Contacts of the strand formed by residues 146 - 152 (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 VAL 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A TRP* 3.6 32.5 - - + +
142A LEU* 3.2 2.9 - - - -
143A VAL 2.8 39.6 + - - +
144A ASP* 3.4 1.3 - - + -
145A ASP* 1.3 91.3 - - - +
147A PRO* 1.4 79.3 - - + +
148A ILE* 3.5 1.6 + - - +
239A ARG* 4.2 17.9 - - + +
243A VAL* 3.9 20.2 - - + -
19B TRP* 4.1 18.6 - - + -
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Residues in contact with PRO 147 (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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140A VAL* 4.1 18.4 - - + -
141A PHE 3.4 7.6 - - - +
142A LEU* 4.2 10.8 - - + -
145A ASP 3.4 10.1 - - - +
146A VAL* 1.4 97.0 - - + +
148A ILE* 1.3 59.1 + - - +
149A ARG 3.6 2.2 - - - +
232A LEU* 4.2 16.4 - - + -
236A GLN* 3.7 42.8 - - + +
239A ARG* 4.3 7.0 - - + +
240A LEU* 3.6 21.0 - - + -
243A VAL* 3.9 1.4 - - - +
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Residues in contact with ILE 148 (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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88A PHE* 4.1 12.8 - - + -
101A LEU* 3.8 18.8 - - + -
103A THR* 4.1 12.6 - - + -
115A GLN* 4.0 0.3 - - - +
117A ILE* 3.9 21.1 - - + +
120A TRP* 3.7 22.2 - - + -
141A PHE* 2.8 23.2 + - + +
143A VAL* 3.7 34.3 - - + -
146A VAL 3.9 2.9 - - - +
147A PRO* 1.3 77.8 - - - +
149A ARG* 1.3 66.8 + - + +
240A LEU* 3.4 6.7 - - - +
243A VAL* 4.2 9.8 - - + +
244A ARG* 2.8 27.7 + - - -
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Residues in contact with ARG 149 (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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103A THR* 3.1 38.5 + - - +
104A ASN 3.5 2.2 - - - +
105A VAL* 3.9 18.9 - - - +
113A ARG* 2.9 40.5 + - - +
115A GLN* 3.2 30.7 + - - +
140A VAL* 3.6 3.1 - - - +
141A PHE* 3.0 58.2 + - + +
147A PRO 3.6 1.2 - - - -
148A ILE* 1.3 88.0 - - + +
150A VAL* 1.3 77.8 + - - +
151A PHE* 4.6 5.5 - - - +
240A LEU* 3.6 6.6 - - - +
244A ARG* 4.2 2.2 - - - +
252A TYR* 3.4 20.2 + - - -
271A ASP* 4.8 3.9 + - - +
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Residues in contact with VAL 150 (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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138A MET* 3.9 32.1 - - + -
139A ILE 3.3 11.0 - - - +
140A VAL* 4.3 5.4 - - + -
147A PRO* 5.2 0.4 - - + -
149A ARG* 1.3 86.3 + - - +
151A PHE* 1.3 63.6 + - - +
152A LYS* 4.1 14.1 - - + -
232A LEU* 3.3 32.8 - - + -
237A TYR* 4.9 4.5 - - + +
240A LEU* 3.8 16.5 - - + +
269A ASP* 3.0 37.9 + - - +
271A ASP* 4.1 5.9 + - - +
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Residues in contact with PHE 151 (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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105A VAL* 4.0 37.9 - - + -
107A THR* 4.2 4.5 - - + -
113A ARG* 3.5 43.1 - - - -
138A MET* 3.4 0.7 - - - -
139A ILE* 2.8 47.0 + - + +
141A PHE* 5.0 2.9 - - + -
149A ARG* 4.6 5.1 - - - +
150A VAL* 1.3 74.1 - - - +
152A LYS* 1.3 67.2 + - - +
159A VAL* 4.4 0.7 - - + -
160A LYS 3.8 24.2 - - - -
161A PHE* 3.5 26.0 - + - -
162A PRO* 4.3 0.7 - - + -
252A TYR* 4.4 4.7 - - - -
265A GLU* 3.8 22.4 - - + -
269A ASP* 3.7 10.8 - - - -
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Residues in contact with LYS 152 (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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137A TYR 3.8 5.8 + - - +
138A MET* 3.8 17.9 - - + -
150A VAL* 4.1 10.5 - - + -
151A PHE* 1.3 85.2 - - - +
153A ASN* 1.3 61.9 + - - +
154A CYS* 3.1 27.2 + - - +
159A VAL* 6.0 0.2 - - - +
161A PHE* 3.7 6.7 - - - -
230A GLN 3.3 16.8 + - - -
231A ASP* 2.7 37.3 + - - +
237A TYR* 3.9 9.0 - - - -
265A GLU* 5.1 0.5 - - - +
268A ARG* 4.3 26.2 - - + +
269A ASP* 2.9 25.1 + - - +
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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