Contacts of the helix formed by residues 96 - 109 (chain B) in PDB entry 1G8I
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 THR 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B TYR* 4.2 7.4 - - + +
95B GLY* 1.3 77.1 - - - +
97B LEU* 1.3 65.3 + - - +
98B ASP* 3.6 7.8 + - - +
99B GLU* 2.9 45.3 + - - +
100B LYS* 2.9 21.9 + - - +
183B LEU 5.1 0.4 - - - -
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Residues in contact with LEU 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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96B THR* 1.3 73.7 - - - +
98B ASP* 1.3 59.7 + - - +
100B LYS* 3.3 2.4 + - - +
101B LEU* 3.0 43.4 + - + +
174B LYS* 4.2 24.2 - - + -
180B VAL* 4.3 28.7 - - + +
183B LEU* 3.2 54.2 + - + +
184B SER* 4.5 7.3 - - - +
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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
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96B THR* 3.2 7.9 + - - +
97B LEU* 1.3 80.4 - - - +
99B GLU* 1.3 61.9 + - + +
101B LEU* 3.3 6.9 + - - +
102B ARG* 3.1 31.0 + - - +
170B GLN* 4.0 15.7 + - - +
174B LYS* 2.5 40.1 + - - -
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Residues in contact with GLU 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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21B TYR* 2.8 32.4 + - - -
91B VAL* 3.4 25.1 - - + +
95B GLY* 3.4 5.7 - - - -
96B THR* 2.9 40.8 + - - +
98B ASP* 1.3 74.3 - - + +
100B LYS* 1.3 65.3 + - - +
102B ARG* 3.3 33.5 + - - +
103B TRP 3.2 17.7 + - - -
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Residues in contact with LYS 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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91B VAL* 3.4 24.0 - - - +
92B THR* 3.4 26.0 - - - +
93B SER 4.2 1.9 + - - -
94B ARG 4.9 0.2 - - - -
95B GLY 3.5 21.9 + - - +
96B THR 2.9 17.0 + - - +
97B LEU 3.6 4.3 - - - +
99B GLU* 1.3 77.4 - - - +
101B LEU* 1.3 58.6 + - - +
103B TRP* 3.4 3.7 + - - +
104B ALA* 3.0 29.3 + - - +
182B ALA 5.6 0.2 + - - -
183B LEU* 2.9 49.8 + - + +
184B SER* 4.1 1.4 - - - +
185B LEU* 2.4 33.6 + - - +
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Residues in contact with LEU 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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97B LEU* 3.0 37.2 + - + +
98B ASP* 3.7 5.2 - - - +
100B LYS* 1.3 77.3 - - - +
102B ARG* 1.3 58.6 + - - +
104B ALA* 4.4 2.0 - - + -
105B PHE* 2.9 26.3 + - - +
166B LEU* 5.1 1.1 - - - -
169B PHE* 3.3 18.1 - - + -
170B GLN* 4.1 27.1 - - + +
173B SER* 3.7 31.9 - - - +
174B LYS* 4.2 15.3 - - + -
183B LEU* 3.1 30.7 - - + -
953B 1PE 4.1 8.5 - - - -
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Residues in contact with ARG 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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98B ASP* 3.1 18.1 + - - +
99B GLU* 3.6 37.3 + - - +
100B LYS 3.3 0.2 - - - -
101B LEU* 1.3 76.0 - - - +
103B TRP* 1.3 62.4 + - - +
105B PHE* 3.4 9.0 + - - +
106B LYS* 3.2 25.7 + - + +
166B LEU* 4.4 19.3 - - + -
170B GLN* 4.1 15.3 - - - +
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Residues in contact with TRP 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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68B VAL* 4.3 10.1 - - + -
