Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 1MS4
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 GLU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA 3.9 0.5 - - - +
68A LYS* 3.0 8.0 - - - +
69A TYR* 2.8 77.7 + - + +
77A TRP* 1.3 74.7 - - - +
79A THR* 1.3 61.5 + - - +
148A THR* 5.8 3.5 - - - +
149A ALA 5.4 0.2 - - - +
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Residues in contact with THR 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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17A LYS 3.7 22.3 + - - +
18A VAL* 3.9 22.4 - - + -
19A PRO* 4.0 10.9 - - + +
66A VAL* 4.1 10.5 - - + -
67A ALA 3.6 2.7 - - - -
68A LYS* 2.3 43.1 + - + +
69A TYR* 5.8 0.4 - - - -
77A TRP 4.7 1.7 + - - -
78A GLU* 1.3 77.6 + - - +
80A GLN* 1.3 65.3 + - - +
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 3.7 13.5 - - + -
66A VAL* 3.2 9.5 - - - +
67A ALA* 3.0 39.0 + - + +
69A TYR* 3.7 19.1 - - + -
79A THR* 1.3 73.9 - - - +
81A ILE* 1.3 67.7 + - - +
151A ILE* 3.3 46.4 + - - +
153A TRP* 2.8 33.7 + - + +
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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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18A VAL* 3.7 23.1 - - + -
19A PRO* 3.3 33.7 - - + +
20A PHE* 5.0 0.2 - - - -
21A GLU* 5.7 0.7 - - + +
52A ALA* 4.7 1.3 - - + -
54A TYR* 3.8 17.5 - - - +
64A ASP* 4.0 16.8 - - + +
65A THR 3.7 8.3 - - - +
66A VAL* 3.9 10.8 - - + -
80A GLN* 1.3 84.3 - - - +
82A ALA* 1.3 61.2 + - - +
83A ILE 3.4 31.2 - - - +
84A LYS* 4.0 7.9 - - + +
87A ARG* 5.5 0.2 - - - +
153A TRP* 4.4 5.5 - - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 5.3 1.3 - - + -
65A THR* 2.9 19.8 + - + +
66A VAL* 4.4 0.2 - - - +
67A ALA* 4.3 10.1 - - + -
80A GLN 3.7 3.2 + - - -
81A ILE* 1.3 74.8 - - - +
83A ILE* 1.3 69.9 + - + +
108A VAL* 5.6 0.7 - - + -
134A ALA* 4.9 1.6 - - - +
153A TRP* 3.3 64.4 - - + +
154A GLY 5.1 2.3 - - - +
156A PRO* 6.0 0.2 - - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.5 1.6 - - - +
65A THR* 2.8 43.8 + - - +
81A ILE* 3.4 8.2 - - - +
82A ALA* 1.3 89.3 - - + +
84A LYS* 1.3 73.5 + - - +
94A VAL* 3.7 16.1 - - + +
108A VAL* 3.6 34.5 - - + +
110A VAL* 3.9 21.3 - - + -
132A LEU* 5.2 1.3 - - + +
134A ALA* 3.8 24.7 - - + +
156A PRO* 3.8 22.9 - - + -
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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