Contacts of the strand formed by residues 55 - 63 (chain A) in PDB entry 3LAW
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS 5.7 3.4 - - - +
7A VAL* 4.3 18.3 - - + +
51A MET* 3.2 8.6 - - - +
52A VAL* 2.8 37.8 + - - +
53A ASP* 3.3 11.4 - - - +
54A ASP* 1.3 88.4 - - + +
56A LEU* 1.3 66.5 + - - +
57A VAL* 3.5 4.3 + - + +
174A LEU* 4.0 36.6 - - + +
177A GLU* 5.2 3.0 + - - -
178A THR* 5.3 9.8 + - - +
130C GLU* 4.6 9.3 + - - -
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Residues in contact with LEU 56 (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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6A LYS* 3.5 30.8 + - + +
7A VAL* 3.3 21.3 + - - +
49A GLU* 4.0 23.1 - - - +
50A VAL 3.5 7.0 - - - +
51A MET* 3.3 28.2 - - + -
54A ASP 5.7 0.7 - - - +
55A ARG* 1.3 72.6 - - - +
57A VAL* 1.3 60.8 + - - +
58A THR* 5.5 0.4 + - - -
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Residues in contact with VAL 57 (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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7A VAL* 3.6 6.5 - - + +
9A LEU* 3.4 32.3 - - + -
49A GLU* 3.3 4.4 - - - +
50A VAL* 2.6 49.2 + - + +
52A VAL* 3.7 21.5 - - + -
55A ARG* 3.8 7.4 - - + +
56A LEU* 1.3 79.2 - - - +
58A THR* 1.3 65.1 + - - +
59A MET* 3.9 23.3 - - + -
170A ALA* 5.4 2.5 - - + +
174A LEU* 4.2 20.0 - - + -
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Residues in contact with THR 58 (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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7A VAL 2.8 11.1 + - - +
8A LEU* 3.5 7.3 - - + +
9A LEU* 2.8 27.9 + - - +
47A THR* 4.3 22.7 - - + +
48A LYS 3.8 6.5 - - - +
49A GLU* 3.5 23.1 + - + +
56A LEU 4.2 0.6 + - - -
57A VAL* 1.3 72.4 - - - +
59A MET* 1.3 62.2 + - - +
60A GLN* 3.7 1.1 + - + +
35C ASN* 5.2 6.7 - - - +
129C PHE* 3.4 37.0 - - + -
157C LYS* 5.3 6.1 - - - -
1400C GNP 5.8 0.9 - - - +
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Residues in contact with MET 59 (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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9A LEU* 3.7 9.4 - - + -
11A VAL* 4.0 21.1 - - - -
28A TYR* 3.4 37.5 - - + +
46A LEU 3.5 1.2 - - - +
47A THR* 3.2 4.5 - - - -
48A LYS* 2.8 42.2 + - + +
50A VAL* 4.3 8.1 - - + -
57A VAL* 3.8 20.2 + - + -
58A THR* 1.3 72.0 - - - +
60A GLN* 1.3 61.1 + - - +
61A ILE* 3.5 22.2 + - + +
166A PHE* 4.1 7.9 - - + +
169A ILE* 4.6 4.5 - - - -
170A ALA* 4.2 25.4 - - + -
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Residues in contact with GLN 60 (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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8A LEU* 4.8 23.5 - - + +
9A LEU 2.8 16.9 + - - +
10A LYS* 4.6 7.8 - - - +
11A VAL* 3.1 26.9 + - - +
45A PHE* 3.3 51.5 - - + -
46A LEU 3.5 2.0 - - - -
47A THR* 4.4 8.9 - - + +
58A THR* 3.7 2.2 + - + -
59A MET* 1.3 70.3 - - - +
61A ILE* 1.3 61.5 + - - +
62A TRP* 3.4 25.3 + - - +
126C LYS* 4.5 16.4 - - - +
1400C GNP 4.7 3.8 + - - -
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Residues in contact with ILE 61 (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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11A VAL* 3.6 13.0 - - + +
13A ILE* 3.4 36.3 - - + -
25A MET* 3.6 17.6 - - + +
28A TYR* 4.1 10.3 - - + -
29A VAL* 3.9 27.6 - - + -
45A PHE* 3.1 5.2 - - - -
46A LEU 2.6 39.9 + - - +
48A LYS* 4.4 2.2 - - + -
59A MET* 3.5 38.8 - - + +
60A GLN* 1.3 75.2 - - - +
62A TRP* 1.3 59.1 + - - +
63A ASP 3.6 1.4 + - - -
166A PHE* 4.6 6.7 - - + -
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Residues in contact with TRP 62 (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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10A LYS* 3.4 39.0 - - + +
11A VAL 2.9 9.9 + - - -
12A ILE* 3.7 21.7 - - + -
13A ILE* 3.2 26.5 + - - +
25A MET* 4.5 1.1 - - - -
43A ALA* 4.1 15.3 - - + -
44A ASP* 3.2 19.3 - - - -
45A PHE* 3.6 33.9 - + + -
60A GLN* 3.4 39.2 + - - +
61A ILE* 1.3 72.0 - - - +
63A ASP* 1.3 61.3 + - - +
64A THR* 4.0 3.3 + - - +
77A PHE* 3.6 31.4 - + + -
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Residues in contact with ASP 63 (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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13A ILE* 5.0 5.4 - - + -
21A LYS* 4.3 6.5 - - - +
22A THR* 2.9 41.8 + - - +
25A MET* 3.1 32.4 - - + +
40A THR* 3.7 12.8 + - + +
43A ALA* 3.4 3.6 - - - -
44A ASP 3.0 29.4 + - - +
61A ILE 3.6 2.2 + - - -
62A TRP* 1.3 72.1 - - - +
64A THR* 1.3 80.6 + - - +
1401A MG 2.8 20.1 - - - -
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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