Contacts of the helix formed by residues 110 - 115 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G CYS* 3.2 22.7 - - - -
109G ILE* 1.3 75.1 - - - +
111G THR* 1.3 63.3 + - - -
112G CYS 3.0 7.4 + - - -
113G ALA 3.1 3.1 + - - -
114G THR* 3.0 25.3 + - - +
145G ILE 2.8 17.6 + - - -
147G GLY 3.2 9.2 - - - -
150G PRO* 3.7 2.0 - - - +
267G SF4 3.6 1.1 - - - -
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Residues in contact with THR 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G GLY* 1.3 71.6 - - - -
112G CYS* 1.3 57.4 + - - +
114G THR* 3.2 9.0 - - - -
115G TYR* 2.9 31.5 + - + -
116G GLY 3.2 5.4 + - - -
117G GLY* 3.5 12.0 + - - +
146G ALA* 4.1 2.6 - - - +
147G GLY 2.7 26.8 + - - +
148G CYS* 4.6 1.3 - - - -
249G CYS 2.8 22.1 + - - +
250G SER* 3.9 2.9 - - - -
251G GLU 4.3 10.1 - - - +
253G ASN 5.7 1.6 - - - +
254G PHE* 4.0 27.6 - - + -
255G TRP* 4.8 1.1 - - + +
267G SF4 3.3 5.9 - - - -
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Residues in contact with CYS 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ALA 4.3 1.3 - - - -
16G GLU* 5.3 0.4 - - - -
74G GLY* 4.0 6.5 - - - +
75G GLY* 3.3 23.3 - - - +
110G GLY 3.0 0.6 - - - -
111G THR* 1.3 80.3 - - - +
113G ALA* 1.3 59.6 + - - +
116G GLY* 2.9 19.2 + - - -
117G GLY* 3.5 18.4 - - - +
118G VAL 3.9 2.5 - - - -
119G GLN* 3.3 31.2 - - - +
130G GLY* 3.9 1.2 - - - -
148G CYS* 5.6 0.4 - - - -
267G SF4 2.2 48.2 - - - -
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Residues in contact with ALA 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ILE 3.2 27.1 - - - +
74G GLY 3.1 23.5 + - - +
108G ALA* 3.9 6.1 - - + -
109G ILE 3.5 21.3 + - - +
110G GLY 3.1 2.6 + - - -
112G CYS* 1.3 77.4 - - - +
114G THR* 1.3 58.7 + - - +
130G GLY* 3.3 0.3 - - - -
131G VAL* 2.8 40.4 + - + +
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Residues in contact with THR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ALA* 3.2 26.9 - - + +
110G GLY 3.1 17.5 + - - +
111G THR* 3.2 12.0 - - - -
113G ALA* 1.3 80.0 - - - +
115G TYR* 1.4 85.2 + - - +
130G GLY* 3.9 6.6 - - - -
131G VAL 4.4 1.6 + - - -
132G ASN* 5.0 5.0 + - - +
133G GLU 5.7 0.5 + - - -
144G ASN* 3.6 32.9 + - + +
145G ILE 3.5 22.7 - - - +
146G ALA* 4.2 1.3 - - - +
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Residues in contact with TYR 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G THR* 2.9 23.6 + - + +
114G THR* 1.4 100.9 - - - +
116G GLY* 1.3 54.1 + - - -
117G GLY 3.7 0.9 - - - +
120G ALA* 5.0 0.7 - - - +
129G VAL* 4.8 1.0 - - - -
130G GLY* 3.9 12.0 + - - -
133G GLU* 5.4 2.6 - - - +
144G ASN* 3.8 11.9 - - - +
146G ALA* 4.0 15.5 - - + -
173G GLN* 2.6 36.6 + - + +
175G ARG* 3.4 20.8 + - - +
250G SER 4.2 1.1 - - - -
251G GLU 4.2 2.2 - - - -
252G PRO* 3.7 53.8 - - + -
253G 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