Contacts of the strand formed by residues 125 - 130 (chain B) in PDB entry 2ARB
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 ILE 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B PHE* 6.3 0.2 - - + -
90B PHE* 6.0 0.2 - - - -
91B PHE* 3.3 2.1 - - - +
92B ILE* 2.9 47.2 + - + +
124B VAL* 1.3 78.9 - - - +
126B ALA* 1.3 67.1 + - - +
127B VAL* 5.9 0.9 - - + -
149B ILE* 5.3 0.9 - - + -
150B ASP 3.3 6.7 - - - +
151B VAL* 4.6 12.6 - - + -
183B LEU* 4.2 26.0 - - + -
201B VAL* 4.6 14.1 - - + -
203B VAL* 4.0 23.3 - - + -
206B VAL* 3.9 23.6 - - + -
207B LEU* 3.6 26.2 - - + +
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Residues in contact with ALA 126 (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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89B ALA* 4.4 4.0 - - + -
90B PHE* 3.1 12.6 - - - +
91B PHE* 3.7 4.9 - - + -
110B LEU* 3.7 31.0 - - + -
111B PHE* 6.0 0.2 - - + -
124B VAL* 4.1 4.2 - - + -
125B ILE* 1.3 77.9 - - - +
127B VAL* 1.3 64.2 + - - +
128B GLU 4.0 0.4 - - - -
149B ILE* 3.6 4.9 - - - +
150B ASP* 2.7 47.4 + - + +
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Residues in contact with VAL 127 (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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89B ALA* 3.2 4.4 - - - -
90B PHE* 2.8 42.0 + - + +
125B ILE* 5.9 0.4 - - + -
126B ALA* 1.3 76.8 - - - +
128B GLU* 1.3 60.8 + - - +
129B PHE* 3.8 28.7 - - + -
147B ILE* 4.2 6.1 - - + -
148B GLY 3.4 9.4 - - - +
149B ILE* 4.8 3.4 - - + -
174B VAL* 4.2 22.0 - - + -
183B LEU* 4.5 13.0 - - + -
185B VAL* 3.8 35.7 - - + -
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Residues in contact with GLU 128 (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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88B ILE 3.6 4.3 - - - +
89B ALA* 4.1 4.5 - - + -
108B LEU* 3.7 27.3 - - + +
126B ALA 4.0 1.0 - - - -
127B VAL* 1.3 73.3 - - - +
129B PHE* 1.3 61.9 + - - +
130B ASP* 3.1 9.3 - - + +
146B HIS* 3.2 8.5 + - - -
147B ILE* 3.2 10.9 - - - +
148B GLY* 2.9 45.4 + - - +
150B ASP* 2.6 30.0 - - - +
154B ILE* 3.8 9.4 - - - +
156B SER* 3.6 8.4 + - - -
262B MN 2.1 36.5 + - - -
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Residues in contact with PHE 129 (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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73B PHE* 4.1 18.8 - + - -
75B PHE* 3.6 30.7 - + + -
77B LEU* 5.4 0.7 - - + +
87B GLY* 3.1 24.6 - - - -
88B ILE* 2.9 24.8 + - + +
89B ALA* 4.9 0.7 - - - -
90B PHE 5.2 0.7 - - - -
108B LEU* 5.9 0.4 - - - -
127B VAL* 3.8 32.8 - - + -
128B GLU* 1.3 71.6 - - - +
130B ASP* 1.3 58.5 + - - +
131B THR* 3.9 1.4 + - - +
146B HIS 3.8 4.3 - - - -
147B ILE* 3.8 30.5 - - + -
162B TRP* 3.9 17.5 - + + -
170B LEU* 3.7 23.1 - - + -
172B VAL* 3.7 27.8 - - + -
185B VAL* 4.7 1.6 - - + -
187B ALA* 4.4 2.0 - - + -
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Residues in contact with ASP 130 (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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86B ASP 3.3 10.2 - - - +
87B GLY* 4.5 0.4 - - - -
106B GLY 5.5 0.9 - - - +
108B LEU* 5.1 7.5 - - + +
128B GLU* 3.1 21.1 - - + +
129B PHE* 1.3 71.8 - - - +
131B THR* 1.3 64.0 + - - +
132B PHE 3.1 8.5 + - - +
140B TRP* 4.9 0.5 + - - -
141B ASP* 3.1 0.2 - - - +
145B PRO* 3.4 4.9 - - - +
146B HIS* 3.0 46.0 + - - +
154B ILE* 5.8 0.7 - - - +
162B TRP* 4.1 1.5 - - - -
262B MN 2.1 30.7 + - - -
264B CA 2.4 30.0 - - - -
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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