Contacts of the strand formed by residues 72 - 78 (chain A) in PDB entry 1LWW
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 GLN 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A SER* 3.8 22.4 + - - +
26A ILE 3.3 1.1 - - - +
27A PRO* 3.0 42.3 - - - +
28A CYS 3.9 4.9 - - - -
68A GLN* 3.1 8.4 - - - +
69A THR* 2.8 42.8 + - - +
71A GLU* 1.3 88.3 - - + +
73A LEU* 1.3 59.4 + - - +
74A HIS* 3.5 18.6 - - + +
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Residues in contact with LEU 73 (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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25A SER* 3.6 2.1 - - - -
26A ILE* 3.1 52.0 + - + +
28A CYS* 4.1 11.6 + - + -
33A LEU* 4.1 19.7 - - + -
35A LEU* 3.8 29.8 - - + -
66A LEU* 4.4 6.5 - - + -
67A THR 3.7 12.8 - - - +
68A GLN* 4.2 6.3 - - + +
72A GLN* 1.3 71.1 - - - +
74A HIS* 1.3 63.6 + - - +
75A CYS* 3.9 8.7 - - - -
96A VAL* 4.2 24.5 - - + -
100A PHE* 4.5 7.6 - - + -
102A LEU* 5.0 7.0 - - + -
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Residues in contact with HIS 74 (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 LEU* 3.3 32.3 - - + +
23A TRP* 3.3 25.3 - - + +
24A ALA 3.6 4.6 + - - +
25A SER* 3.1 24.2 + - - -
66A LEU* 3.4 4.9 - - - +
67A THR* 2.6 45.8 + - + +
68A GLN* 4.2 0.9 - - - -
69A THR* 3.2 37.1 + - + +
72A GLN* 3.5 17.3 - - + +
73A LEU* 1.3 72.0 - - - +
75A CYS* 1.3 60.5 + - - +
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Residues in contact with CYS 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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23A TRP* 3.3 3.9 - - - -
24A ALA 2.8 41.4 + - - +
26A ILE* 3.6 28.7 - - - -
64A TRP* 3.8 19.5 - - + -
65A THR 3.8 4.5 - - - -
66A LEU* 3.7 18.8 - - + -
73A LEU* 3.7 10.3 - - - -
74A HIS* 1.3 78.5 - - - +
76A THR* 1.3 59.7 + - - +
87A ARG* 3.3 3.3 + - - -
88A PRO* 3.4 4.1 - - - +
93A LEU* 3.9 11.0 - - + -
96A VAL* 4.1 11.0 - - - -
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Residues in contact with THR 76 (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 ARG* 2.8 35.8 + - - -
22A LEU 2.6 27.2 + - - -
23A TRP* 3.7 18.4 - - + -
64A TRP* 3.3 10.4 - - - -
65A THR* 3.1 49.4 + - - +
75A CYS* 1.3 72.9 - - - +
77A VAL* 1.3 58.4 + - - +
78A TYR* 4.1 3.8 - - + +
87A ARG* 3.1 7.2 + - - +
88A PRO* 3.8 0.9 - - - -
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Residues in contact with VAL 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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14A ARG* 3.0 18.8 + - - -
62A GLN* 3.7 34.5 - - + +
63A VAL 3.5 12.1 - - - +
64A TRP* 3.8 20.2 - - + -
76A THR* 1.3 76.9 + - - +
78A TYR* 1.3 66.3 + - - +
79A ARG* 3.7 34.3 + - + +
86A SER 4.4 4.2 + - - +
87A ARG* 4.2 3.4 + - - +
88A PRO* 3.8 16.5 - - + +
92A GLU* 3.7 10.1 - - - +
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Residues in contact with TYR 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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12A GLY 4.3 2.5 - - - -
13A HIS* 3.9 2.3 - - - -
14A ARG* 2.9 69.6 + - + +
62A GLN* 4.5 2.9 - - - +
63A VAL* 2.9 50.1 + - + +
64A TRP* 4.0 2.5 - - - -
65A THR* 2.6 41.5 + - - -
76A THR* 4.1 4.7 - - + -
77A VAL* 1.3 73.4 - - - +
79A ARG* 1.3 64.9 + - - +
171A ILE* 4.4 14.2 - - + +
173A LEU* 3.5 36.1 - - + -
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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