Contacts of the strand formed by residues 11 - 19 (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 VAL 11 (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* 1.3 70.0 - - - +
12A ALA* 1.3 69.2 + - - +
13A ARG* 3.9 8.3 + - + +
53A CYS* 6.1 2.2 - - - -
60A ARG* 3.4 28.5 - - + +
61A VAL 4.4 0.9 - - - -
62A GLU* 4.2 19.3 - - + +
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Residues in contact with ALA 12 (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 VAL* 3.3 4.1 + - + -
11A VAL* 1.3 73.7 - - - +
13A ARG* 1.3 58.1 + - - +
59A GLN* 4.1 22.9 - - - +
60A ARG 2.8 14.3 + - - +
61A VAL* 3.2 14.5 - - + +
62A GLU* 2.6 33.4 + - - +
188A LEU* 5.6 6.7 - - + -
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Residues in contact with ARG 13 (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* 3.9 7.3 + - + +
12A ALA* 1.3 80.1 - - - +
14A CYS* 1.3 64.0 + - - +
61A VAL* 4.8 0.2 - - - -
62A GLU* 3.4 30.8 + - + +
86A ASP* 4.1 6.1 - - - +
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Residues in contact with CYS 14 (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 ALA* 6.2 0.2 - - + -
13A ARG* 1.3 77.3 - - - +
15A LYS* 1.3 60.3 + - - +
16A LEU* 3.9 14.8 + - - -
61A VAL* 3.8 11.0 - - + -
62A GLU 3.0 5.9 + - - -
63A LEU* 3.4 28.8 - - + +
64A SER* 2.9 27.9 + - - +
86A ASP* 3.3 12.1 - - - -
184A SER* 4.6 8.3 - - - +
187A CYS* 3.7 30.1 - - + -
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Residues in contact with LYS 15 (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* 1.3 69.4 - - - +
16A LEU* 1.3 63.4 + - - +
17A VAL* 4.1 6.5 - - + -
64A SER* 3.4 15.0 - - - +
66A TRP* 3.8 35.4 - - + +
81A CYS* 3.1 28.3 + - - +
83A SER* 2.6 32.0 + - - +
84A ASP* 3.6 21.2 - - + +
85A SER* 3.6 7.1 - - - -
86A ASP* 2.7 38.5 + - - +
87A ALA 3.4 6.4 + - - +
80B LEU* 5.9 2.8 - - - +
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Residues in contact with LEU 16 (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* 4.0 18.2 - - - -
15A LYS* 1.3 78.7 - - - +
17A VAL* 1.3 63.2 + - - +
18A LEU* 4.3 2.5 + - + +
63A LEU* 4.2 16.2 - - + -
64A SER 3.0 7.4 + - - +
65A LEU* 3.4 19.7 - - + +
66A TRP* 2.9 25.5 + - - +
87A ALA* 3.4 31.4 - - + +
89A LEU* 4.2 14.4 - - + -
180A PHE* 3.9 29.6 - - + -
183A ALA* 4.1 18.4 - - + -
184A SER* 5.0 0.9 - - - +
187A CYS* 4.0 5.6 - - - -
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Residues in contact with VAL 17 (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* 4.1 4.7 - - - -
16A LEU* 1.3 77.2 - - - +
18A LEU* 1.3 61.0 + - - +
19A VAL* 4.3 1.8 - - + -
66A TRP* 3.6 21.1 - - + +
68A THR* 4.0 20.4 - - + -
81A CYS* 3.5 25.4 - - - +
82A TYR* 4.0 23.6 - - + -
85A SER* 3.9 20.0 - - - +
87A ALA 3.1 6.5 + - - -
88A VAL* 3.3 14.9 - - + +
89A LEU 2.7 32.9 + - - -
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Residues in contact with LEU 18 (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* 4.7 6.7 - - + +
17A VAL* 1.3 81.6 - - - +
19A VAL* 1.3 57.0 + - - +
26A LYS* 4.0 28.4 - - + +
29A MET* 3.9 28.9 - - + -
30A LEU* 4.0 29.4 - - + -
65A LEU* 4.9 1.6 - - + -
66A TRP 3.0 11.7 + - - +
67A ASP* 5.0 1.3 - - - +
68A THR* 2.6 36.2 + - - +
89A LEU* 3.4 31.6 - - + +
91A CYS* 4.1 10.1 - - - -
180A PHE* 4.3 13.2 - - + -
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Residues in contact with VAL 19 (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* 4.3 3.6 - - + -
18A LEU* 1.3 79.0 - - - +
20A GLY* 1.3 54.7 + - - +
26A LYS* 3.5 6.3 - - - -
68A THR* 3.7 12.8 - - - +
78A ARG* 4.1 4.7 - - - -
82A TYR* 3.5 36.6 - - + +
88A VAL* 3.8 22.4 - - + -
89A LEU 3.0 8.8 + - - +
90A LEU* 3.7 7.7 - - + -
91A CYS* 2.8 34.0 + - - +
107A TRP* 3.9 23.6 - - + -
111A ILE* 4.1 13.2 - - + -
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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