Contacts of the strand formed by residues 77 - 81 (chain A) in PDB entry 1LBA
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 ILE 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.4 28.9 - - - +
11A THR* 3.8 16.2 - - + -
13A ALA 3.0 6.7 + - - -
14A ILE* 4.0 18.8 - - + -
15A PHE* 2.8 26.9 + - - -
47A HIS* 3.6 19.7 - - + -
48A PHE* 4.1 15.7 - - + -
62A GLU* 3.5 17.3 - - + +
68A HIS* 3.8 5.7 - - - -
76A SER* 1.3 74.0 + - - +
78A GLY* 1.3 63.1 + - - +
79A VAL* 4.2 5.2 - - + -
110A LEU* 4.2 14.6 - - + -
114A TYR* 4.1 20.0 - - + -
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Residues in contact with GLY 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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15A PHE 3.6 3.4 - - - -
17A HIS* 4.0 4.3 - - - -
46A TYR* 3.8 4.4 - - - +
47A HIS* 2.9 36.9 + - - +
48A PHE 3.3 6.6 + - - -
68A HIS* 3.5 29.2 + - - -
77A ILE* 1.3 75.5 - - - +
79A VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 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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14A ILE* 3.7 28.7 - - + -
15A PHE 2.8 10.8 + - - +
16A VAL* 3.5 8.4 - - + +
17A HIS* 2.8 31.6 + - - +
48A PHE* 3.5 13.2 - - + +
50A ILE* 3.9 26.9 - - + -
77A ILE* 4.2 4.3 - - + -
78A GLY* 1.3 78.6 - - - +
80A CYS* 1.3 63.1 + - - +
81A LEU* 6.1 0.2 - - + -
103A LEU* 4.0 13.2 - - + -
106A LEU* 4.1 10.8 - - + -
107A LEU* 4.4 4.0 - - + -
110A LEU* 4.2 15.5 - - + -
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Residues in contact with CYS 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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17A HIS 3.4 2.5 - - - -
18A CYS 3.6 5.4 - - - -
19A SER* 3.4 41.1 - - - -
32A ILE* 4.8 6.3 - - - -
46A TYR* 3.7 42.6 - - + -
48A PHE 2.8 13.0 + - - +
49A ILE* 3.4 7.1 - - + +
50A ILE* 2.9 27.4 + - - +
78A GLY 4.2 0.2 - - - -
79A VAL* 1.3 77.5 - - - +
81A LEU* 1.3 63.9 + - - +
82A VAL 3.9 1.0 + - - -
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Residues in contact with LEU 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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16A VAL* 4.3 4.9 - - + -
17A HIS 2.8 19.8 + - - +
18A CYS* 3.0 3.8 - - - +
19A SER 2.9 25.6 + - - -
50A ILE* 4.0 30.3 - - + -
79A VAL* 6.1 0.4 - - + -
80A CYS* 1.3 73.7 - - - +
82A VAL* 1.3 61.2 + - - +
83A GLY 3.2 0.7 + - - -
95A PHE* 3.6 31.6 - - + -
99A GLN* 4.2 21.3 - - + +
100A MET* 4.4 4.9 - - - -
103A LEU* 4.1 24.5 - - + -
131A PRO* 5.2 0.2 - - + -
133A PHE* 3.7 30.1 - - + -
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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