Contacts of the helix formed by residues 110 - 115 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C CYS* 3.2 22.7 - - - -
109C ILE* 1.3 75.3 - - - +
111C THR* 1.3 62.4 + - - -
112C CYS 3.0 7.1 + - - -
113C ALA 3.1 3.3 + - - -
114C THR* 3.0 24.4 + - - +
145C ILE 2.8 17.2 + - - -
147C GLY 3.2 9.4 - - - -
150C PRO* 3.7 1.7 - - - +
267C SF4 3.6 1.3 - - - -
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Residues in contact with THR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLY* 1.3 70.6 - - - -
112C CYS* 1.3 58.1 + - - +
114C THR* 3.2 10.1 - - - -
115C TYR* 2.9 32.6 + - + -
116C GLY 3.2 5.2 + - - -
117C GLY* 3.5 13.0 + - - +
146C ALA* 4.1 2.3 - - - +
147C GLY 2.7 25.9 + - - +
148C CYS* 4.6 1.8 - - - -
249C CYS 2.8 21.7 + - - -
250C SER* 3.9 3.1 - - - -
251C GLU 4.3 9.2 - - - +
252C PRO* 5.6 0.2 - - + -
253C ASN 5.7 1.6 - - - +
254C PHE* 4.0 28.0 - - + -
255C TRP* 4.8 0.9 - - + +
267C SF4 3.3 5.4 - - - -
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Residues in contact with CYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ALA 4.3 1.6 - - - -
16C GLU* 5.3 0.4 - - - -
74C GLY* 4.0 7.0 - - - +
75C GLY* 3.3 23.3 - - - +
110C GLY 3.0 1.0 - - - -
111C THR* 1.3 79.6 - - - +
113C ALA* 1.3 60.2 + - - +
116C GLY* 2.9 19.6 + - - -
117C GLY* 3.5 18.2 - - - +
118C VAL 3.9 3.1 - - - -
119C GLN* 3.3 31.4 - - - +
130C GLY* 3.9 0.7 - - - -
148C CYS* 5.6 0.2 - - - -
267C SF4 2.2 47.5 - - - -
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE 3.2 27.1 - - - +
74C GLY 3.1 23.2 + - - +
75C GLY* 4.4 0.2 - - - -
108C ALA* 3.9 4.9 - - + -
109C ILE 3.5 21.3 - - - +
110C GLY 3.1 2.6 + - - -
112C CYS* 1.3 78.1 - - - +
114C THR* 1.3 61.8 + - - +
131C VAL* 2.8 40.7 + - + +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA* 3.2 26.9 - - + +
110C GLY 3.1 16.9 + - - +
111C THR* 3.2 12.0 - - - -
113C ALA* 1.3 78.9 - - - +
115C TYR* 1.4 85.7 + - - +
130C GLY* 3.9 6.6 - - - -
131C VAL 4.4 1.9 + - - -
132C ASN* 5.0 5.2 + - - +
133C GLU 5.7 0.3 + - - -
144C ASN* 3.6 32.7 + - + +
145C ILE 3.5 23.1 - - - +
146C ALA* 4.2 1.1 - - - +
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C THR* 2.9 22.5 + - + +
114C THR* 1.4 102.1 - - - +
116C GLY* 1.3 54.4 + - - -
117C GLY 3.7 1.6 - - - +
120C ALA* 5.0 0.7 - - - +
129C VAL* 4.8 1.0 - - - -
130C GLY* 3.9 10.1 + - - -
133C GLU* 5.4 3.3 - - - +
144C ASN* 3.8 12.2 - - - +
146C ALA* 4.0 14.8 - - + -
173C GLN* 2.6 36.8 + - + +
175C ARG* 3.4 20.1 - - - +
250C SER 4.2 2.0 - - - -
251C GLU 4.2 2.5 - - - -
252C PRO* 3.7 52.5 - - + -
253C ASN* 4.8 12.7 + - - +
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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