Contacts of the helix formed by residues 110 - 115 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I CYS* 3.2 23.3 - - - -
109I ILE* 1.3 75.7 - - - +
111I THR* 1.3 63.0 + - - -
112I CYS 3.0 6.9 + - - -
113I ALA 3.1 3.3 + - - -
114I THR* 3.0 24.0 + - - +
145I ILE 2.8 17.6 + - - -
147I GLY 3.2 8.3 - - - -
150I PRO* 3.7 2.4 - - - +
267I SF4 3.6 0.7 - - - -
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Residues in contact with THR 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I GLY* 1.3 70.1 - - - -
112I CYS* 1.3 58.5 + - - +
114I THR* 3.2 10.1 - - - -
115I TYR* 2.9 32.1 + - + -
116I GLY 3.2 4.9 + - - -
117I GLY* 4.3 12.3 - - - +
146I ALA* 4.1 2.6 - - - +
147I GLY 2.7 26.1 + - - +
148I CYS* 4.6 1.8 - - - -
249I CYS 2.8 22.0 + - - +
250I SER* 3.9 2.9 - - - -
251I GLU 4.3 10.1 - - - +
253I ASN 5.7 1.3 - - - +
254I PHE* 4.0 27.4 - - + -
255I TRP* 4.8 1.3 - - + +
267I SF4 3.3 5.9 - - - -
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Residues in contact with CYS 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ALA 4.3 1.8 - - - -
16I GLU* 5.3 0.2 - - - -
74I GLY* 4.0 6.3 - - - +
75I GLY* 3.3 23.0 - - - +
110I GLY 3.0 1.2 - - - -
111I THR* 1.3 80.4 - - - +
113I ALA* 1.3 60.1 + - - +
116I GLY* 2.9 18.9 + - - -
117I GLY* 3.5 17.9 - - - +
118I VAL 3.9 3.1 - - - -
119I GLN* 3.3 30.7 - - - +
130I GLY* 3.9 1.0 - - - -
148I CYS* 5.6 0.2 - - - -
267I SF4 2.2 47.7 - - - -
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Residues in contact with ALA 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ILE 3.2 26.7 - - - +
74I GLY 3.1 24.1 + - - +
75I GLY* 4.4 0.4 - - - -
108I ALA* 3.9 5.4 - - + -
109I ILE 3.5 21.3 - - - +
110I GLY 3.1 2.4 + - - -
112I CYS* 1.3 77.6 - - - +
114I THR* 1.3 59.5 - - - +
131I VAL* 2.8 41.0 + - + +
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Residues in contact with THR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ALA* 3.2 27.1 - - - +
110I GLY 3.1 17.3 + - - +
111I THR* 3.2 12.1 - - - -
113I ALA* 1.3 79.0 - - - +
115I TYR* 1.4 86.0 + - - +
130I GLY* 3.9 6.5 - - - -
131I VAL 4.4 1.6 + - - -
132I ASN* 5.0 5.5 + - - +
133I GLU 5.7 0.3 + - - -
144I ASN* 3.6 32.9 + - + +
145I ILE 3.5 22.7 - - - +
146I ALA* 4.2 1.5 - - - +
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Residues in contact with TYR 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I THR* 2.9 22.9 + - + +
114I THR* 1.4 101.9 - - - +
116I GLY* 1.3 54.5 + - - -
117I GLY 3.7 1.1 - - - +
120I ALA* 5.0 0.9 - - - +
129I VAL* 4.8 1.2 - - - -
130I GLY* 3.9 10.7 + - - -
133I GLU* 5.4 2.6 - - - +
144I ASN* 3.8 12.4 - - - +
146I ALA* 4.0 15.5 - - + -
173I GLN* 2.6 36.9 + - + +
175I ARG* 3.4 20.3 - - - +
250I SER 4.2 1.6 - - - -
251I GLU 4.2 2.2 - - - -
252I PRO* 3.7 54.0 - - + +
253I ASN* 4.8 13.1 + - - +
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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