Contacts of the strand formed by residues 70 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.6 28.7 - - + -
63B VAL* 4.5 5.0 - - - +
67B SER* 2.8 31.6 + - - +
68B ALA 3.8 6.5 - - - +
69B GLY* 1.3 80.7 - - - +
71B VAL* 1.3 66.2 + - - +
72B THR* 5.1 0.2 + - - -
90B PHE 3.6 1.6 - - - +
91B LEU* 3.7 1.2 - - - -
92B GLY 3.0 25.1 + - - -
99B TYR* 4.2 7.1 + - - -
173B LEU* 4.4 7.6 - - - +
174B TRP 3.6 3.6 - - - -
175B ASN* 4.6 0.4 - - - +
180B ALA* 4.2 1.2 - - - +
188B THR* 4.5 4.3 - - + +
195B PHE* 4.0 24.0 - - + -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 1.3 78.9 - - - +
72B THR* 1.3 65.5 + - - +
73B ALA 4.6 0.2 - - - +
89B GLU* 3.9 30.7 - - + +
90B PHE 3.3 5.2 - - - +
91B LEU* 4.0 10.3 - - + -
173B LEU* 3.4 2.9 - - - +
174B TRP* 2.9 66.7 + - + +
176B ALA* 3.6 28.3 - - + -
179B TRP* 4.1 6.7 - - + -
180B ALA* 3.8 12.1 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B MET* 3.8 10.5 - - + -
62B LEU* 3.5 33.9 - - + +
63B VAL* 4.2 5.5 - - - +
70B THR* 5.1 0.7 + - - -
71B VAL* 1.3 72.3 - - - +
73B ALA* 1.3 58.5 + - - +
89B GLU* 3.5 0.2 - - - -
90B PHE* 2.7 41.9 + - - -
99B TYR* 4.3 2.8 + - - -
172B SER 3.4 4.9 - - - +
173B LEU* 3.3 19.3 - - + +
197B ALA* 3.9 17.0 - - + +
199B TYR* 3.3 25.1 - - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B MET* 5.0 0.7 - - - -
71B VAL 4.0 0.2 - - - -
72B THR* 1.3 75.4 - - - +
74B PHE* 1.3 59.4 - - - +
75B TYR* 3.8 18.2 - - + -
88B PHE 3.3 8.7 - - - +
89B GLU* 4.1 13.5 - - + +
171B SER* 3.1 9.3 - - - -
172B SER* 2.8 49.0 + - - +
174B TRP* 4.1 11.7 - - + +
199B TYR* 3.6 4.4 + - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 4.8 0.9 - - - -
56B PHE* 4.2 20.0 - - + -
57B SER 4.2 5.4 - - - -
58B MET* 3.9 31.4 - - + -
60B MET* 3.9 21.3 - - + +
72B THR 4.4 0.2 + - - -
73B ALA* 1.3 73.2 - - - +
75B TYR* 1.3 62.4 + - - +
76B LEU* 5.2 5.8 - - + -
88B PHE* 2.9 64.4 + + + +
90B PHE* 5.4 0.2 - - - -
130B TYR* 3.4 32.5 - - + -
131B SER* 4.6 0.2 - - - -
132B VAL* 4.8 3.8 - - + -
169B ILE* 3.7 23.8 - - + -
170B TYR 3.4 5.8 - - - -
171B SER* 3.7 15.9 - - - +
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 3.8 28.3 - - + -
74B PHE* 1.3 76.1 - - - +
76B LEU* 1.3 65.6 - - - +
77B SER* 4.1 14.8 - - - -
85B GLU* 3.8 10.3 - - - -
86B ILE 3.2 9.6 - - - +
87B ASP* 3.2 31.2 - - + +
88B PHE 4.5 0.7 - - - +
89B GLU* 6.0 0.2 - - + -
169B ILE* 3.5 5.1 - - - +
170B TYR* 2.7 84.7 + + + +
171B SER 4.7 0.9 - - - -
172B SER* 4.2 13.5 + - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.9 42.4 - - + -
74B PHE* 5.2 4.0 - - + -
75B TYR* 1.3 80.4 - - - +
77B SER* 1.3 61.3 + - - +
85B GLU* 3.2 7.3 - - - +
86B ILE* 2.9 39.2 + - + +
132B VAL* 4.3 26.2 - - + -
134B TRP* 4.1 19.7 - - + -
167B MET* 3.9 20.9 - - + +
168B LYS 3.2 5.4 - - - +
169B ILE* 4.0 25.6 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 4.1 10.3 - - - -
76B LEU* 1.3 76.2 - - - +
78B SER* 1.3 70.3 + - - +
79B GLN* 3.1 9.0 - - - +
83B HIS* 3.2 22.7 - - - -
84B ASP 3.4 6.3 - - - -
85B GLU* 4.1 10.1 + - - -
167B MET* 3.5 8.0 - - - +
168B LYS 3.0 28.6 + - - +
170B TYR* 3.8 15.8 - - - -
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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