Contacts of the strand formed by residues 87 - 93 (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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LYS 3.4 2.9 + - - +
16B LEU* 3.4 23.9 - - + +
17B VAL 3.0 22.9 + - - -
85B SER* 3.4 6.5 - - - -
86B ASP* 1.3 82.0 - - - +
88B VAL* 1.3 62.8 + - - +
89B LEU* 4.1 0.6 + - + -
118B THR* 4.8 1.6 - - - -
119B ARG* 3.4 23.8 - - + +
121B LEU* 4.1 15.9 - - + -
187B CYS* 3.7 9.2 - - - -
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Residues in contact with VAL 88 (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* 3.3 13.5 - - + +
19B VAL* 3.7 22.7 - - + -
82B TYR* 4.1 21.8 - - + -
85B SER* 4.4 4.9 - - - +
87B ALA* 1.3 75.5 - - - +
89B LEU* 1.3 65.4 + - - +
90B LEU 3.7 0.7 + - - -
111B ILE* 3.6 40.4 - - + -
118B THR* 3.6 22.7 - - + -
119B ARG 2.9 9.3 + - - +
120B VAL* 3.4 5.5 - - + +
121B LEU 3.0 24.3 + - - +
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Residues in contact with LEU 89 (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* 4.1 25.8 - - + -
17B VAL 2.7 14.1 + - - +
18B LEU* 3.5 19.3 - - + -
19B VAL* 3.0 28.1 + - - +
29B MET* 5.7 0.2 - - + -
87B ALA* 4.3 1.1 - - + +
88B VAL* 1.3 76.4 - - - +
90B LEU* 1.3 59.6 + - - +
91B CYS* 3.5 3.7 + - - -
121B LEU* 3.4 33.9 - - + -
123B ILE* 3.8 28.0 - - + -
179B ILE* 4.7 4.9 - - + -
180B PHE* 3.8 35.7 - - + -
183B ALA* 4.9 3.4 - - + -
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Residues in contact with LEU 90 (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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19B VAL* 3.8 9.9 - - + +
88B VAL 3.7 1.4 + - - -
89B LEU* 1.3 69.6 - - - +
91B CYS* 1.3 64.5 - - - +
104B LEU* 3.3 48.0 - - + +
107B TRP* 3.6 24.7 - - + -
108B ARG* 4.2 17.0 - - + +
111B ILE* 4.2 11.0 - - + -
120B VAL* 4.0 19.3 - - + -
121B LEU 2.8 13.6 + - - +
122B LEU* 3.3 20.2 - - + +
123B ILE 2.8 23.8 + - - -
159B LEU* 4.3 9.0 - - + -
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Residues in contact with CYS 91 (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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18B LEU* 4.3 9.2 - - - -
19B VAL 2.8 14.4 + - - +
20B GLY* 3.5 18.7 - - - -
21B ASP 4.3 1.6 + - - -
24B CYS* 3.7 18.8 - - - -
26B LYS* 3.9 11.0 - - + -
29B MET* 3.8 25.8 - - - -
89B LEU* 3.6 18.2 - - - -
90B LEU* 1.3 79.9 - - - +
92B PHE* 1.3 63.5 + - - +
104B LEU* 4.1 1.7 - - - +
123B ILE* 3.2 15.7 - - - +
125B CYS* 4.2 6.5 - - - -
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Residues in contact with PHE 92 (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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21B ASP* 5.8 0.9 - - - +
24B CYS* 4.1 12.3 - - - -
91B CYS* 1.3 76.1 - - - +
93B ASP* 1.3 70.9 + - - +
94B ILE* 3.8 18.2 - - + -
99B THR* 4.9 6.7 - - - +
100B VAL* 3.8 18.8 - - + -
104B LEU* 4.0 23.1 - - + -
122B LEU* 3.7 32.3 - - + -
123B ILE 3.1 10.8 + - - +
124B GLY* 4.0 4.0 - - - -
125B CYS* 2.9 27.0 + - - +
147B ILE* 3.8 25.8 - - + -
152B GLY* 4.7 3.6 - - - -
155B ILE* 4.8 2.0 - - + -
164B TYR* 3.6 36.8 - + - -
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Residues in contact with ASP 93 (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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23B GLN 4.2 1.2 - - - +
24B CYS* 3.8 23.6 - - + +
92B PHE* 1.3 79.3 - - - +
94B ILE* 1.3 58.3 + - - +
95B SER* 2.5 43.1 + - - -
96B ARG* 3.0 45.2 + - + +
99B THR* 4.6 2.3 + - - -
125B CYS 3.8 4.0 - - - -
126B LYS* 3.1 39.3 + - - +
129B LEU* 5.0 0.2 - - - +
147B ILE* 5.1 0.2 - - - +
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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