7 + - - +
76A LEU* 5.4 2.9 - - + -
88A PHE* 2.9 62.3 + + + +
130A TYR* 3.4 32.5 - - + -
131A SER* 4.7 0.7 - - - -
132A VAL* 4.9 5.2 - - + -
169A ILE* 3.5 25.6 - - + -
170A TYR 3.4 9.6 - - - -
171A SER* 3.9 4.0 - - - +
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Residues in contact with TYR 75 (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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73A ALA* 3.8 28.3 - - + -
74A PHE* 1.3 75.3 - - - +
76A LEU* 1.3 71.8 + - - +
77A SER* 4.1 9.2 - - - -
85A GLU* 3.7 18.4 - - - -
86A ILE 3.2 9.0 - - - +
87A ASP* 3.2 23.6 - - + +
88A PHE 4.5 0.7 - - - +
89A GLU* 6.0 0.4 - - + -
169A ILE* 3.4 4.6 - - - +
170A TYR* 2.8 83.4 + + + +
171A SER* 4.8 0.2 - - - -
172A SER* 4.3 11.8 + - - -
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Residues in contact with LEU 76 (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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51A TYR* 5.9 0.2 - - + -
56A PHE* 3.8 39.7 - - + -
74A PHE* 5.4 4.0 - - + -
75A TYR* 1.3 78.8 - - - +
77A SER* 1.3 61.9 + - - +
85A GLU* 3.1 6.9 - - - +
86A ILE* 2.9 39.5 + - + +
132A VAL* 4.2 29.6 - - + -
134A TRP* 4.0 20.6 - - + -
167A MET* 3.9 20.4 - - + +
168A LYS 3.2 5.4 - - - +
169A ILE* 3.9 23.6 - - + -
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Residues in contact with SER 77 (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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75A TYR* 4.1 14.8 - - - -
76A LEU* 1.3 76.7 - - - +
78A SER* 1.3 73.1 + - - +
83A HIS* 3.4 19.8 - - - -
84A ASP 3.4 6.7 - - - -
85A GLU* 4.1 6.2 + - - -
167A MET* 3.6 5.8 - - - -
168A LYS* 3.0 30.1 + - - +
170A TYR* 3.8 20.9 + - - -
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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