Contacts of the strand formed by residues 64 - 70 (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 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B PRO* 3.6 25.1 - - + +
7B GLU* 3.1 26.2 - - - +
63B GLY* 1.3 76.6 - - - -
65B HIS* 1.3 66.1 + - - +
133B PHE* 3.3 24.7 - - + -
134B LEU 3.2 4.7 - - - -
135B ASP* 2.8 64.8 + - - +
137B GLY* 4.9 5.5 - - - +
138B MSE 4.2 9.1 - - - +
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Residues in contact with HIS 65 (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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6B PRO 4.2 0.2 - - - -
7B GLU* 3.3 27.7 + - - -
9B GLN* 3.0 15.9 + - - +
60B PHE* 3.3 50.7 - + + +
61B THR 5.2 0.2 + - - -
62B SER 2.7 23.9 + - - -
63B GLY* 3.4 21.1 + - - -
64B ARG* 1.3 82.6 + - - +
66B TYR* 1.3 61.2 + - - +
67B TRP* 4.2 8.4 - - + -
132B ILE 3.7 0.7 - - - +
133B PHE* 3.2 7.3 - - - -
134B LEU* 2.8 45.7 + - + +
136B VAL* 4.7 0.2 - - + -
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Residues in contact with TYR 66 (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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1B GLY 5.9 0.2 - - - -
2B PRO* 4.2 27.6 - - + +
3B LEU* 5.3 1.8 - - + -
6B PRO 3.7 6.1 - - - +
7B GLU 3.0 7.7 + - - -
8B PHE* 3.5 35.9 - + + -
9B GLN* 3.2 25.0 + - - +
65B HIS* 1.3 75.8 - - - +
67B TRP* 1.3 68.3 - - - +
68B GLU* 2.6 46.4 + - + +
131B GLY* 3.6 22.3 - - - -
132B ILE 3.3 20.2 - - - -
133B PHE* 4.1 15.9 - + + -
144B TYR* 5.4 7.5 - + + +
146B VAL* 3.8 5.5 - - - +
186B VAL* 3.5 16.4 - - + +
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Residues in contact with TRP 67 (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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9B GLN* 4.5 5.8 - - + +
12B MSE 3.7 34.1 - - + -
60B PHE* 3.5 27.4 - + - -
65B HIS* 4.2 3.4 - - + -
66B TYR* 1.3 93.6 - - - +
68B GLU* 1.3 65.8 + - - +
69B VAL* 3.9 17.9 - - + +
80B GLY 3.6 15.4 + - - -
81B VAL* 3.4 22.7 - - + -
130B VAL 3.8 0.2 - - - +
131B GLY* 3.7 1.7 - - - -
132B ILE* 2.9 66.1 + - + +
134B LEU* 4.1 20.0 - - + -
166B PRO* 3.6 19.5 - - + -
168B PHE* 4.0 15.6 - + - -
183B ILE* 5.3 5.2 - - + -
186B VAL* 5.5 1.8 - - - -
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Residues in contact with GLU 68 (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* 5.5 0.2 - - - +
66B TYR* 2.6 43.3 + - + +
67B TRP* 1.3 74.5 - - - +
69B VAL* 1.3 69.5 + - - +
129B ARG* 3.2 34.3 + - + -
130B VAL 3.3 9.9 - - - +
146B VAL* 3.6 18.1 - - + +
183B ILE* 3.4 8.0 - - - +
184B CYS* 2.9 43.3 + - + +
186B VAL* 3.7 25.5 - - + +
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Residues in contact with VAL 69 (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* 3.9 15.0 - - + +
68B GLU* 1.3 81.6 - - - +
70B ASP* 1.3 67.5 + - - +
71B VAL* 4.0 4.4 + - + +
79B VAL* 3.9 27.1 - - + -
128B HIS 3.7 0.5 - - - +
129B ARG* 3.2 4.9 - - - -
130B VAL* 2.7 41.8 + - + +
132B ILE* 4.3 9.6 - - + -
168B PHE* 3.3 30.7 - - + -
181B LEU* 4.1 18.4 - - + -
182B SER 3.5 9.4 - - - +
183B ILE* 4.9 0.7 - - + -
184B CYS* 4.5 0.2 - - - -
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Residues in contact with ASP 70 (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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69B VAL* 1.3 71.9 - - - +
71B VAL* 1.3 60.0 + - - +
72B GLY* 2.9 31.9 + - - -
128B HIS* 3.2 31.9 + - - +
129B ARG* 3.3 24.8 + - - +
180B ILE 3.8 1.0 - - - +
181B LEU* 3.4 4.9 - - - +
182B SER* 2.9 38.5 + - - +
184B CYS* 3.4 21.6 - - - -
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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