Contacts of the helix formed by residues 110 - 115 (chain E) in PDB entry 2FRV
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 GLY 110 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E CYS* 3.2 22.4 - - - -
109E ILE* 1.3 75.9 - - - +
111E THR* 1.3 64.2 + - - -
112E CYS 3.0 7.0 + - - -
113E ALA 3.1 3.3 + - - -
114E THR* 3.0 24.2 + - - +
145E ILE 2.8 17.2 + - - -
147E GLY 3.2 8.7 - - - -
150E PRO* 3.7 2.4 - - - +
267E SF4 3.6 1.3 - - - -
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Residues in contact with THR 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E GLY* 1.3 71.6 - - - -
112E CYS* 1.3 58.6 + - - +
114E THR* 3.2 9.2 - - - -
115E TYR* 2.9 32.4 + - + -
116E GLY 3.2 5.2 + - - -
117E GLY* 3.5 12.7 + - - +
146E ALA* 4.1 2.4 - - - +
147E GLY 2.7 26.8 + - - +
148E CYS* 4.6 1.6 - - - -
249E CYS 2.8 22.2 + - - +
250E SER* 3.9 3.3 - - - -
251E GLU 4.3 9.0 - - - +
252E PRO* 5.6 0.2 - - + -
253E ASN 5.7 1.8 - - - +
254E PHE* 4.0 28.0 - - + -
255E TRP* 4.8 1.1 - - + +
267E SF4 3.3 5.7 - - - -
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Residues in contact with CYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA 4.3 1.3 - - - -
16E GLU* 5.3 0.4 - - - -
74E GLY* 4.0 7.0 - - - +
75E GLY* 3.3 23.1 - - - +
110E GLY* 3.0 1.6 - - - -
111E THR* 1.3 80.7 - - - +
113E ALA* 1.3 58.5 + - - +
116E GLY 2.9 19.2 + - - -
117E GLY* 3.5 18.8 - - - +
118E VAL 3.9 3.1 - - - -
119E GLN* 3.3 29.8 - - - +
130E GLY* 3.9 0.9 - - - -
148E CYS* 5.6 0.4 - - - -
267E SF4 2.2 46.9 - - - -
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Residues in contact with ALA 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ILE 3.2 27.4 - - - +
74E GLY 3.1 23.7 + - - +
75E GLY* 4.4 0.4 - - - -
108E ALA* 3.9 5.6 - - + -
109E ILE 3.5 20.6 - - - +
110E GLY 3.1 2.4 + - - -
112E CYS* 1.3 77.2 - - - +
114E THR* 1.3 60.2 - - - +
130E GLY* 3.3 0.2 - - - -
131E VAL* 2.8 40.5 + - + +
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Residues in contact with THR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ALA 3.2 26.7 - - - +
110E GLY 3.0 17.9 + - - +
111E THR* 3.2 11.8 - - - -
113E ALA* 1.3 78.3 - - - +
115E TYR* 1.4 85.5 + - - +
130E GLY* 3.9 7.2 - - - -
131E VAL 4.4 1.7 + - - -
132E ASN* 5.0 5.5 + - - +
133E GLU 5.7 0.3 + - - -
144E ASN* 3.6 33.1 + - + +
145E ILE 3.5 23.3 - - - +
146E ALA* 4.2 1.3 - - - +
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Residues in contact with TYR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E THR* 2.9 22.9 + - + +
114E THR* 1.4 100.6 - - - +
116E GLY* 1.3 54.7 + - - +
117E GLY 3.7 1.8 - - - +
120E ALA* 5.0 1.4 - - - +
129E VAL* 4.8 1.0 - - - -
130E GLY* 3.9 11.2 + - - -
133E GLU* 5.4 2.6 - - - +
144E ASN* 3.8 13.0 - - - +
146E ALA* 4.0 14.8 - - + -
173E GLN* 2.6 36.3 + - + +
175E ARG* 3.4 19.9 - - - +
250E SER 4.2 1.6 - - - -
251E GLU 4.2 2.2 - - - -
252E PRO* 3.7 54.7 - - + +
253E ASN* 4.8 12.9 + - - +
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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