Contacts of the helix formed by residues 64 - 72 (chain A) in PDB entry 5MQI
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 ASP 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A CYS 4.3 4.0 - - - +
17A LEU* 3.7 26.3 - - + +
18A GLY 3.5 14.0 - - - +
19A TYR* 5.0 0.7 - - - -
25A TYR* 3.1 26.3 + - - +
60A ILE* 2.8 39.6 + - - +
62A GLN 3.3 0.4 - - - -
63A SER* 1.3 87.1 - - - +
65A LEU* 1.3 60.0 + - - +
67A PRO* 3.1 7.1 - - - +
68A ILE* 2.9 32.9 + - - +
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Residues in contact with LEU 65 (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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17A LEU* 4.4 11.7 - - + -
35A VAL* 4.6 7.4 - - + -
60A ILE* 3.0 18.7 + - + +
61A LEU* 3.5 19.5 - - - +
64A ASP* 1.3 73.4 - - - +
66A LEU* 1.3 59.2 + - - +
68A ILE* 3.2 12.9 + - + +
69A LEU* 2.8 29.3 + - - +
82A VAL* 3.7 22.9 - - + +
85A LEU* 3.4 42.2 - - + -
86A MET* 4.2 17.5 - - + -
89A LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 66 (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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61A LEU* 2.8 32.8 + - + +
62A GLN* 4.3 6.1 - - + +
65A LEU* 1.3 70.5 - - - +
67A PRO* 1.3 71.8 - - + +
69A LEU* 3.2 13.2 + - + +
70A THR* 3.0 32.8 + - + +
86A MET* 4.8 2.7 - - - -
123A ALA* 3.6 42.0 - - + +
124A PHE* 4.1 20.0 - - + +
126A SER* 5.4 0.9 - - - +
129A ALA* 3.9 26.9 - - + -
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Residues in contact with PRO 67 (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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20A LEU* 4.3 14.6 - - + -
25A TYR* 3.4 30.1 - - + -
62A GLN 3.1 20.9 - - - +
63A SER 3.4 19.7 - - - +
64A ASP 3.1 10.8 - - - +
66A LEU* 1.3 88.8 - - + +
68A ILE* 1.3 62.6 + - - +
70A THR* 3.3 6.4 + - - +
71A GLN* 2.9 34.2 + - + +
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Residues in contact with ILE 68 (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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17A LEU* 4.6 9.9 - - + -
25A TYR* 3.5 29.8 - - + +
27A LYS* 5.0 1.6 - - + -
31A CYS* 3.7 24.9 - - - -
35A VAL* 4.7 1.3 - - + -
64A ASP 2.9 24.5 + - - +
65A LEU* 3.2 15.5 + - + +
67A PRO* 1.3 74.0 - - - +
69A LEU* 1.3 59.9 + - - +
72A HIS* 2.9 40.9 + - + +
78A LEU* 3.6 28.9 - - + -
79A PHE* 5.5 2.5 - - - +
82A VAL* 3.7 19.7 - - + -
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Residues in contact with LEU 69 (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 LEU 2.8 17.9 + - - +
66A LEU* 3.2 22.4 + - + +
68A ILE* 1.3 80.7 - - - +
70A THR* 1.3 61.1 + - + +
73A HIS* 3.4 22.2 - - - +
79A PHE* 3.3 34.1 - - + +
82A VAL* 4.6 8.7 - - + +
83A ILE* 3.5 24.0 - - + -
86A MET* 3.8 20.9 - - + -
124A PHE* 4.9 3.1 - - + -
129A ALA* 4.4 22.9 - - + +
132A VAL* 3.6 6.7 - - + +
133A LEU* 4.5 10.8 - - + -
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Residues in contact with THR 70 (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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66A LEU* 3.0 22.3 + - + +
67A PRO* 3.3 8.1 + - - +
69A LEU* 1.3 82.4 - - + +
71A GLN* 1.3 67.5 + - - +
73A HIS* 2.9 23.6 + - - -
126A SER* 5.5 0.7 - - - +
128A LYS* 3.3 33.2 + - + +
129A ALA* 3.9 36.8 - - + +
132A VAL* 4.0 5.8 - - + -
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Residues in contact with GLN 71 (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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20A LEU* 4.2 7.1 - - - +
23A ASP* 3.7 16.4 + - - -
24A THR* 3.8 9.0 - - - +
25A TYR* 2.9 46.1 + - - +
67A PRO* 2.9 18.6 + - - +
70A THR* 1.3 87.5 + - - +
72A HIS* 1.3 72.5 + - + +
73A HIS* 3.6 6.5 + - - -
128A LYS* 5.3 1.6 - - - +
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Residues in contact with HIS 72 (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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25A TYR* 2.9 37.6 + + - -
26A HIS* 5.1 0.4 - - - -
27A LYS* 3.1 58.5 + - + +
68A ILE* 2.9 27.3 + - + +
71A GLN* 1.3 94.0 + - + +
73A HIS* 1.3 62.0 + - - +
74A GLN* 3.2 5.4 + - - -
75A ASP* 3.4 18.8 + - + +
78A LEU* 4.6 3.4 - - + +
79A PHE* 4.7 2.4 - - - +
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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