Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 1ITB
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 LYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.8 4.2 - - - +
74A LYS 3.1 29.4 + - - +
75A ASP* 3.1 6.7 - - + +
76A ASP* 1.3 81.9 - - - +
78A PRO* 1.3 88.6 + - + +
79A THR* 3.2 13.7 - - + +
120A TRP* 3.6 30.3 - - + -
134A LEU 5.1 1.6 + - - -
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Residues in contact with PRO 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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72A VAL 3.7 6.3 - - - +
73A LEU* 4.3 9.2 - - + -
76A ASP 4.4 2.2 - - - +
77A LYS* 1.3 94.7 + - + +
79A THR* 1.3 65.3 + - - +
117A PHE* 3.7 38.8 - - + -
120A TRP* 3.5 58.2 - - + +
134A LEU* 4.3 8.3 - - + +
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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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71A CYS* 3.4 3.5 - - - -
72A VAL* 2.9 40.7 + - - +
74A LYS* 3.1 37.6 - - + +
77A LYS* 3.2 26.2 - - + +
78A PRO* 1.3 79.9 - - - +
80A LEU* 1.3 66.6 + - - +
81A GLN* 4.0 1.0 + - - +
134A LEU* 4.1 10.8 - - - +
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Residues in contact with LEU 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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26A LEU* 6.2 0.7 - - + -
69A LEU* 4.1 24.7 - - + -
70A SER 3.3 17.9 - - - +
79A THR* 1.3 77.7 - - - +
81A GLN* 1.3 67.5 + - - +
82A LEU* 5.3 6.1 - - + -
101A PHE* 4.1 22.9 - - + -
122A ILE* 4.7 8.3 - - + -
132A VAL* 3.8 37.9 - - + +
133A PHE* 3.9 12.3 - - - +
134A LEU* 3.7 33.5 - - + +
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Residues in contact with GLN 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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24A TYR 5.4 1.3 - - - +
69A LEU* 3.6 3.8 - - - -
70A SER* 3.0 46.4 + - - +
72A VAL* 3.1 35.9 - - + +
74A LYS* 5.5 2.9 - - - +
79A THR* 5.0 1.8 - - - +
80A LEU* 1.3 80.6 - - - +
82A LEU* 1.3 70.2 + - - +
83A GLU* 4.1 21.0 + - - +
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Residues in contact with LEU 82 (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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20A MET* 4.5 2.0 - - - -
24A TYR* 3.6 42.6 + - + +
25A GLU* 3.7 23.3 - - - +
26A LEU* 4.2 25.1 - - + +
62A LEU* 4.0 14.4 - - + -
67A LEU* 3.7 26.7 - - + -
68A TYR 3.8 3.8 - - - +
69A LEU* 4.2 24.2 - - + -
80A LEU* 5.3 6.5 - - + -
81A GLN* 1.3 85.9 + - - +
83A GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 83 (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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24A TYR* 4.7 2.0 - - - -
67A LEU* 3.5 5.1 - - - +
68A TYR* 2.9 32.4 + - - +
70A SER* 2.8 23.2 + - - +
72A VAL* 4.9 2.4 - - - +
81A GLN* 4.1 17.7 + - - +
82A LEU* 1.3 75.0 - - - +
84A SER* 1.3 70.0 + - - +
85A VAL* 4.0 3.4 + - + +
98A ARG* 3.6 24.8 + - - -
99A PHE* 3.6 29.2 - - + -
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Residues in contact with SER 84 (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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24A TYR* 3.1 21.2 + - - -
66A ASN* 3.2 19.1 - - - -
67A LEU* 3.5 10.7 - - - +
83A GLU* 1.3 84.0 - - - +
85A VAL* 1.3 68.2 + - - +
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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