Contacts of the helix formed by residues 110 - 115 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A CYS* 3.2 23.1 - - - -
109A ILE* 1.3 75.4 - - - +
111A THR* 1.3 62.7 + - - -
112A CYS 3.0 7.4 + - - -
113A ALA 3.1 3.1 + - - -
114A THR* 3.0 24.9 + - - +
145A ILE 2.8 17.6 + - - -
147A GLY 3.2 9.4 - - - -
150A PRO* 3.7 2.4 - - - +
267A SF4 3.6 1.1 - - - -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY* 1.3 70.1 - - - -
112A CYS* 1.3 56.6 + - - +
114A THR* 3.2 9.9 - - - -
115A TYR* 2.9 32.8 + - + -
116A GLY 3.2 5.5 + - - -
117A GLY* 4.3 13.0 - - - +
146A ALA* 4.1 2.6 - - - +
147A GLY 2.7 26.9 + - - +
148A CYS* 4.6 1.6 - - - -
249A CYS 2.8 22.2 + - - -
250A SER* 3.9 3.3 - - - -
251A GLU 4.3 9.6 - - - +
253A ASN 5.7 1.1 - - - +
254A PHE* 4.0 27.8 - - + -
255A TRP* 4.8 0.9 - - + +
267A SF4 3.3 6.3 - - - -
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA 4.3 1.6 - - - -
16A GLU* 5.3 0.4 - - - -
74A GLY* 4.0 6.7 - - - +
75A GLY* 3.3 23.6 - - - +
110A GLY 3.0 1.4 - - - -
111A THR* 1.3 80.1 - - - +
113A ALA* 1.3 59.2 + - - +
116A GLY* 2.9 19.2 + - - -
117A GLY* 3.5 17.9 - - - +
118A VAL 3.9 2.5 - - - -
119A GLN* 3.3 30.5 - - - +
130A GLY* 3.9 0.9 - - - -
148A CYS* 5.6 0.4 - - - -
267A SF4 2.2 47.3 - - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE 3.2 27.1 - - - +
74A GLY 3.1 22.6 + - - +
75A GLY* 4.4 0.4 - - - -
108A ALA* 3.9 5.8 - - + -
109A ILE 3.5 21.5 + - - +
110A GLY 3.1 2.8 + - - -
112A CYS* 1.3 78.0 - - - +
114A THR* 1.3 59.7 + - - +
131A VAL* 2.8 41.5 + - + +
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA 3.2 26.5 - - - +
110A GLY 3.1 16.9 + - - +
111A THR* 3.2 12.0 - - - -
113A ALA* 1.3 80.2 - - - +
115A TYR* 1.4 86.2 + - - +
130A GLY* 3.9 6.6 - - - -
131A VAL 4.4 1.6 + - - -
132A ASN* 5.0 5.5 + - - +
133A GLU 5.7 0.5 + - - -
144A ASN* 3.6 31.7 + - + +
145A ILE 3.5 23.8 - - - +
146A ALA* 4.2 1.7 - - - +
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR* 2.9 22.9 + - + +
114A THR* 1.4 105.0 - - - +
116A GLY* 1.3 54.1 + - - -
117A GLY 3.7 1.3 - - - +
120A ALA* 5.0 0.9 - - - +
129A VAL* 4.6 1.4 - - - -
130A GLY* 3.9 10.6 + - - -
133A GLU* 5.4 2.8 - - - +
144A ASN* 3.8 12.9 - - - +
146A ALA* 4.0 14.8 - - + -
173A GLN* 2.6 36.6 + - + +
175A ARG* 3.4 20.4 - - - +
250A SER 4.2 2.2 - - - -
251A GLU 4.2 2.0 - - - -
252A PRO* 3.7 53.8 - - + -
253A ASN* 4.8 12.8 + - - +
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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