Contacts of the strand formed by residues 12 - 19 (chain B) 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 ALA 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B VAL* 1.3 79.2 + - - +
13B ARG* 1.3 54.7 + - - +
59B GLN* 4.2 13.0 - - - -
60B ARG 3.4 17.7 + - - +
61B VAL* 3.5 23.1 - - + -
62B GLU* 2.6 36.6 + - - +
188B LEU* 5.8 4.9 - - + -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL 3.5 8.0 + - - +
12B ALA* 1.3 73.5 - - - +
14B CYS* 1.3 58.9 + - - +
61B VAL* 4.5 0.4 - - - +
62B GLU* 3.5 13.5 - - + +
64B SER* 6.5 0.7 - - - -
86B ASP* 3.9 7.1 - - - +
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Residues in contact with CYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 1.3 74.0 - - - +
15B LYS* 1.3 60.1 + - - +
16B LEU* 3.8 19.6 + - - -
61B VAL* 4.0 12.6 - - + -
62B GLU 2.9 7.9 + - - -
63B LEU* 3.4 30.3 - - + +
64B SER* 2.9 28.5 + - - +
86B ASP* 3.2 8.3 - - - +
184B SER* 4.6 6.1 - - - +
187B CYS* 3.9 29.8 - - + -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG 4.3 0.2 + - - -
14B CYS* 1.3 69.9 - - - +
16B LEU* 1.3 63.9 + - - +
17B VAL* 3.9 10.1 - - + -
64B SER* 3.4 10.3 - - - +
66B TRP* 3.6 47.5 - - + +
81B CYS 2.8 28.2 + - - -
83B SER* 2.6 34.0 + - - +
84B ASP* 3.7 16.6 - - + +
85B SER* 3.6 8.3 - - - -
86B ASP* 2.6 42.9 + - - +
87B ALA 3.4 5.7 + - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B CYS* 3.8 9.6 + - - -
15B LYS* 1.3 78.9 - - - +
17B VAL* 1.3 62.7 + - - +
18B LEU* 4.3 3.1 - - + +
63B LEU* 4.3 19.1 - - + -
64B SER 3.0 7.3 + - - +
65B LEU* 3.5 14.7 - - + -
66B TRP* 3.0 24.8 + - - +
87B ALA* 3.4 32.3 - - + +
89B LEU* 4.1 14.6 - - + -
180B PHE* 4.0 22.2 - - + -
183B ALA* 4.0 24.2 - - + -
184B SER* 4.9 0.9 - - - +
187B CYS* 3.8 17.9 - - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS* 3.9 14.6 - - - -
16B LEU* 1.3 77.6 - - - +
18B LEU* 1.3 59.9 + - - +
19B VAL* 4.2 3.4 - - + -
66B TRP* 3.6 16.8 - - + +
68B THR* 4.0 21.5 - - + -
81B CYS* 3.5 26.9 - - + +
82B TYR* 4.1 26.9 - - + -
85B SER* 4.0 13.9 - - - -
87B ALA 3.0 8.3 + - - +
88B VAL* 3.3 8.1 - - + +
89B LEU* 2.7 32.3 + - - +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.3 9.0 - - + +
17B VAL* 1.3 76.1 - - - +
19B VAL* 1.3 55.1 + - - +
26B LYS* 3.7 40.8 - - + +
29B MET* 3.8 24.5 - - + -
30B LEU* 3.9 31.9 - - + -
65B LEU* 4.8 3.1 - - + -
66B TRP 3.0 18.9 + - - +
67B ASP* 4.7 3.6 - - - +
68B THR* 2.7 34.5 + - - +
89B LEU* 3.5 24.7 - - + +
91B CYS* 4.3 2.0 - - - -
180B PHE* 4.4 10.5 - - + -
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.9 6.7 + - + -
18B LEU* 1.3 79.0 - - - +
20B GLY* 1.3 59.6 + - - +
26B LYS* 3.5 6.3 - - - -
68B THR* 3.5 15.0 - - + +
78B ARG* 4.2 6.7 - - - -
82B TYR* 3.6 32.8 - - + +
88B VAL* 3.7 21.5 - - + -
89B LEU 3.0 9.1 + - - +
90B LEU* 4.3 9.4 - - + -
91B CYS* 2.8 30.0 + - - +
107B TRP* 4.0 21.3 - - + -
111B ILE* 4.1 12.3 - - + -
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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