Contacts of the strand formed by residues 130 - 136 (chain B) in PDB entry 2BEW
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 LEU 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 4.7 4.0 - - + +
83B GLY* 3.9 23.8 - - - +
84B ILE* 3.7 29.8 - - + +
87B ALA* 3.8 10.4 - - + +
93B ALA* 3.4 11.7 - - + +
95B ALA* 4.4 7.6 - - + -
114B ALA* 4.5 11.4 - - + -
127B CYS* 3.2 15.0 + - + +
129B SER* 1.3 78.5 - - - +
131B THR* 1.3 72.4 + - - +
132B ILE* 4.2 28.0 - - + -
184B PRO* 3.4 9.1 - - + +
185B CYS 3.2 15.5 + - - +
1343B K 3.0 15.1 - - - -
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Residues in contact with THR 131 (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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92B THR* 6.6 0.2 - - - -
93B ALA 3.0 10.6 + - - +
94B ILE* 3.5 10.5 - - + -
95B ALA 2.9 25.3 + - - +
129B SER 3.9 1.1 + - - -
130B LEU* 1.3 76.6 + - - +
132B ILE* 1.3 70.9 - - - +
133B ARG* 4.1 1.1 - - + +
175B LEU* 4.2 17.9 - - + -
178B CYS* 3.2 40.9 + - + +
179B ILE* 3.4 18.0 + - + -
185B CYS* 3.3 11.1 - - + +
187B PHE* 4.6 3.8 - - + -
1343B K 3.5 0.7 - - - -
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Residues in contact with ILE 132 (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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80B VAL* 4.1 18.6 - - + -
95B ALA* 3.4 13.0 - - + +
97B ILE* 3.7 30.3 - - + -
103B ILE* 4.3 14.6 - - + -
110B ILE* 3.9 32.8 - - + -
130B LEU* 4.2 22.0 - - + -
131B THR* 1.3 78.6 - - - +
133B ARG* 1.3 64.2 + - - +
134B SER* 5.2 0.7 - - - -
184B PRO* 6.2 1.3 - - + -
185B CYS 2.9 11.4 + - - +
186B ILE* 3.4 16.6 - - + +
187B PHE 2.9 24.4 + - - +
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Residues in contact with ARG 133 (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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27B VAL* 3.6 9.4 - - - +
31B LEU* 4.0 23.4 - - - +
43B ILE* 5.1 4.8 - - - +
56B CYS* 3.5 23.5 - - - +
57B THR* 4.6 5.5 - - - +
94B ILE* 4.0 23.3 - - + -
95B ALA 2.8 18.1 + - - +
96B GLU* 2.8 46.5 + - - +
97B ILE* 3.1 22.2 + - - +
131B THR* 5.1 0.7 - - + -
132B ILE* 1.3 74.2 - - - +
134B SER* 1.3 62.1 + - - +
135B PRO* 5.3 2.4 - - - +
175B LEU* 4.2 12.1 - - + -
187B PHE* 3.2 15.3 - - + +
189B GLU* 2.8 44.7 + - - +
194B TYR* 4.1 2.4 + - - -
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Residues in contact with SER 134 (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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97B ILE* 2.9 26.2 + - - +
99B PHE 3.2 1.2 + - - -
100B ALA* 3.0 30.6 + - - -
103B ILE* 5.1 4.3 - - - -
132B ILE* 4.3 1.5 + - - -
133B ARG* 1.3 78.0 - - - +
135B PRO* 1.3 66.8 - - - +
186B ILE* 5.6 0.4 - - - -
187B PHE 3.0 7.1 + - - -
188B PHE* 3.4 24.6 - - - -
189B GLU* 2.9 25.5 + - - -
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Residues in contact with PRO 135 (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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54B PHE* 3.7 21.3 - - + -
96B GLU* 5.0 7.9 - - + +
97B ILE 3.4 7.6 - - - +
98B GLN* 3.1 28.5 - - - +
99B PHE* 3.9 1.4 - - - -
100B ALA* 2.8 32.2 + - - +
133B ARG* 4.7 2.9 - - - +
134B SER* 1.3 84.4 - - - +
136B TRP* 1.3 58.7 + - - +
189B GLU* 3.3 9.2 - - - +
191B LYS* 3.7 25.3 + - + -
194B TYR* 3.5 20.2 - - - +
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Residues in contact with TRP 136 (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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100B ALA* 4.3 0.4 - - - -
134B SER 4.1 0.4 - - - +
135B PRO* 1.3 76.2 - - - +
137B GLY* 1.3 74.0 + - - +
148B GLN 4.1 3.8 - - - -
149B SER* 3.3 17.3 - - - -
150B PRO* 3.6 21.5 - - + -
151B GLU* 2.9 34.8 + - - -
164B ILE* 3.8 23.2 - - + +
188B PHE* 3.4 38.3 - + + -
189B GLU 2.8 11.2 + - - +
190B PRO* 3.4 33.4 - - + +
191B LYS* 3.0 29.0 + - - +
192B ILE 4.8 0.2 + - - -
227B TRP* 4.0 17.3 - + - -
228B GLY* 4.2 11.7 - - - -
229B THR* 4.3 5.2 - - - -
230B GLN* 5.8 1.1 - - + -
279B HIS* 6.4 0.2 - - + -
280B GLU* 4.3 19.5 - - + -
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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