71B VAL* 3.4 32.7 + - + +
72B PHE* 3.9 34.3 - + - -
88B ALA* 4.4 17.5 - - + +
91B VAL* 4.0 27.1 - - + -
92B THR* 3.8 24.2 - - + +
99B GLU 3.2 10.9 + - - +
100B LYS* 3.7 8.1 - - - +
102B ARG* 1.3 77.4 - - - +
104B ALA* 1.3 71.3 + - + +
106B LYS* 2.9 36.7 + - + +
107B LEU* 3.0 32.0 + - + -
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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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100B LYS 3.0 17.8 + - - +
101B LEU* 3.8 6.5 - - + +
103B TRP* 1.3 84.2 - - + +
105B PHE* 1.3 65.1 + - - +
107B LEU* 3.0 8.9 + - + +
108B TYR* 3.0 37.6 + - + -
169B PHE* 4.0 14.8 - - + -
183B LEU* 5.3 5.2 - - + -
953B 1PE 4.9 9.4 - - - -
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Residues in contact with PHE 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 LEU 2.9 18.5 + - - +
102B ARG 3.4 7.2 - - - +
104B ALA* 1.3 78.3 - - - +
106B LYS* 1.3 60.5 + - + +
108B TYR* 3.2 2.4 + - - +
109B ASP* 2.9 49.2 + - + +
114B GLY* 3.6 23.3 - - - -
115B TYR 4.1 0.2 - - - -
116B ILE* 3.4 34.3 - - + -
164B LEU 3.6 7.0 - - - -
165B THR 3.6 7.0 - - - -
166B LEU* 3.5 51.4 - - + -
169B PHE* 3.6 22.1 - + + -
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Residues in contact with LYS 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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71B VAL* 4.2 33.9 + - + +
74B GLU* 4.9 14.5 - - - +
102B ARG 3.2 14.7 + - - +
103B TRP* 2.9 25.9 + - + +
105B PHE* 1.3 83.3 - - + +
107B LEU* 1.3 63.0 + - - +
109B ASP* 3.7 18.8 + - - +
110B LEU* 5.2 0.2 - - - -
112B ASN* 5.8 3.6 - - - +
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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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64B PHE* 4.3 24.2 - - + -
67B PHE* 3.4 42.4 - - + +
68B VAL* 3.9 12.8 - - + +
71B VAL* 3.7 17.3 - - + +
103B TRP* 3.0 27.5 + - + +
104B ALA* 3.0 12.7 + - + +
106B LYS* 1.3 77.5 - - - +
108B TYR* 1.3 68.4 - - + +
110B LEU* 3.6 20.1 + - - +
124B ILE* 3.8 12.5 - - + +
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Residues in contact with TYR 108 (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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64B PHE* 5.9 0.2 - - - -
104B ALA* 3.0 33.8 + - + +
105B PHE 3.8 0.4 - - - +
107B LEU* 1.3 80.9 - - + +
109B ASP* 1.3 53.4 + - - +
110B LEU* 2.8 21.3 + - - +
116B ILE* 3.5 27.8 - - + +
120B GLU* 3.5 22.5 - - - +
121B MET* 4.1 29.6 - - + -
124B ILE* 3.1 44.4 - - + +
125B VAL* 4.9 0.4 - - + -
128B ILE* 4.3 4.0 - - - +
169B PHE* 3.9 17.5 - + - -
953B 1PE 3.5 53.6 + - - -
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Residues in contact with ASP 109 (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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105B PHE* 2.9 31.0 + - + +
106B LYS* 3.7 13.5 + - - +
107B LEU 3.5 0.6 - - - -
108B TYR* 1.3 72.3 - - - +
110B LEU* 1.3 64.9 + - - +
111B ASP* 3.1 5.2 - - - +
112B ASN* 2.8 21.4 + - - +
113B ASP* 2.8 10.9 + - - +
114B GLY* 2.6 31.7 + - - -
115B TYR 3.6 8.3 - - - +
116B ILE* 4.1 2.6 - - + +
120B GLU* 4.1 5.2 - - - -
1601B CA 2.5 29.2 - - - -
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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