Contacts of the strand formed by residues 75 - 80 (chain A) in PDB entry 4MYF
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 LEU 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 15.0 - - + -
13A LEU* 2.9 35.0 + - + +
14A PHE* 3.3 55.4 - - + -
16A ALA* 3.9 9.5 - - - +
22A ALA* 4.1 0.9 - - - -
24A ILE* 3.5 34.1 - - + +
26A ILE* 5.1 0.9 - - + -
73A LEU* 4.5 4.5 - - + -
74A LYS* 1.3 85.6 - - - +
76A TYR* 1.3 64.1 + - - +
291A PHE* 4.1 25.4 - - + -
295A VAL* 4.6 4.0 - - + -
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Residues in contact with TYR 76 (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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14A PHE* 3.9 6.7 - - - -
16A ALA* 4.0 17.0 - - + -
17A GLN 4.1 11.1 + - - -
18A ARG* 3.9 5.5 - - - -
19A GLU* 3.5 51.9 + - + +
22A ALA* 3.5 20.0 - - + -
24A ILE 3.1 5.4 + - - +
25A VAL* 3.4 4.8 - - + -
26A ILE* 2.8 33.1 + - - +
75A LEU* 1.3 76.3 - - - +
77A ASP* 1.3 75.3 + - - +
78A ALA* 3.8 11.3 + - + -
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Residues in contact with ASP 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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14A PHE* 3.8 18.1 - - + -
26A ILE* 3.7 15.4 - - - +
52A ARG* 2.7 43.4 + - - +
55A LEU* 4.6 7.2 - - - +
76A TYR* 1.3 85.7 - - - +
78A ALA* 1.3 60.3 + - - +
79A GLY* 2.9 24.7 + - - -
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Residues in contact with ALA 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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19A GLU* 3.8 21.3 - - - +
25A VAL* 3.8 13.2 - - + -
26A ILE 2.8 17.3 + - - +
27A ILE* 4.3 6.1 - - + -
76A TYR* 3.8 10.5 + - + -
77A ASP* 1.3 71.0 - - - +
79A GLY* 1.3 60.8 + - - +
80A ASP 4.9 1.9 - - - +
96A LYS* 4.1 15.8 - - + +
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Residues in contact with GLY 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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27A ILE* 3.7 6.1 - - - +
28A GLY 2.9 21.3 + - - -
52A ARG* 3.2 17.6 + - - -
77A ASP* 2.9 13.0 + - - -
78A ALA* 1.3 81.1 - - - +
80A ASP* 1.3 60.5 + - - -
81A ILE* 4.2 0.3 + - - +
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Residues in contact with ASP 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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28A GLY* 3.2 13.1 - - - -
30A PRO* 3.7 32.6 - - + +
48A PRO* 3.9 4.0 - - - +
49A ALA 5.8 0.2 + - - -
52A ARG* 2.7 34.5 + - - -
78A ALA 4.9 2.3 - - - +
79A GLY* 1.3 74.3 - - - -
81A ILE* 1.3 66.9 + - - +
82A THR* 3.5 12.0 + - - +
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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