Contacts of the helix formed by residues 97 - 105 (chain V) in PDB entry 1G3I
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 ASP 97 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95V GLU* 3.7 14.9 - - - +
96V VAL* 1.3 74.2 - - - +
98V SER* 1.3 51.4 + - - +
99V ILE 2.9 5.8 - - - -
100V ILE* 2.7 29.6 + - - +
101V ARG* 3.1 23.4 + - - +
285V LEU* 3.8 23.6 - - - +
291V VAL* 4.0 25.8 - - + +
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Residues in contact with SER 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V GLU* 3.5 32.3 + - - +
96V VAL 4.4 0.2 - - - -
97V ASP* 1.3 75.8 - - - +
99V ILE* 1.3 63.8 + - - +
100V ILE 3.1 0.4 - - - -
101V ARG* 3.0 25.9 - - - +
102V ASP* 3.0 41.4 + - - +
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Residues in contact with ILE 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V ILE* 3.9 10.1 - - + +
81V VAL* 3.9 38.8 - - + -
95V GLU 5.2 1.8 - - - +
96V VAL* 3.2 20.9 - - - +
97V ASP 2.8 0.6 + - - -
98V SER* 1.3 83.0 - - - +
100V ILE* 1.3 61.8 + - + +
102V ASP* 4.2 1.1 - - - -
103V LEU* 3.5 18.7 + - - +
254V VAL* 3.4 33.2 - - + +
256V ILE* 5.8 0.7 - - + -
282V LEU* 3.6 31.2 - - + -
285V LEU* 4.3 11.9 - - + -
305V PHE* 5.8 0.2 - - + -
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Residues in contact with ILE 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97V ASP 2.7 8.9 + - - +
99V ILE* 1.3 79.1 - - + +
101V ARG* 1.3 57.1 + - - +
102V ASP 2.9 4.5 - - - -
103V LEU* 2.7 34.6 + - + +
104V THR* 3.1 12.2 + - - +
248V VAL* 5.8 1.1 - - + -
254V VAL* 5.1 5.8 - - + -
285V LEU* 4.1 21.1 - - + -
291V VAL* 3.5 41.7 - - + -
293V THR* 4.2 1.3 - - + -
298V VAL* 3.8 22.7 - - + -
300V THR* 3.8 6.7 - - + -
303V ILE* 3.5 31.9 - - + -
305V PHE* 5.6 1.6 - - + -
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Residues in contact with ARG 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V GLU* 4.5 9.7 - - - +
97V ASP* 3.1 19.4 + - - +
98V SER* 3.0 34.5 - - - +
100V ILE* 1.3 78.8 - - - +
102V ASP* 1.3 64.5 - - - +
104V THR* 3.9 3.3 + - - -
105V ASP* 2.8 31.9 + - - +
291V VAL* 4.7 4.7 - - + +
292V SER* 4.6 15.3 + - - -
293V THR* 3.7 25.7 - - + +
294V LYS* 5.4 8.5 - - + +
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Residues in contact with ASP 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V ILE* 4.3 23.0 - - + +
98V SER* 3.0 27.9 + - - +
99V ILE* 4.5 1.8 - - - +
100V ILE 2.9 0.6 - - - -
101V ARG* 1.3 89.7 - - - +
103V LEU* 1.3 62.8 + - - +
104V THR 3.1 2.2 + - - -
105V ASP* 3.4 18.8 + - + +
106V SER* 3.5 15.1 + - - -
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Residues in contact with LEU 103 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77V PRO* 3.2 57.1 - - + +
78V PHE 3.8 3.6 - - - -
79V ILE* 3.4 25.8 - - + -
99V ILE 3.5 14.1 + - - +
100V ILE* 2.7 24.6 + - + +
102V ASP* 1.3 78.4 - - - +
104V THR* 1.3 61.7 + - - +
106V SER* 3.7 4.3 + - - -
107V ALA* 3.7 2.6 - - - +
248V VAL* 4.1 19.8 - - + +
252V GLY* 4.3 4.9 - - - -
253V ILE 3.8 3.8 - - - +
254V VAL* 4.3 6.5 - - + -
303V ILE* 4.2 26.2 - - + -
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Residues in contact with THR 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100V ILE 3.1 12.0 + - - -
101V ARG 4.0 6.1 - - - -
102V ASP 3.1 0.4 - - - -
103V LEU* 1.3 77.6 - - - +
105V ASP* 1.3 57.0 + - - +
106V SER 3.0 5.2 - - - -
107V ALA* 3.0 25.2 + - + +
108V MET* 3.5 12.7 + - + +
244V ALA 5.8 1.1 - - - +
245V ILE* 5.3 7.5 - - + +
248V VAL* 4.2 20.5 - - + +
293V THR* 3.9 20.0 - - - +
295V HIS* 4.1 37.7 - - + +
298V VAL* 4.4 7.6 - - - +
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Residues in contact with ASP 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290U THR* 5.5 0.9 - - - +
292U SER* 4.7 5.7 - - - -
297U MET* 3.5 45.0 - - + +
101V ARG* 2.8 26.3 + - - +
102V ASP* 3.4 16.0 + - + +
104V THR* 1.3 77.4 - - - +
106V SER* 1.3 56.8 + - - +
107V ALA 3.4 1.5 + - - -
108V MET* 4.8 7.2 + - - +
109V LYS* 4.7 10.9 + - - +
293V THR* 6.1 0.3 - - - -
294V LYS* 3.8 30.5 + - - +
295V HIS* 4.6 7.8 - - - -
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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