Contacts of the helix formed by residues 110 - 115 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20S CYS* 3.2 22.7 - - - -
109S ILE* 1.3 75.7 - - - +
111S THR* 1.3 62.7 + - - -
112S CYS 3.0 7.0 + - - -
113S ALA 3.1 3.5 + - - -
114S THR* 3.0 24.0 + - - +
145S ILE 2.8 17.4 + - - -
147S GLY 3.2 9.6 - - - -
150S PRO* 3.7 2.0 - - - +
267S SF4 3.6 1.1 - - - -
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Residues in contact with THR 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S GLY* 1.3 71.6 - - - -
112S CYS* 1.3 57.6 + - - +
114S THR* 3.2 9.2 - - - -
115S TYR* 2.9 32.0 + - + -
116S GLY 3.2 5.0 + - - -
117S GLY* 3.5 12.3 + - - +
146S ALA* 4.1 2.6 - - - +
147S GLY 2.7 26.4 + - - +
148S CYS* 4.6 1.8 - - - -
249S CYS 2.8 22.5 + - - +
250S SER* 3.9 2.8 - - - -
251S GLU 4.3 9.4 - - - +
253S ASN 5.7 1.3 - - - +
254S PHE* 4.0 28.3 - - + -
255S TRP* 4.8 1.1 - - + +
267S SF4 3.3 6.1 - - - -
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Residues in contact with CYS 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S ALA 4.3 1.3 - - - -
16S GLU* 5.3 0.4 - - - -
74S GLY* 4.0 6.7 - - - +
75S GLY* 3.3 23.5 - - - +
110S GLY 3.0 1.0 - - - -
111S THR* 1.3 80.5 - - - +
113S ALA* 1.3 59.4 + - - +
116S GLY* 2.9 19.2 + - - -
117S GLY* 3.5 18.8 - - - +
118S VAL* 3.9 2.9 - - - -
119S GLN* 3.3 30.3 - - - +
130S GLY* 3.9 0.9 - - - -
148S CYS* 5.6 0.4 - - - -
267S SF4 2.2 48.0 - - - -
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Residues in contact with ALA 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S ILE 3.2 27.6 - - - +
74S GLY 3.1 23.1 + - - +
75S GLY* 4.4 0.2 - - - -
108S ALA* 3.9 5.6 - - + -
109S ILE 3.5 20.6 + - - +
110S GLY 3.1 2.8 + - - -
112S CYS* 1.3 77.3 - - - +
114S THR* 1.3 59.2 - - - +
130S GLY* 3.3 0.2 - - - -
131S VAL* 2.8 40.7 + - + +
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Residues in contact with THR 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108S ALA* 3.2 26.5 - - + +
110S GLY 3.1 17.6 + - - +
111S THR* 3.2 11.3 - - - -
113S ALA* 1.3 79.8 - - - +
115S TYR* 1.4 86.6 + - - +
130S GLY* 3.9 6.6 - - - -
131S VAL 4.4 1.7 + - - -
132S ASN* 5.0 5.2 + - - +
133S GLU 5.7 0.3 + - - -
144S ASN* 3.6 32.0 + - + +
145S ILE 3.5 24.0 - - - +
146S ALA* 4.3 0.9 - - - +
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Residues in contact with TYR 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111S THR* 2.9 24.0 + - + +
114S THR* 1.4 101.8 - - - +
116S GLY* 1.3 54.8 + - - -
117S GLY 3.7 1.6 - - - +
120S ALA* 5.0 0.9 - - - +
129S VAL* 4.8 1.0 - - - -
130S GLY* 3.9 11.1 + - - -
133S GLU* 5.4 2.8 - - - +
144S ASN* 3.8 12.2 - - - +
146S ALA* 4.0 15.3 - - + -
173S GLN* 2.6 37.6 + - + +
175S ARG* 3.4 20.1 - - - +
250S SER 4.2 1.3 - - - -
251S GLU 4.2 2.5 - - - -
252S PRO* 3.7 53.4 - - + -
253S ASN* 4.8 12.5 + - - +
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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