Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 4MT5
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 THR 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.3 31.8 - - + +
6A LYS* 3.8 35.7 - - + +
18A GLN* 5.2 1.7 + - - +
62A THR 3.9 2.5 + - - -
63A PRO* 1.3 73.0 - - - +
65A TYR* 1.3 77.6 + - - +
66A GLU* 4.2 7.3 + - + +
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Residues in contact with TYR 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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3A ALA* 4.6 11.0 - - + -
4A TYR 2.8 20.4 + - - +
5A VAL* 3.4 7.1 - - + +
6A LYS 2.7 31.7 + - - -
29A ILE* 4.9 0.4 - - + -
51A GLY 3.7 19.3 - - - -
52A PHE* 4.2 36.1 - + + +
56A THR* 3.6 33.9 - - + +
57A LYS 4.6 3.8 + - - -
63A PRO* 4.1 30.3 - - + +
64A THR* 1.3 79.5 - - - +
66A GLU* 1.3 57.6 + - - +
67A VAL* 5.6 0.2 - - - -
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Residues in contact with GLU 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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6A LYS* 3.1 44.7 + - + +
8A VAL* 4.9 1.0 - - + +
49A SER* 4.1 1.6 + - - +
50A ASP* 3.8 0.5 - - - -
51A GLY* 2.8 31.1 + - - -
64A THR* 4.2 8.4 - - + +
65A TYR* 1.3 78.0 - - - +
67A VAL* 1.3 62.8 + - - +
68A HIS* 2.8 39.9 + - + +
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Residues in contact with VAL 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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5A VAL* 4.5 9.2 - - + -
6A LYS 2.8 10.0 + - - +
7A TYR* 3.3 20.9 - - + -
8A VAL* 2.8 27.6 + - - -
33A THR* 3.9 18.8 - - + -
37A ILE* 4.0 9.0 - - + -
47A LEU* 3.7 19.1 - - + -
49A SER 3.4 4.7 - - - +
50A ASP* 3.3 22.9 - - + +
51A GLY 4.8 0.2 - - - +
52A PHE* 5.2 1.6 - - + -
66A GLU* 1.3 75.4 - - - +
68A HIS* 1.3 61.1 + - - +
69A PHE* 3.4 26.7 - - + -
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Residues in contact with HIS 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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8A VAL* 3.5 26.3 - - + +
10A ASP* 2.7 35.5 + - - +
47A LEU* 3.4 9.4 - - - +
48A VAL* 2.8 28.4 + - + -
49A SER* 2.8 32.0 + - - +
66A GLU* 2.8 40.9 + - + +
67A VAL* 1.3 72.9 - - - +
69A PHE* 1.3 59.5 + - - +
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Residues in contact with PHE 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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7A TYR* 3.7 19.3 - + + -
8A VAL 2.7 18.8 + - - +
9A ASP* 4.5 0.9 - - - -
10A ASP* 2.7 35.8 + - - +
16A LEU* 4.5 6.3 - - + -
37A ILE* 3.9 32.5 - - + -
40A TYR* 3.9 21.1 - + + -
41A GLU* 4.8 2.7 - - + -
45A TYR* 3.9 30.1 - + + -
46A VAL 3.1 9.0 - - - +
47A LEU* 3.9 26.7 - - + -
48A VAL* 3.6 4.7 - - - -
67A VAL* 3.4 35.2 - - + -
68A HIS* 1.3 75.5 - - - +
70A LYS* 1.3 57.0 - - - +
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Residues in contact with LYS 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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9A ASP* 4.4 2.5 - - - -
10A ASP* 4.8 6.3 - - + -
11A THR* 3.9 10.3 - - - +
45A TYR* 3.5 4.4 - - - -
46A VAL* 2.6 65.9 + - + +
47A LEU 5.1 0.7 - - - -
48A VAL* 3.8 19.3 - - + -
69A PHE* 1.3 74.7 - - - +
71A HIS* 1.3 70.1 + - - +
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Residues in contact with HIS 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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9A ASP* 3.0 34.2 + - - -
11A THR* 3.0 33.1 + - + +
12A THR* 4.2 10.3 - - + +
44A GLY 4.2 2.2 - - - -
45A TYR* 3.4 19.8 + + - -
46A VAL* 4.8 0.9 - - - +
70A LYS* 1.3 84.5 - - - +
72A GLY* 1.3 65.0 + - - +
73A MET* 3.7 16.1 + - + +
119A ASP* 2.7 39.2 + - - +
121A VAL* 3.8 13.4 - - + +
122A THR* 3.8 20.9 - - + -
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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