Contacts of the helix formed by residues 148 - 154 (chain A) in PDB entry 5UPE
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 ILE 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.0 27.1 - - + -
70A LEU* 4.1 18.2 - - + -
112A LEU* 4.4 3.6 - - + -
114A ILE* 4.0 23.8 - - + -
116A ILE* 4.6 0.2 - - + -
134A VAL* 3.9 16.8 - - + -
144A LEU* 3.6 16.2 - - + +
145A THR 3.4 14.4 - - - +
147A TRP* 1.3 83.3 - - + +
149A GLU* 1.3 63.4 + - - +
150A THR 3.3 2.0 - - - -
151A ILE* 3.1 15.9 - - + +
152A LEU* 3.1 44.2 + - + +
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Residues in contact with GLU 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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19A LYS* 2.8 25.5 + - - +
145A THR 3.9 0.8 + - - -
146A ASN* 3.2 34.1 + - - +
148A ILE* 1.3 77.7 - - - +
150A THR* 1.3 57.2 + - - +
152A LEU* 3.2 1.8 + - - +
153A VAL* 2.8 47.9 + - + +
399A PHE* 3.5 56.3 + - + +
400A LYS* 4.8 2.3 + - - -
196B ARG* 3.2 26.7 + - - +
246B GLU* 3.9 3.5 - - - +
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Residues in contact with THR 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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14A ALA 4.3 0.7 - - - +
15A THR* 3.7 11.1 + - - -
16A ASP* 2.7 36.2 + - - +
19A LYS* 3.7 9.0 - - - -
147A TRP 4.2 1.6 + - - -
148A ILE 3.3 0.8 - - - -
149A GLU* 1.3 79.6 - - - +
151A ILE* 1.4 60.9 + - - +
153A VAL 3.6 0.3 + - - -
154A GLN* 3.5 22.8 + - - +
195B TYR* 3.5 49.4 - - + -
196B ARG* 3.7 18.1 - - - +
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Residues in contact with ILE 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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9A PHE* 3.7 11.9 - - + -
11A ILE* 5.4 4.3 - - + -
14A ALA* 4.4 11.5 + - + +
65A ILE* 3.8 27.8 - - + +
69A TYR* 3.5 36.3 - - + -
70A LEU* 4.0 15.0 - - + -
148A ILE* 3.1 36.8 - - + +
150A THR* 1.4 76.1 - - - +
152A LEU* 1.3 63.8 + - + +
154A GLN* 3.4 17.8 + - - +
201B GLN* 3.3 35.2 - - + +
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Residues in contact with LEU 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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62A LEU* 3.8 27.8 - - + -
65A ILE* 4.0 11.2 - - + +
70A LEU* 3.7 23.3 - - + -
116A ILE* 4.2 7.0 - - + -
132A PHE* 3.9 19.2 - - + -
134A VAL* 3.7 30.1 - - + -
148A ILE* 3.1 37.3 + - + +
149A GLU 3.9 2.2 - - - +
151A ILE* 1.3 74.2 - - + +
153A VAL* 1.4 59.3 + - - +
154A GLN 3.1 2.0 - - - -
155A SER* 2.9 32.2 + - - -
399A PHE* 4.4 7.6 - - + -
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Residues in contact with VAL 153 (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 PHE* 4.1 14.0 - - + -
149A GLU* 2.8 34.4 + - + +
150A THR 4.1 4.3 - - - +
151A ILE 3.4 0.4 - - - -
152A LEU* 1.4 66.6 - - - +
154A GLN* 1.4 50.9 + - - +
155A SER* 3.0 5.4 + - - -
156A TRP* 2.8 30.8 + - - +
392A ARG* 3.6 34.5 - - - +
397A CYS 4.9 1.1 - - - +
399A PHE* 3.3 38.6 - - + +
196B ARG* 3.7 20.4 - - + +
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Residues in contact with GLN 154 (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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65A ILE* 4.3 6.4 - - + +
69A TYR* 5.8 0.3 - - - -
150A THR 3.5 10.7 + - - +
151A ILE* 3.4 12.8 + - - +
152A LEU 3.1 0.8 - - - -
153A VAL* 1.4 72.2 - - - +
155A SER* 1.4 58.5 + - - +
156A TRP* 2.9 13.2 + - - +
157A TYR* 3.2 16.6 + - - +
158A PRO* 3.5 8.5 - - - +
195B TYR* 2.8 36.5 + - - +
196B ARG 3.8 7.6 - - - +
198B VAL* 3.5 29.2 - - - +
199B SER 4.5 6.1 - - - +
200B SER* 3.6 14.1 + - - -
201B GLN* 3.0 35.6 + - - +
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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