Contacts of the helix formed by residues 97 - 105 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95S GLU* 3.8 15.1 - - - +
96S VAL* 1.3 74.8 - - - +
98S SER* 1.3 53.5 + - - +
99S ILE 2.8 5.8 - - - -
100S ILE* 2.6 30.6 + - - +
101S ARG* 3.1 22.9 + - - +
285S LEU* 3.8 23.2 - - - +
291S VAL* 4.1 26.1 - - + +
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Residues in contact with SER 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S GLU* 3.5 31.8 + - - +
97S ASP* 1.3 75.6 - - - +
99S ILE* 1.3 63.2 + - - +
100S ILE 3.1 0.7 - - - -
101S ARG* 3.0 27.4 - - - +
102S ASP* 3.0 41.1 + - - +
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Residues in contact with ILE 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S ILE* 3.9 10.1 - - + +
81S VAL* 4.0 38.6 - - + -
95S GLU 5.2 2.0 - - - +
96S VAL* 3.2 20.9 - - - +
97S ASP 2.8 0.4 + - - -
98S SER* 1.3 83.0 - - - +
100S ILE* 1.3 60.8 + - + +
102S ASP* 4.2 1.3 - - - -
103S LEU* 3.5 18.9 + - - +
254S VAL* 3.4 33.4 - - + +
256S ILE* 5.8 0.9 - - + -
282S LEU* 3.6 31.2 - - + -
285S LEU* 4.3 12.3 - - + -
305S PHE* 5.8 0.2 - - + -
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Residues in contact with ILE 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S ASP 2.6 9.1 + - - +
99S ILE* 1.3 80.4 - - + +
101S ARG* 1.3 55.8 + - - +
102S ASP 2.9 4.0 - - - -
103S LEU* 2.7 35.6 + - + +
104S THR* 3.1 12.8 + - - +
248S VAL* 5.8 0.4 - - + -
254S VAL* 5.2 5.8 - - + -
285S LEU* 4.1 21.1 - - + -
291S VAL* 3.5 39.7 - - + -
293S THR* 4.2 1.8 - - + -
298S VAL* 3.8 22.4 - - + -
300S THR* 3.8 6.5 - - + -
303S ILE* 3.5 32.3 - - + -
305S PHE* 5.6 1.1 - - + -
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Residues in contact with ARG 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S GLU* 4.5 10.3 - - - +
97S ASP* 3.1 18.6 + - - +
98S SER* 3.0 34.7 - - - +
100S ILE* 1.3 78.9 - - - +
102S ASP* 1.3 65.0 + - - +
104S THR* 3.9 3.0 + - - -
105S ASP* 2.8 32.3 + - - +
291S VAL* 4.7 4.7 - - + +
292S SER* 4.7 15.5 + - - -
293S THR* 3.7 24.7 - - + +
294S LYS* 5.4 8.0 - - + +
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Residues in contact with ASP 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S ILE* 4.3 23.3 - - + +
98S SER* 3.0 28.4 + - - +
99S ILE* 4.5 1.6 - - - +
100S ILE 2.9 0.8 - - - -
101S ARG* 1.3 87.1 - - - +
103S LEU* 1.3 65.0 + - - +
104S THR 3.1 2.6 + - - -
105S ASP* 3.4 18.5 + - + +
106S SER* 3.4 14.6 + - - -
290X THR 6.1 1.3 - - - -
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Residues in contact with LEU 103 (chain S).
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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77S PRO* 3.2 56.3 - - + +
78S PHE 3.9 2.9 - - - -
79S ILE* 3.4 26.2 - - + -
99S ILE 3.5 13.6 + - - +
100S ILE* 2.7 29.4 + - + +
102S ASP* 1.3 73.7 - - - +
104S THR* 1.3 60.9 + - - +
106S SER* 3.7 6.3 + - - -
107S ALA* 3.9 0.9 + - - +
248S VAL* 4.1 19.8 - - + +
252S GLY* 4.3 5.2 - - - -
253S ILE 3.8 3.8 - - - +
254S VAL* 4.3 6.5 - - + -
303S ILE* 4.1 26.5 - - + -
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Residues in contact with THR 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S ILE* 3.1 11.1 + - - +
101S ARG 4.0 6.1 - - - -
102S ASP 3.1 0.4 - - - -
103S LEU* 1.3 76.7 - - - +
105S ASP* 1.3 57.3 + - - +
106S SER 3.0 5.6 - - - -
107S ALA* 3.1 20.3 + - - +
108S MET* 3.8 17.6 + - + +
244S ALA 6.4 0.4 - - - -
245S ILE* 5.5 7.0 - - + +
248S VAL* 4.1 26.2 - - + +
293S THR* 3.9 20.1 - - - +
295S HIS* 4.2 33.7 - - + +
298S VAL* 4.4 6.6 - - - +
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Residues in contact with ASP 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S ARG* 2.8 26.5 + - - +
102S ASP* 3.4 15.1 + - - +
104S THR* 1.3 77.5 - - - +
106S SER* 1.3 57.1 + - - +
107S ALA 3.4 1.6 - - - -
108S MET* 4.5 13.5 + - - +
109S LYS* 4.8 5.5 - - - +
293S THR* 6.1 0.2 - - - -
294S LYS* 3.8 32.4 + - - +
295S HIS* 4.5 7.8 - - - -
290X THR* 5.1 1.0 - - - +
292X SER* 4.4 5.5 - - - -
297X MET* 3.1 50.0 - - + +
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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