Contacts of the helix formed by residues 82 - 95 (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 PHE 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B SER 5.7 1.5 + - - +
8B LEU* 4.3 7.0 - - + -
16B LEU* 3.6 30.1 - - + -
27B VAL* 3.5 31.0 - - + -
30B TRP* 3.7 14.1 - - + -
31B TYR* 3.4 52.9 - + + -
34B PHE* 3.7 33.7 - + + -
41B GLY 4.2 1.8 + - - +
81B GLU* 1.3 73.7 - - - +
83B SER* 1.3 56.6 + - - +
85B PHE* 4.1 16.2 - + - -
86B ILE* 2.8 47.7 + - + +
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Residues in contact with SER 83 (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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15B GLU* 5.0 4.7 + - - -
16B LEU* 4.1 22.1 - - - +
81B GLU* 3.6 23.0 + - - +
82B PHE* 1.3 77.6 - - - +
84B GLU* 1.3 64.5 + - - +
86B ILE* 3.6 0.9 - - - +
87B GLN* 3.1 48.0 + - - +
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Residues in contact with GLU 84 (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 PHE* 3.4 18.8 - - - +
73B ASP* 3.8 0.6 - - - +
74B GLU* 3.8 20.6 - - + +
75B ASN* 2.8 29.0 + - - +
79B ARG 3.0 3.5 - - - +
80B ILE* 3.2 7.4 - - + -
81B GLU* 2.9 35.5 + - + +
83B SER* 1.3 75.6 - - - +
85B PHE* 1.3 67.3 + - - +
87B GLN* 4.1 4.2 - - - +
88B ALA* 3.1 26.2 + - - +
1600B CA 2.5 30.9 - - - -
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Residues in contact with PHE 85 (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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30B TRP* 4.0 22.2 - + + -
34B PHE* 3.7 41.7 - + + -
43B LEU* 4.7 12.1 - - + -
48B PHE* 5.6 1.8 - + - -
51B ILE* 5.3 9.9 - - + -
72B PHE* 4.1 20.3 - + - -
80B ILE* 3.8 12.5 - - + +
81B GLU 3.0 13.9 + - - +
82B PHE* 3.4 19.5 - + - +
84B GLU* 1.3 78.0 - - - +
86B ILE* 1.3 63.4 + - - +
88B ALA* 3.8 2.1 - - - +
89B LEU* 3.0 56.5 + - + +
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Residues in contact with ILE 86 (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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16B LEU* 3.9 24.9 - - + -
20B THR* 4.3 6.7 - - + -
22B PHE* 3.4 35.6 - - + -
27B VAL* 4.8 9.6 - - + -
30B TRP* 3.8 35.7 - - + -
82B PHE* 2.8 45.8 + - + +
83B SER 3.6 6.1 - - - +
85B PHE* 1.3 75.5 - - + +
87B GLN* 1.3 63.7 + - + +
89B LEU* 3.6 7.2 - - + +
90B SER* 2.8 28.1 + - - -
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Residues in contact with GLN 87 (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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15B GLU* 5.5 1.2 + - - -
16B LEU* 4.3 7.4 - - + +
19B LYS* 4.0 31.5 - - + +
20B THR* 4.0 22.0 - - + -
74B GLU* 5.1 11.4 + - - +
83B SER* 3.1 39.2 + - - +
84B GLU* 4.2 3.9 - - - +
86B ILE* 1.3 76.1 - - + +
88B ALA* 1.3 66.2 + - - +
90B SER* 3.4 1.4 + - - -
91B VAL* 3.2 29.7 + - + +
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Residues in contact with ALA 88 (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 PHE* 3.5 44.6 - - + -
84B GLU 3.1 18.9 + - - +
87B GLN* 1.3 76.1 - - - +
89B LEU* 1.3 64.1 + - - +
90B SER 3.4 0.2 + - - -
91B VAL* 3.4 2.1 + - - +
92B THR* 3.0 29.0 + - - -
103B TRP* 4.4 18.3 + - + +
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Residues in contact with LEU 89 (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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22B PHE* 4.2 3.1 - - + -
30B TRP* 3.7 48.9 - - + +
72B PHE* 4.7 8.9 - - + -
85B PHE* 3.0 37.0 + - + +
86B ILE* 3.6 11.7 - - + +
88B ALA* 1.3 77.4 - - - +
90B SER* 1.3 56.6 + - - +
92B THR* 4.9 5.4 - - + -
93B SER* 2.9 40.6 + - - +
902B EDO 3.7 23.1 - - - +
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Residues in contact with SER 90 (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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19B LYS 4.7 1.2 + - - -
20B THR* 3.3 23.6 - - - -
21B TYR* 3.0 33.3 + - - +
22B PHE* 3.6 13.0 - - - -
86B ILE 2.8 18.1 + - - -
87B GLN 3.6 6.5 - - - -
88B ALA 3.3 0.4 - - - -
89B LEU* 1.3 76.1 - - - +
91B VAL* 1.3 60.0 + - - +
93B SER* 4.6 0.2 - - - -
94B ARG* 2.9 31.1 + - - +
95B GLY 3.2 5.2 + - - -
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Residues in contact with VAL 91 (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* 5.4 4.3 - - + -
87B GLN 3.2 17.4 + - - +
88B ALA 4.1 2.2 - - - +
90B SER* 1.3 76.6 - - - +
92B THR* 1.3 60.5 + - - +
95B GLY* 3.0 26.5 + - - +
99B GLU* 3.4 40.2 - - + +
100B LYS* 3.4 8.6 - - - +
103B TRP* 4.0 26.0 - - + -
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Residues in contact with THR 92 (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 PHE* 5.6 3.4 - - + -
88B ALA 3.0 18.7 + - - -
89B LEU* 4.3 5.4 - - + -
91B VAL* 1.3 77.8 - - - +
93B SER* 1.3 60.0 + - - +
100B LYS* 3.4 20.0 - - - +
103B TRP* 3.8 34.9 - - + +
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Residues in contact with SER 93 (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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22B PHE* 4.5 0.5 - - - -
89B LEU* 2.9 26.4 + - - -
92B THR* 1.3 79.8 - - - +
94B ARG* 1.3 70.4 + - - +
95B GLY 3.8 0.9 - - - -
100B LYS* 4.2 3.6 - - - -
185B LEU 3.4 4.3 - - - +
186B TYR* 3.3 6.9 - - - -
187B ASP* 2.8 36.7 + - - +
188B GLY 5.3 2.2 - - - +
902B EDO 3.4 31.2 - - - -
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Residues in contact with ARG 94 (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* 2.9 48.5 + - + -
22B PHE* 3.5 25.3 - - - -
26B GLU* 2.9 42.0 + - - -
90B SER 2.9 11.7 + - - +
93B SER* 1.3 78.5 - - - +
95B GLY* 1.3 68.7 + - - +
100B LYS* 4.9 0.2 - - - +
186B TYR* 3.3 49.8 + - + +
187B ASP* 2.9 40.5 + - - +
902B EDO 4.2 7.9 + - - -
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Residues in contact with GLY 95 (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* 3.9 7.4 - - - -
90B SER 3.2 2.9 + - - -
91B VAL* 3.0 23.6 + - - -
93B SER 3.8 0.6 - - - -
94B ARG* 1.3 83.1 - - - +
96B THR* 1.3 69.7 + - - +
99B GLU* 3.4 14.1 - - - -
100B LYS* 3.5 17.1 + - - +
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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