Contacts of the strand formed by residues 129 - 135 (chain B) in PDB entry 2FBE
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 ARG 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B GLU* 3.2 30.1 + - + +
69B VAL 3.2 13.7 - - - +
70B ASP* 3.3 20.7 + - - +
127B LEU* 3.9 2.9 - - - +
128B HIS* 1.3 87.5 + - + +
130B VAL* 1.3 61.5 + - - +
144B TYR 3.7 0.7 - - - +
145B ASN* 3.8 5.6 + - - +
146B VAL* 3.0 43.7 + - + +
147B SER* 4.8 8.8 + - - +
184B CYS* 3.3 33.9 - - - +
185B SER 4.5 7.9 + - - -
186B VAL 5.6 2.0 + - - -
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Residues in contact with VAL 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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67B TRP 3.8 0.5 - - - +
68B GLU* 3.3 4.9 - - - -
69B VAL* 2.7 41.9 + - + +
71B VAL* 5.5 2.5 - - + -
77B TRP* 3.9 33.4 - - + -
79B VAL* 4.3 11.7 - - + -
103B VAL* 4.5 4.0 - - + -
127B LEU* 4.2 14.6 - - + -
128B HIS 5.2 1.6 - - - -
129B ARG* 1.3 75.5 - - - +
131B GLY* 1.3 71.5 + - - +
132B ILE* 3.9 15.9 + - + +
143B PHE* 4.1 19.5 - - + -
144B TYR 3.3 9.0 - - - +
146B VAL* 4.0 2.2 - - - -
152B ILE* 4.5 3.6 - - + -
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Residues in contact with GLY 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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66B TYR* 3.6 28.5 - - - -
67B TRP 3.7 3.1 - - - -
68B GLU* 4.0 0.4 - - - -
130B VAL* 1.3 73.2 - - - +
132B ILE* 1.3 61.3 + - - -
142B ALA 3.7 0.9 - - - +
143B PHE* 3.2 6.2 - - - -
144B TYR* 2.7 44.1 + - - -
146B VAL* 3.6 7.3 - - - +
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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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65B HIS 3.7 0.7 - - - +
66B TYR* 3.3 8.3 - - - -
67B TRP* 2.9 77.5 + - + +
69B VAL* 4.3 7.6 - - + -
79B VAL* 4.2 15.5 - - + -
80B GLY* 4.0 23.1 - - - +
130B VAL* 4.0 7.0 - - + +
131B GLY* 1.3 77.0 - - - -
133B PHE* 1.3 61.3 + - - +
134B LEU 4.1 0.2 - - - -
141B ILE* 3.7 31.2 - - + -
142B ALA 3.5 2.7 - - - -
143B PHE* 3.8 19.7 - - + -
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Residues in contact with PHE 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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2B PRO 5.1 0.7 - - - -
3B LEU* 4.2 24.7 - - + -
6B PRO* 3.3 31.4 - - + -
64B ARG* 3.3 36.6 - - + -
65B HIS 3.2 18.6 - - - -
66B TYR* 4.1 15.9 - + + -
131B GLY 4.2 0.2 + - - -
132B ILE* 1.3 73.0 - - - +
134B LEU* 1.3 59.6 + - - +
135B ASP* 3.7 22.4 + - + +
140B SER 4.4 0.2 - - - -
141B ILE* 3.1 7.2 - - - -
142B ALA* 2.7 44.0 + - + +
144B TYR* 4.8 7.6 - + + -
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Residues in contact with LEU 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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60B PHE* 3.6 43.3 - - + -
63B GLY 3.5 2.1 - - - +
64B ARG* 3.2 3.5 - - - -
65B HIS* 2.8 44.3 + - + +
67B TRP* 4.1 17.2 - - + -
81B VAL* 4.7 3.1 - - + -
132B ILE 4.1 1.0 + - - -
133B PHE* 1.3 72.1 - - - +
135B ASP* 1.3 61.0 + - - +
136B VAL* 3.8 20.4 - - + +
140B SER 3.8 9.6 - - - +
141B ILE* 4.1 16.2 - - + +
158B ILE* 3.9 21.1 - - + -
164B TRP* 4.1 17.7 - - + -
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Residues in contact with ASP 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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63B GLY 4.1 0.2 - - - -
64B ARG* 2.8 52.0 + - + +
133B PHE* 3.7 18.0 + - + +
134B LEU* 1.3 70.6 - - - +
136B VAL* 1.3 51.4 + - - +
137B GLY 3.3 3.1 + - - -
138B MSE 2.7 45.1 + - + +
139B ARG 2.7 31.5 + - - -
140B SER* 2.8 24.4 + - - +
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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