Contacts of the strand formed by residues 146 - 152 (chain A) in PDB entry 5C7G
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 ARG 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ARG 3.6 16.4 - - - +
34A SER* 3.1 5.6 - - - -
35A ARG 3.5 18.2 - - - +
36A LEU* 4.3 1.3 - - - -
37A ASN* 3.6 17.8 + - - +
38A TYR* 2.9 27.2 + - - +
41A ASN 3.5 18.8 + - - -
42A GLY* 4.0 3.8 - - - -
69A THR* 3.3 2.8 - - - -
70A GLN* 2.8 62.6 + - + +
71A GLY 2.8 25.2 + - - +
72A ALA* 4.2 6.3 - - - +
73A ILE 5.3 0.2 - - - +
115A PRO 3.3 15.4 + - - -
116A THR* 4.3 7.1 - - - +
145A MET* 1.3 80.1 - - - +
147A PHE* 1.3 64.6 + - - +
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A MET* 3.2 33.2 - - + +
19A ILE* 4.6 0.7 - - + -
34A SER* 2.7 42.4 + - - +
36A LEU* 3.0 24.9 + - - +
54A ILE* 3.9 27.4 - - + -
55A GLN* 4.5 7.4 - - - -
56A VAL* 4.0 17.9 - - + -
67A VAL* 4.6 0.2 - - + -
68A GLY 3.0 14.8 - - - +
69A THR* 4.1 10.8 - - + -
132A VAL* 5.5 1.6 - - + -
134A ILE* 3.8 25.8 - - + -
145A MET* 5.1 4.9 - - + -
146A ARG* 1.3 76.3 - - - +
148A GLU* 1.3 64.3 + - - +
149A VAL* 3.9 27.1 - - + -
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Residues in contact with GLU 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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6A ALA* 3.6 24.2 - - + +
7A LEU 4.2 0.3 - - - -
8A GLY* 3.4 8.7 + - - -
9A MET* 2.9 27.2 + - - +
10A GLU* 3.0 33.3 + - - +
11A SER 4.7 0.2 + - - -
14A ILE* 4.7 0.3 - - - +
36A LEU* 4.0 15.5 - - + +
67A VAL* 3.3 10.2 - - - +
68A GLY 2.9 27.2 + - - +
147A PHE* 1.3 74.8 - - - +
149A VAL* 1.3 82.6 + - - +
150A TYR* 3.6 32.5 - - + +
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Residues in contact with VAL 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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6A ALA* 3.5 2.3 - - - -
7A LEU* 2.8 44.0 + - + +
9A MET* 4.3 3.5 - - + +
14A ILE* 5.5 0.7 - - + -
56A VAL* 3.8 27.6 - - + -
58A LEU* 4.6 7.9 - - + -
64A VAL* 3.5 28.9 - - + -
66A ALA 3.8 5.6 - - - +
67A VAL* 4.3 10.3 - - + -
132A VAL* 4.3 13.2 - - + -
147A PHE* 3.9 14.4 - - + -
148A GLU* 1.3 86.3 + - - +
150A TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 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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4A MET* 3.5 40.2 - - + -
5A GLU 3.2 4.9 - - - +
6A ALA* 3.6 20.2 - - + -
7A LEU* 4.1 3.1 - - - -
36A LEU* 4.2 11.3 - - - +
64A VAL* 3.5 7.3 - - - +
65A THR* 2.9 22.6 + - - -
66A ALA* 2.9 30.1 + - + +
67A VAL 3.9 1.3 - - - -
68A GLY* 3.4 30.6 - - - -
118A VAL* 4.6 6.4 - - - +
120A VAL* 4.5 15.7 - - + +
148A GLU* 3.6 28.6 - - + +
149A VAL* 1.3 75.6 - - - +
151A GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 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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3A CYS* 3.4 19.1 - - - -
5A GLU* 2.9 33.8 + - - +
7A LEU* 3.9 7.7 - - - +
63A PHE 3.1 14.4 - - - -
65A THR* 3.8 2.2 + - - -
150A TYR* 1.3 76.8 - - - +
152A CYS* 1.3 65.7 + - - +
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Residues in contact with CYS 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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2A LYS 4.8 2.0 - - - +
3A CYS* 2.1 45.8 - - + -
5A GLU* 3.6 23.6 - - - +
7A LEU* 3.9 9.0 - - - +
62A ARG* 3.8 8.2 - - - +
63A PHE* 2.9 42.4 + - - +
151A GLY* 1.3 72.1 - - - +
153A LYS* 1.3 73.3 + - + +
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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