Contacts of the helix formed by residues 96 - 107 (chain B) in PDB entry 3GA1
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B GLN* 5.3 6.4 + - - +
92B MET* 4.6 8.0 - - + +
93B ASN* 2.9 38.5 + - - +
95B GLY* 1.3 85.4 - - - +
97B GLN* 1.3 63.7 + - - +
98B ASP 3.3 0.2 + - - -
99B LEU* 3.6 11.1 + - + +
100B LEU* 3.1 22.4 + - - +
128B NO3 3.2 11.0 + - - -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.9 19.6 - - + +
92B MET* 3.9 14.4 - - - -
93B ASN 3.9 2.0 + - - -
94B VAL* 3.6 13.5 - - - +
95B GLY* 2.9 24.6 + - - +
96B ASP* 1.3 78.3 + - - +
98B ASP* 1.3 70.2 + - - +
100B LEU* 3.4 0.9 + - - +
101B MET* 2.9 36.3 + - + +
127B NO3 3.7 30.9 + - - +
128B NO3 3.3 13.3 + - - -
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 1.3 92.2 + - - +
99B LEU* 1.3 58.2 + - - +
101B MET* 3.3 7.2 + - - +
102B TYR* 2.9 29.7 + - - +
128B NO3 2.9 27.1 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA 5.5 1.1 - - - +
74B GLN* 3.6 40.8 - - + +
76B GLN* 6.1 3.1 - - + -
77B SER* 2.9 24.2 - - - +
96B ASP* 3.9 13.5 - - + +
98B ASP* 1.3 75.7 - - - +
100B LEU* 1.3 56.1 + - - +
102B TYR* 3.4 12.1 + - + +
103B THR* 2.8 38.9 + - - +
128B NO3 2.9 17.5 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B SER* 3.9 13.2 + - - +
80B GLN* 3.8 34.3 - - + +
81B ILE* 3.7 23.8 - - + -
90B LEU* 3.7 21.8 - - + -
92B MET* 3.9 24.5 - - + -
96B ASP 3.1 18.2 + - - +
97B GLN 3.8 3.1 - - - +
99B LEU* 1.3 76.3 - - - +
101B MET* 1.3 92.2 + - + +
103B THR* 3.2 2.1 + - - -
104B ALA* 2.9 25.8 + - - +
112B ILE* 4.6 0.9 - - + -
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B MET* 5.5 0.9 - - - -
97B GLN* 2.9 24.9 + - - +
98B ASP* 3.6 5.6 - - - +
100B LEU* 1.3 114.6 - - + +
102B TYR* 1.3 63.0 + - - +
104B ALA* 3.5 3.0 + - + +
105B GLY* 3.0 19.8 + - - -
112B ILE* 3.8 27.4 - - + +
113B MET* 4.5 19.7 - - - +
119B PHE* 3.9 19.1 - - + -
127B NO3 4.1 16.8 - - - +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 3.7 37.9 - - + +
73B VAL* 5.7 0.9 - - + -
98B ASP 2.9 16.7 + - - +
99B LEU* 3.6 14.1 - - + +
101B MET* 1.3 75.4 - - - +
103B THR* 1.3 66.7 + - - +
105B GLY* 3.2 2.5 + - - -
106B PHE* 2.9 50.0 + + - +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 4.3 18.1 - - + -
74B GLN* 4.9 4.2 + - - +
77B SER* 3.2 27.2 + - - -
78B PHE 4.1 7.6 - - - +
81B ILE* 4.0 16.8 - - + -
99B LEU* 2.8 25.0 + - - +
100B LEU 3.6 4.0 - - - -
102B TYR* 1.3 80.3 - - - +
104B ALA* 1.3 64.8 + - - +
106B PHE* 3.3 4.6 + - - +
107B LEU* 3.0 37.4 + - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.9 11.1 - - + +
100B LEU 2.9 16.1 + - - +
101B MET* 3.7 8.1 - - + +
103B THR* 1.3 76.2 - - - +
105B GLY* 1.3 57.0 + - - +
108B GLN 2.9 21.3 + - - -
109B ILE* 2.9 22.1 + - + +
112B ILE* 3.7 42.8 - - + -
113B MET* 6.4 0.2 - - + -
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET 3.0 15.6 + - - -
102B TYR* 3.6 3.6 - - - -
103B THR 3.2 0.2 - - - -
104B ALA* 1.3 74.8 - - - +
106B PHE* 1.3 65.5 + - - +
108B GLN* 2.9 22.1 + - - +
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 3.4 45.4 - + - +
70B PRO* 3.8 30.7 - - + -
72B ALA* 3.9 19.1 - - + -
73B VAL* 3.7 27.1 - - + -
102B TYR* 2.9 38.2 + + + +
103B THR* 3.5 11.2 - - - +
105B GLY* 1.3 76.9 - - - +
107B LEU* 1.3 62.0 + - + +
108B GLN* 3.4 7.6 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER* 2.6 30.1 + - - +
54B TYR* 3.4 32.8 - - + +
55B PHE* 4.2 12.8 - - + -
69B LEU* 4.4 12.6 - - + -
73B VAL* 4.8 2.9 - - + -
78B PHE* 3.6 33.0 - - + -
81B ILE* 3.9 17.9 - - + -
103B THR* 3.0 27.3 + - + +
106B PHE* 1.3 84.5 - - + +
108B GLN* 1.3 69.4 + - - +
109B ILE* 3.3 16.2 + - + -
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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