Contacts of the helix formed by residues 90 - 104 (chain B) in PDB entry 1I3R
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 GLN 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B LEU 5.6 0.2 + - - -
86B ASN* 2.6 46.4 + - - +
87B TRP* 3.2 22.7 + - - +
88B ASN 3.3 0.9 - - - -
89B SER* 1.3 81.3 - - - +
91B PRO* 1.3 68.0 - - - +
92B GLU* 3.3 2.5 - - + -
93B PHE* 3.0 30.7 + - + +
94B LEU* 3.2 10.8 + - - +
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Residues in contact with PRO 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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89B SER 3.0 15.5 - - - +
90B GLN* 1.3 82.2 - - - +
92B GLU* 1.3 69.0 + - + +
94B LEU* 3.3 10.8 + - + +
95B GLU* 3.1 25.2 + - - +
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Residues in contact with GLU 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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90B GLN* 3.3 1.7 - - + -
91B PRO* 1.3 83.2 - - + +
93B PHE* 1.3 62.9 + - - +
95B GLU* 3.5 10.6 + - - +
96B GLN* 3.2 22.8 + - - +
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Residues in contact with PHE 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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9B ASN* 4.4 17.9 - - - -
10B GLU 4.8 0.4 - - - -
11B GLY* 3.8 32.1 - - - -
56B TYR* 5.8 0.9 - - - -
73B PHE* 3.9 20.6 - + - -
87B TRP* 3.6 48.5 - + + -
90B GLN* 3.0 29.6 + - + +
92B GLU* 1.3 77.3 - - - +
94B LEU* 1.3 60.5 + - - +
96B GLN* 3.2 21.8 + - - +
97B LYS* 2.9 39.6 + - + +
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Residues in contact with LEU 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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66B PHE* 4.4 4.5 - - + -
71B GLY 4.0 16.4 - - - +
72B GLU* 4.0 17.5 - - - +
73B PHE* 4.0 22.2 - - + -
87B TRP 3.7 11.0 - - - +
88B ASN* 3.5 44.9 - - - +
90B GLN 3.2 7.6 + - - +
91B PRO* 3.3 10.3 + - + +
93B PHE* 1.3 75.7 - - - +
95B GLU* 1.3 67.0 + - - +
97B LYS* 3.2 3.6 + - - +
98B ARG* 2.8 49.8 + - - +
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Residues in contact with GLU 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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91B PRO 3.1 14.6 + - - +
92B GLU* 3.6 13.8 - - - +
94B LEU* 1.3 77.2 - - - +
96B GLN* 1.3 64.6 + - - +
98B ARG* 3.2 13.7 + - - +
99B ALA* 2.9 24.8 + - + +
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Residues in contact with GLN 96 (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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9B ASN* 3.2 43.8 + - - +
92B GLU 3.2 10.6 + - - +
93B PHE* 3.3 25.7 - - - +
95B GLU* 1.3 79.6 - - - +
97B LYS* 1.3 64.1 + - - +
99B ALA* 3.0 17.5 + - - +
100B GLU* 3.1 28.2 + - + +
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Residues in contact with LYS 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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8B PHE* 4.4 6.3 - - - +
9B ASN 2.7 31.8 + - - +
10B GLU* 4.3 8.3 + - - -
39B SER* 5.4 0.8 + - - -
52B LEU* 4.0 12.3 - - - +
54B VAL* 4.3 22.1 - - - +
56B TYR* 4.9 5.1 + - - -
66B PHE* 4.0 29.6 - - + -
73B PHE* 4.0 25.4 - - + -
93B PHE* 2.9 25.4 + - + +
94B LEU* 3.6 8.3 - - - +
96B GLN* 1.3 77.2 - - - +
98B ARG* 1.3 62.9 + - - +
100B GLU* 2.8 39.9 + - - +
101B VAL* 4.3 0.5 + - - +
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Residues in contact with ARG 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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66B PHE* 4.1 12.6 - - + -
68B SER* 6.2 0.4 - - - -
71B GLY* 2.8 37.2 + - - +
72B GLU* 3.7 18.8 + - - +
94B LEU* 2.8 41.3 + - - +
95B GLU* 3.5 10.1 - - - +
97B LYS* 1.3 75.0 - - - +
99B ALA* 1.3 61.1 + - - +
100B GLU 3.3 0.2 - - - -
101B VAL* 3.5 20.9 + - - +
102B ASP* 5.8 0.2 - - - +
2C LYS* 6.2 0.2 - - - +
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Residues in contact with ALA 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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95B GLU* 2.9 13.9 + - + +
96B GLN* 3.0 13.2 + - - +
98B ARG* 1.3 75.8 - - - +
100B GLU* 1.3 56.9 + - - +
101B VAL 3.0 6.1 - - - -
102B ASP* 2.8 25.2 + - + +
103B THR* 2.9 24.5 + - + +
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Residues in contact with GLU 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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7B ALA 4.7 0.7 - - - +
8B PHE* 3.3 25.9 - - + -
9B ASN* 3.2 28.8 + - - +
52B LEU* 4.4 5.1 - - + +
96B GLN* 3.1 24.9 + - + +
97B LYS* 2.8 47.3 + - - +
99B ALA* 1.3 72.1 - - - +
101B VAL* 1.3 56.2 + - - +
102B ASP 3.0 5.8 - - - -
103B THR* 3.3 13.7 - - - +
104B VAL* 2.9 32.1 + - + +
105B CYS* 3.0 13.2 + - - +
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Residues in contact with VAL 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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50B VAL* 4.0 33.4 - - + +
52B LEU* 3.9 15.9 - - + +
68B SER* 3.7 28.7 - - - +
97B LYS 4.6 0.7 - - - +
98B ARG* 3.5 19.7 - - - +
99B ALA 3.0 0.4 - - - -
100B GLU* 1.3 77.7 - - - +
102B ASP* 1.3 58.4 + - + +
105B CYS* 3.4 10.8 - - + +
106B ARG* 3.2 38.7 + - - +
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Residues in contact with ASP 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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99B ALA* 2.8 11.2 + - + +
101B VAL* 1.3 80.7 - - + +
103B THR* 1.3 70.6 + - + +
104B VAL 3.2 1.3 - - - -
106B ARG* 3.7 24.6 + - - +
107B HIS* 3.2 23.7 + - - +
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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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6B THR* 3.0 18.9 + - - +
99B ALA* 2.9 31.2 + - + +
100B GLU* 3.3 13.5 - - - +
102B ASP* 1.3 78.9 - - - +
104B VAL* 1.3 64.4 + - - +
107B HIS* 3.3 16.1 - - - +
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Residues in contact with VAL 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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6B THR* 3.7 16.8 - - - +
7B ALA 4.0 15.9 - - - +
8B PHE* 3.4 42.4 - - + +
41B CYS* 5.1 0.2 - - - -
100B GLU* 2.9 28.5 + - + +
102B ASP 3.2 0.2 - - - -
103B THR* 1.3 95.1 - - - +
105B CYS* 1.3 60.0 + - - +
106B ARG 3.7 0.2 - - - -
108B ASN* 3.0 50.3 + - - +
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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