Contacts of the strand formed by residues 74 - 80 (chain A) in PDB entry 1Y7M
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 ARG 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 3.2 3.8 - - - -
71A LEU* 2.8 38.2 + - + +
72A ASN* 3.3 33.9 + - - +
73A ASN* 1.3 76.6 - - - +
75A VAL* 1.3 68.6 + - - +
76A MSE 3.4 1.4 + - + +
3B THR* 6.3 0.2 - - - +
5B GLN* 3.8 0.2 - - - +
40B GLY 3.2 4.0 - - - -
41B GLN* 4.3 4.3 - - - -
42B SER* 3.7 33.4 + - - +
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Residues in contact with VAL 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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68A THR* 3.7 30.5 - - + -
69A LEU 3.6 4.3 - - - -
70A SER* 3.8 3.6 + - - +
74A ARG* 1.3 74.6 - - - +
76A MSE 1.3 60.9 - - - +
77A LYS 4.5 4.7 - - - +
78A THR* 4.7 12.3 - - + -
5B GLN* 4.0 15.7 - - - +
40B GLY* 2.8 42.4 + - - +
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Residues in contact with MSE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 4.0 19.3 - - + +
69A LEU* 2.8 24.9 + - + +
70A SER* 4.9 0.2 - - - -
71A LEU* 3.9 34.8 - - + -
74A ARG* 3.4 2.4 + - + +
75A VAL* 1.3 76.5 - - - +
77A LYS* 1.3 69.2 + - + +
149A GLU* 5.8 2.0 - - - +
153A ILE* 4.4 23.8 - - + -
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Residues in contact with LYS 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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67A LEU 4.0 0.3 - - - +
68A THR* 3.5 4.2 - - - +
69A LEU* 2.9 34.3 + - + +
75A VAL* 3.9 0.6 - - - +
76A MSE 1.3 89.6 - - + +
78A THR* 1.3 81.5 + - - +
79A TYR* 3.6 39.7 - - + +
146A ASP* 5.2 2.5 + - - -
149A GLU* 2.9 30.3 + - - +
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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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66A THR* 4.3 16.5 - - - +
67A LEU 3.5 3.1 - - - -
68A THR* 3.8 25.0 + - + -
75A VAL* 4.7 10.1 - - + -
77A LYS* 1.3 90.6 - - - +
79A TYR* 1.3 63.4 + - - +
80A PRO* 4.6 1.9 - - - +
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Residues in contact with TYR 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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66A THR* 3.3 7.1 - - - -
67A LEU* 2.9 47.8 + - + +
69A LEU* 4.8 4.4 - - + +
77A LYS* 3.6 41.6 - - + +
78A THR* 1.3 75.6 + - - +
80A PRO* 1.3 71.6 - - + +
142A MSE 3.3 30.5 - - + -
146A ASP* 3.4 39.3 - - + +
149A GLU* 2.7 40.6 + - - +
150A LEU* 4.3 21.2 + - + +
153A ILE* 5.0 4.2 - - - +
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Residues in contact with PRO 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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65A LYS 3.5 8.3 - - - +
66A THR* 4.7 1.6 - - + -
78A THR 4.6 2.0 - - - +
79A TYR* 1.3 91.3 - - + +
81A ILE* 1.3 65.1 + - - +
131A ILE* 3.7 21.5 - - + +
132A GLY* 5.1 6.1 - - - +
141A ARG 4.3 1.6 - - - +
142A MSE 4.5 6.4 - - - +
143A HIS* 4.4 14.4 + - + +
146A ASP* 4.1 11.8 - - - +
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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