Contacts of the helix formed by residues 121 - 131 (chain N) in PDB entry 5U07
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 GLU 121 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53N ARG* 2.9 39.1 + - - +
54N TYR* 4.2 10.6 - - - -
55N LYS 4.8 0.5 - - - +
57N LEU* 4.9 8.1 - - - +
120N PRO* 1.3 96.9 - - + +
122N ALA* 1.3 52.8 + - - +
123N ASP* 2.6 7.2 + - - -
124N THR* 2.6 56.6 + - + +
125N ILE* 3.6 9.9 + - + +
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Residues in contact with ALA 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N SER* 5.4 0.4 - - - -
3N GLY* 4.4 11.9 - - - +
4N PHE* 3.3 25.7 - - + -
57N LEU* 4.6 4.5 - - + +
117N VAL* 4.4 10.5 - - + -
119N GLY* 4.1 25.4 + - - +
120N PRO 3.6 1.2 - - - -
121N GLU* 1.3 77.7 - - - +
123N ASP* 1.3 57.4 + - - +
125N ILE* 3.0 18.1 - - + +
126N ALA* 3.0 23.7 + - - +
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Residues in contact with ASP 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N SER* 3.8 22.4 - - - -
3N GLY* 3.7 18.4 + - - +
4N PHE* 5.1 0.2 - - - -
120N PRO 5.6 0.8 - - - +
121N GLU* 2.6 7.2 + - - +
122N ALA* 1.3 76.2 - - - +
124N THR* 1.3 57.7 + - + +
126N ALA* 3.3 7.5 + - - +
127N ASP* 2.9 34.1 + - - +
153N ARG 4.2 5.7 - - - +
154N ARG* 3.4 39.1 + - - +
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Residues in contact with THR 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N GLN* 3.8 12.2 + - - -
53N ARG* 4.8 4.9 + - - -
121N GLU* 2.6 44.3 + - + +
123N ASP* 1.3 72.6 - - + +
125N ILE* 1.3 64.3 + - - -
127N ASP* 3.1 16.4 + - - +
128N ALA* 3.0 19.9 + - - +
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Residues in contact with ILE 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N PHE* 3.2 33.2 - - + -
39N PHE* 3.8 39.2 - - + -
42N ALA* 5.0 0.9 - - + +
43N GLN* 3.1 27.1 - - + +
53N ARG* 5.9 0.2 - - - +
54N TYR* 3.9 20.0 - - + -
57N LEU* 5.7 4.3 - - + -
117N VAL* 5.1 2.0 - - + -
121N GLU* 4.4 14.1 - - + +
122N ALA* 3.0 27.1 + - + +
124N THR* 1.3 78.1 + - - +
126N ALA* 1.3 60.0 + - - +
128N ALA* 2.9 6.3 + - - +
129N LEU* 2.9 30.2 + - + +
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Residues in contact with ALA 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N PHE* 3.9 23.1 - - + -
122N ALA 3.0 13.8 + - - +
123N ASP* 3.5 9.0 - - - +
125N ILE* 1.3 80.7 - - - +
127N ASP* 1.3 62.8 + - - +
129N LEU* 3.0 9.2 + - - +
130N ALA* 3.0 23.6 + - - +
150N VAL* 5.3 6.3 - - + +
153N ARG* 4.0 22.4 + - + +
154N ARG* 4.3 6.7 - - - +
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Residues in contact with ASP 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N ASP* 2.9 13.3 + - - +
124N THR* 3.1 19.5 + - - +
126N ALA* 1.3 76.0 - - - +
128N ALA* 1.3 57.8 + - - +
130N ALA* 3.9 8.1 + - - +
131N ALA* 3.8 15.6 + - - +
153N ARG* 3.2 10.5 + - - +
154N ARG* 2.5 44.4 + - - -
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Residues in contact with ALA 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N ALA* 3.5 17.9 - - + +
43N GLN* 3.5 32.5 - - + +
124N THR 3.0 7.4 + - - +
125N ILE 2.9 10.5 + - - +
127N ASP* 1.3 76.0 - - - +
129N LEU* 1.3 60.7 + - - +
130N ALA 3.2 1.3 - - - -
131N ALA 2.9 30.8 - - - -
132N PRO* 3.0 8.3 - - - +
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Residues in contact with LEU 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ARG* 3.8 12.8 - - - +
4N PHE* 4.4 7.9 - - + -
6N LEU* 3.9 16.8 - - + -
38N MET* 4.4 7.4 - - + +
39N PHE* 4.0 22.2 - - + -
42N ALA* 4.0 18.2 - - + -
125N ILE 2.9 16.2 + - - +
126N ALA* 3.0 7.1 + - - +
128N ALA* 1.3 73.2 - - - +
130N ALA* 1.3 66.5 + - - +
131N ALA 3.3 0.2 + - - -
132N PRO* 3.6 12.0 - - - +
136N PRO* 4.3 17.0 - - + +
149N LEU* 3.9 23.4 - - + +
150N VAL* 3.7 33.2 - - + -
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Residues in contact with ALA 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ASP* 2.9 26.2 - - - +
292D ARG* 3.8 11.6 - - - +
126N ALA 3.0 14.3 + - - +
127N ASP* 3.9 9.6 - - - +
128N ALA 3.2 0.2 - - - -
129N LEU* 1.3 77.9 - - - +
131N ALA* 1.3 58.8 + - + +
150N VAL* 5.8 5.3 - - + +
153N ARG* 4.8 16.6 - - - +
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Residues in contact with ALA 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D PHE 5.0 4.5 - - - +
291D ASP* 3.4 10.5 - - - +
42N ALA 4.4 1.4 - - - +
127N ASP 3.8 6.3 + - - +
128N ALA* 2.9 13.5 + - - +
130N ALA* 1.3 79.6 - - + +
132N PRO* 1.3 69.5 - - - +
133N TYR 3.7 0.3 + - - -
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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