Contacts of the strand formed by residues 146 - 152 (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 VAL 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B TRP* 3.7 28.9 - - + +
142B LEU* 3.2 2.6 - - - -
143B VAL 2.8 37.7 + - - +
144B ASP* 3.4 1.1 - - + -
145B ASP* 1.3 92.7 - - - +
147B PRO* 1.3 78.7 - - + +
148B ILE* 3.4 1.7 + - - +
239B ARG* 3.8 32.8 - - + +
243B VAL* 3.7 22.2 - - + -
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Residues in contact with PRO 147 (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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140B VAL* 4.0 20.4 - - + -
141B PHE 3.3 7.2 - - - +
142B LEU* 4.0 9.8 - - + -
145B ASP 3.6 7.9 - - - +
146B VAL* 1.3 90.9 - - + +
148B ILE* 1.3 59.8 + - - +
149B ARG 4.7 2.9 - - - +
232B LEU* 4.1 14.1 - - + -
236B GLN* 3.7 43.7 - - + +
239B ARG* 4.1 8.7 - - + -
240B LEU* 3.5 23.7 - - + +
243B VAL* 4.0 0.9 - - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 4.2 2.5 - - + -
101B LEU* 3.8 23.8 - - + +
103B THR* 3.8 29.6 - - + +
115B GLN* 4.2 0.3 - - - +
117B ILE* 3.9 21.7 - - + +
120B TRP* 3.7 21.5 - - + -
141B PHE* 2.8 28.1 + - + +
143B VAL* 3.7 23.8 - - + -
146B VAL 3.9 3.6 - - - +
147B PRO* 1.3 76.5 - - - +
149B ARG* 1.3 63.5 + - + +
240B LEU* 3.4 7.0 - - - +
243B VAL* 4.1 11.1 - - + +
244B ARG* 2.9 27.9 + - - -
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Residues in contact with ARG 149 (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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103B THR* 3.0 40.2 + - - +
104B ASN 3.6 1.8 - - - +
105B VAL* 4.0 17.4 - - - +
113B ARG* 2.8 39.2 + - - +
115B GLN* 3.3 29.0 + - - +
140B VAL* 3.5 6.1 - - - +
141B PHE* 3.0 56.9 + - + +
147B PRO* 3.5 2.3 - - - -
148B ILE* 1.3 88.6 - - + +
150B VAL* 1.3 71.0 + - - +
151B PHE* 4.8 5.9 - - - +
240B LEU* 3.6 8.7 - - - +
244B ARG* 4.3 2.5 - - - +
252B TYR* 3.3 21.8 + - - -
271B ASP* 4.8 4.6 + - - +
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Residues in contact with VAL 150 (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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138B MET* 3.8 33.7 - - + -
139B ILE 3.3 10.1 - - - +
140B VAL* 4.2 5.6 - - + -
149B ARG* 1.3 81.1 + - - +
151B PHE* 1.3 62.8 + - - +
152B LYS* 4.2 13.2 - - + -
232B LEU* 4.5 12.6 - - + -
237B TYR* 4.6 11.0 - - + -
240B LEU* 4.3 12.2 - - + +
269B ASP* 3.0 54.2 + - - +
271B ASP* 4.1 5.9 + - - +
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Residues in contact with PHE 151 (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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105B VAL* 3.9 39.3 - - + -
107B THR* 4.1 5.6 - - + -
113B ARG* 3.6 41.1 - - - -
138B MET* 3.4 1.1 - - - -
139B ILE* 2.8 48.5 + - + +
141B PHE* 5.0 2.7 - - + -
149B ARG* 4.8 5.4 - - - +
150B VAL* 1.3 72.9 - - - +
152B LYS* 1.3 67.9 + - - +
159B VAL* 4.3 5.8 - - + -
160B LYS 3.8 19.1 - - - -
161B PHE* 3.4 30.3 - + - -
162B PRO* 4.4 0.4 - - + -
252B TYR* 4.4 3.1 - - - -
265B GLU* 3.8 17.0 - - + -
269B ASP* 3.6 11.0 - - - -
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Residues in contact with LYS 152 (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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137B TYR 3.7 11.4 - - - +
138B MET* 4.2 10.3 - - + -
150B VAL* 4.2 13.0 - - + +
151B PHE* 1.3 87.1 - - - +
153B ASN* 1.3 61.4 + - - +
154B CYS* 3.2 25.0 + - - +
159B VAL* 5.9 0.2 - - - +
160B LYS 5.4 0.3 - - - +
161B PHE* 3.8 6.9 - - - -
230B GLN 5.7 1.1 - - - -
231B ASP* 3.5 17.5 + - - +
237B TYR* 2.4 33.2 + - - -
265B GLU* 4.9 0.5 - - - +
268B ARG* 2.7 49.8 + - + +
269B ASP* 2.9 17.4 + - - +
270B ARG* 4.0 6.1 - - - +
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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