Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 3MX7
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 ALA 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 3.7 1.4 - - - +
70A ILE* 3.0 39.3 + - + +
71A SER 3.6 15.3 - - - +
72A GLY 4.3 3.1 - - - +
73A PHE* 1.3 77.3 - - - +
75A TYR* 1.3 77.0 + - - +
89A TYR* 6.1 0.4 - - + -
90A MET 5.9 3.1 - - - +
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Residues in contact with TYR 75 (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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23A HIS* 5.2 0.2 - - - -
25A THR* 4.5 15.3 - - + -
48A LEU* 3.6 37.5 - - + +
49A VAL* 3.8 22.7 - - + -
67A ILE* 4.2 11.7 - - + -
68A ASP 3.3 16.2 - - - +
69A ALA* 3.7 16.6 - - + +
70A ILE* 4.1 4.7 - - - +
73A PHE* 3.8 37.5 - + - -
74A ALA* 1.3 82.4 - - - +
76A GLU* 1.3 60.7 + - - +
77A TYR* 3.7 32.6 - - + +
89A TYR* 3.5 17.5 - - - +
90A MET 5.0 0.5 + - - -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 3.5 1.2 - - - +
67A ILE* 3.5 4.5 - - - -
68A ASP* 2.8 52.5 + - + +
70A ILE* 3.8 26.7 - - + +
75A TYR* 1.3 75.4 - - - +
77A TYR* 1.3 65.1 + - - +
78A THR* 4.7 6.0 + - - +
87A LYS* 3.8 32.4 - - + +
88A LYS 3.4 10.3 - - - +
89A TYR* 4.1 19.8 - - + -
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Residues in contact with TYR 77 (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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5A VAL* 3.6 37.9 - - + +
6A ALA* 4.3 4.5 - - + -
8A TRP* 3.6 24.6 - - + -
21A PHE* 3.7 26.2 - + - -
23A HIS* 2.7 40.7 - + - +
25A THR* 4.7 4.0 - - - +
65A ILE* 4.7 1.3 - - + -
66A ASN 3.3 3.4 - - - -
67A ILE* 3.7 19.1 - - + -
75A TYR* 3.7 32.7 - - + +
76A GLU* 1.3 74.0 - - - +
78A THR* 1.3 61.6 + - - +
87A LYS* 3.5 0.9 - - - -
88A LYS 2.8 46.0 + - - +
89A TYR* 4.8 2.5 - - - -
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Residues in contact with THR 78 (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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8A TRP* 4.1 2.0 - - - -
64A THR 3.4 2.1 - - - +
65A ILE* 3.3 3.7 - - - +
66A ASN* 2.8 48.1 + - + +
68A ASP* 5.0 4.1 + - - -
76A GLU* 4.7 6.9 + - - +
77A TYR* 1.3 74.7 + - - +
79A LEU* 1.3 62.4 + - - +
80A GLU* 3.8 3.7 + - + +
85A SER* 3.8 28.9 - - - +
86A LEU 3.6 4.7 - - - +
87A LYS* 3.3 35.7 - - + +
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Residues in contact with LEU 79 (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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8A TRP* 3.3 55.6 - - + +
10A VAL* 4.3 7.2 - - + -
19A ILE* 3.7 19.1 - - + -
54A PHE* 4.1 7.0 - - + -
63A ALA* 4.0 23.6 - - + -
64A THR 3.4 14.1 - - - +
65A ILE* 3.8 16.4 - - + +
78A THR* 1.3 72.9 - - - +
80A GLU* 1.3 61.3 - - - +
81A ILE* 4.2 14.5 + - + -
84A LYS 3.8 0.2 - - - +
85A SER* 3.0 25.1 - - - -
86A LEU 3.1 12.2 + - - -
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Residues in contact with GLU 80 (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 LYS 4.2 0.5 - - - +
63A ALA* 3.4 2.4 - - - -
64A THR* 2.9 44.5 + - + +
66A ASN* 5.3 8.1 + - - +
78A THR* 3.8 4.0 + - + +
79A LEU* 1.3 73.9 - - - +
81A ILE* 1.3 68.8 + - - +
82A ASN 5.1 0.2 - - - +
83A GLY* 3.6 24.6 - - - +
84A LYS 3.3 17.7 - - - +
85A SER* 4.1 8.7 - - - -
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Residues in contact with ILE 81 (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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10A VAL* 4.4 17.5 - - + -
12A LEU* 4.2 17.7 - - + -
19A ILE* 4.3 10.3 - - + -
56A VAL* 5.0 2.0 - - + -
61A THR* 3.6 28.7 - - + -
62A LYS 3.7 4.0 - - - +
63A ALA* 3.7 24.2 - - + -
79A LEU* 4.2 22.6 - - + -
80A GLU* 1.3 81.0 - - - +
82A ASN* 1.3 83.3 + - - +
83A GLY 3.2 1.6 - - - -
84A LYS* 2.9 23.8 + - - +
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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