Contacts of the strand formed by residues 66 - 71 (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 THR 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA 3.8 0.7 + - - +
60A VAL* 3.4 2.9 - - - -
61A SER* 2.9 44.2 + - - -
64A ALA* 3.5 23.6 - - + +
65A LYS* 1.3 78.6 - - - +
67A LEU* 1.3 60.1 + - - +
68A THR* 4.3 9.4 + - - -
78A THR* 4.3 16.4 - - - +
79A TYR 3.3 9.4 - - - +
80A PRO* 5.3 0.9 - - + -
81A ILE* 3.7 7.7 - - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.5 31.6 - - + -
59A ALA 3.5 2.5 - - - -
60A VAL* 4.1 14.8 - - + +
66A THR* 1.3 73.9 - - - +
68A THR* 1.3 68.3 + - - +
69A LEU 4.2 1.1 - - - +
78A THR* 3.5 1.2 - - - -
79A TYR* 2.9 48.3 + - + +
81A ILE* 3.8 16.3 - - + +
122A ILE* 4.3 13.2 - - + -
140A ILE* 4.3 13.0 - - + -
142A MSE 4.3 11.0 - - + -
150A LEU* 4.2 27.8 - - + -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS 3.6 1.4 - - - +
58A ILE* 3.4 3.8 - - - -
59A ALA* 2.8 49.7 + - + +
66A THR* 4.3 10.2 + - - -
67A LEU* 1.3 79.5 - - - +
69A LEU* 1.3 62.9 + - - +
70A SER* 3.9 3.6 + - - +
75A VAL* 3.7 36.8 - - + -
77A LYS 3.5 8.3 - - - +
78A THR* 3.8 15.1 + - + +
5B GLN* 5.7 0.9 - - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.8 16.6 - - + -
57A HIS 3.8 2.5 - - - +
58A ILE* 3.8 17.5 - - + +
67A LEU* 4.2 2.2 + - + +
68A THR* 1.3 72.1 - - - +
70A SER* 1.3 62.8 + - - +
75A VAL* 3.6 2.1 - - - -
76A MSE 2.8 53.1 + - + +
77A LYS* 2.9 23.0 + - + +
79A TYR* 4.8 7.6 - - + +
150A LEU* 4.2 21.1 - - + -
153A ILE* 4.3 28.7 - - + -
154A VAL* 3.6 23.3 - - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO 4.3 0.2 - - - -
56A TYR* 3.3 13.9 - - - +
57A HIS* 2.9 44.0 + - - -
59A ALA* 5.8 2.8 - - - +
68A THR* 4.7 4.3 + - - +
69A LEU* 1.3 77.4 - - - +
71A LEU* 1.3 59.4 + - - +
72A ASN 4.2 0.7 - - - -
73A ASN* 4.8 3.6 - - - -
74A ARG 3.2 9.9 - - - -
75A VAL* 3.8 8.5 - - - +
76A MSE 5.0 0.7 - - - -
5B GLN* 2.8 36.5 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO* 3.5 23.6 - - + +
56A TYR* 3.8 24.0 - - + +
70A SER* 1.3 73.6 - - - +
72A ASN* 1.3 102.9 + - + +
73A ASN 3.2 0.4 - - - -
74A ARG* 2.8 26.1 + - + +
76A MSE 3.9 24.4 - - + -
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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