Contacts of the strand formed by residues 60 - 68 (chain A) in PDB entry 2CLS
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL 3.6 6.8 + - - +
11A VAL* 3.4 27.3 - - + -
12A ALA* 2.8 26.3 + - - +
54A LEU 3.6 7.2 - - - +
55A GLU* 4.5 3.1 - - + +
59A GLN* 1.3 73.2 - - - +
61A VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 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* 4.4 3.6 - - - -
12A ALA* 3.2 17.5 - - + +
14A CYS* 3.8 27.1 - - + -
52A ALA 3.9 0.3 - - - +
53A CYS* 3.4 6.6 - - - +
54A LEU* 2.8 43.1 + - + +
56A THR* 3.9 28.3 - - - -
59A GLN* 4.2 11.7 - - + +
60A ARG* 1.3 80.9 - - - +
62A GLU* 1.3 63.0 + - - +
63A LEU* 3.9 12.7 + - + -
184A SER* 4.3 11.9 - - - +
188A LEU* 5.9 4.3 - - + -
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Residues in contact with GLU 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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11A VAL* 4.2 11.6 - - + +
12A ALA 2.6 14.2 + - - +
13A ARG* 3.4 27.7 + - + +
14A CYS 3.0 24.4 + - - -
51A THR* 3.7 20.8 + - - -
52A ALA 3.7 1.3 - - - +
53A CYS* 4.0 21.4 - - - +
61A VAL* 1.3 71.7 - - - +
63A LEU* 1.3 74.4 + - - +
64A SER* 3.9 4.5 + - - -
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Residues in contact with LEU 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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14A CYS* 3.4 31.6 - - + +
16A LEU* 4.2 7.9 - - + -
33A LEU* 4.6 4.7 - - + -
50A TYR 3.7 0.3 - - - +
51A THR* 3.3 7.4 - - - -
52A ALA* 2.7 41.7 + - + +
54A LEU* 4.5 14.6 - - + -
61A VAL* 4.0 7.0 - - + +
62A GLU* 1.3 77.7 - - - +
64A SER* 1.3 59.8 + - - +
65A LEU* 3.9 29.8 - - + -
180A PHE* 4.1 23.8 - - + -
184A SER* 3.2 27.1 - - - +
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Residues in contact with SER 64 (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 CYS 2.9 12.5 + - - -
15A LYS* 3.4 9.1 - - - +
16A LEU 3.0 26.0 + - - +
49A ASN* 3.7 7.3 + - - -
50A TYR 3.6 4.4 + - - -
51A THR* 5.0 1.1 - - - +
62A GLU* 3.9 6.1 + - - -
63A LEU* 1.3 71.6 - - - +
65A LEU* 1.3 60.6 + - - +
66A TRP* 3.4 22.9 + - - -
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Residues in contact with LEU 65 (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* 3.4 20.6 - - + +
18A LEU* 4.9 2.0 - - + -
30A LEU* 4.1 17.5 - - + -
33A LEU* 3.7 20.4 - - + -
34A ALA* 5.1 0.9 - - + -
48A GLU 3.9 0.5 - - - +
49A ASN* 3.3 6.6 + - - -
50A TYR* 2.8 62.3 + - + +
52A ALA* 3.9 20.4 - - + +
63A LEU* 4.0 16.6 - - + -
64A SER* 1.3 75.0 + - - +
66A TRP* 1.3 62.7 + - - +
67A ASP 3.9 0.6 + - - -
180A PHE* 3.7 35.2 - - + -
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Residues in contact with TRP 66 (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 LYS* 3.8 31.7 - - + +
16A LEU 2.9 15.2 + - - +
17A VAL* 4.0 18.4 - - + +
18A LEU* 3.0 29.3 + - - +
30A LEU* 4.6 2.7 - - - -
47A PHE* 5.4 5.6 - + + -
48A GLU 3.7 6.5 - - - -
49A ASN* 3.1 38.7 - - - +
64A SER* 3.4 21.7 + - - -
65A LEU* 1.3 72.3 - - - +
67A ASP* 1.3 61.2 + - - +
68A THR* 4.7 0.2 - - - -
81A CYS* 3.3 32.1 - - + -
76B ASN* 3.9 25.4 - - + -
77B VAL* 4.4 10.5 - - + -
80B LEU* 4.6 13.0 - - + -
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Residues in contact with ASP 67 (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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18A LEU* 4.6 1.9 - - - +
26A LYS* 3.8 17.2 - - - +
27A THR* 2.7 38.2 + - - +
30A LEU* 3.5 23.6 - - + +
45A THR* 3.7 10.7 + - + +
47A PHE* 3.5 11.4 - - - -
48A GLU* 2.9 38.9 + - + +
50A TYR* 4.0 12.2 + - + -
65A LEU 3.9 1.4 + - - -
66A TRP* 1.3 73.1 - - - +
68A THR* 1.3 74.9 + - - +
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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
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17A VAL* 4.0 14.8 - - + -
18A LEU 2.6 28.1 + - - +
19A VAL* 3.7 11.9 - - + +
26A LYS* 3.2 20.4 - - - -
45A THR* 4.1 6.5 - - - +
46A VAL 4.0 2.0 - - - -
47A PHE* 3.7 22.9 - - + -
66A TRP 4.4 1.6 - - - +
67A ASP* 1.3 83.3 + - - +
69A SER* 1.3 60.6 + - - +
78A ARG* 3.8 23.4 - - + -
81A CYS* 3.7 16.6 - - - -
500A GTP 3.9 1.7 + - - -
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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