Contacts of the helix formed by residues 93 - 108 (chain B) in PDB entry 1IC8
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 SER 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B GLU* 2.8 41.2 + - - +
91B ASN 3.5 2.6 + - - -
92B LEU* 1.3 74.1 - - - +
94B PRO* 1.3 78.3 - - - +
95B GLU* 3.7 4.7 + - - +
96B GLU* 3.1 32.3 + - - +
97B ALA* 3.1 22.9 + - - +
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Residues in contact with PRO 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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90B GLU* 5.0 2.0 - - - +
92B LEU 4.3 2.9 - - - +
93B SER* 1.3 91.2 - - - +
95B GLU* 1.3 73.9 - - + +
97B ALA* 3.8 2.5 - - + +
98B ALA* 3.0 23.1 + - - +
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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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93B SER* 4.4 4.0 - - - +
94B PRO* 1.3 88.1 - - + +
96B GLU* 1.3 58.3 + - - +
98B ALA* 2.8 29.7 + - - +
99B HIS* 2.8 22.0 + - + +
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Residues in contact with GLU 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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90B GLU* 4.2 14.9 - - + +
91B ASN* 4.7 8.3 - - - +
93B SER* 3.1 32.2 + - - +
95B GLU* 1.3 79.2 - - - +
97B ALA* 1.3 56.9 + - - +
99B HIS* 3.6 8.9 + - - +
100B GLN* 3.1 37.7 + - - +
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Residues in contact with ALA 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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91B ASN 5.7 2.2 - - - +
92B LEU* 5.6 8.7 - - + -
93B SER 3.1 21.0 + - - +
94B PRO* 3.8 2.2 - - + +
96B GLU* 1.3 73.3 - - - +
98B ALA* 1.3 69.6 + - - +
100B GLN* 2.7 32.3 + - + +
101B LYS* 2.9 14.0 + - - +
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Residues in contact with ALA 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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94B PRO 3.0 15.0 + - - +
95B GLU* 2.8 19.2 + - - +
97B ALA* 1.3 76.3 - - - +
99B HIS* 1.3 63.1 + - + +
101B LYS* 3.2 9.0 + - - +
102B ALA* 3.1 21.5 + - - +
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Residues in contact with HIS 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* 2.8 20.4 + - + +
96B GLU* 3.7 13.8 - - - +
98B ALA* 1.3 76.3 - - + +
100B GLN* 1.3 61.5 + - - +
102B ALA* 3.1 10.1 + - + +
103B VAL* 2.9 34.0 + - + +
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Residues in contact with GLN 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 ASN 5.0 6.6 - - - +
96B GLU* 3.1 28.4 + - - +
97B ALA* 2.7 27.7 + - - +
99B HIS* 1.3 71.5 - - + +
101B LYS* 1.3 60.2 + - - +
103B VAL* 2.8 29.6 + - - +
104B VAL* 3.2 12.2 + - + +
167B VAL* 4.2 17.5 + - + +
168B ARG* 4.1 32.5 - - + +
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Residues in contact with LYS 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 ALA 2.9 10.3 + - - +
98B ALA* 3.6 11.2 - - - +
100B GLN* 1.3 76.6 - - - +
102B ALA* 1.3 55.5 + - - +
104B VAL* 3.1 17.4 - - + +
105B GLU* 2.8 32.8 - - + +
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Residues in contact with ALA 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 ALA 3.1 11.8 + - - +
99B HIS* 3.5 15.3 - - + +
100B GLN 3.1 0.6 - - - -
101B LYS* 1.3 76.3 - - - +
103B VAL* 1.3 60.7 + - + +
105B GLU* 3.0 10.5 - - - +
106B THR* 2.8 30.8 + - - +
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Residues in contact with VAL 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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99B HIS* 2.9 23.9 + - + +
100B GLN* 2.8 30.5 - - - +
102B ALA* 1.3 74.8 - - + +
104B VAL* 1.3 62.6 + - - +
106B THR* 2.7 27.2 + - - -
107B LEU* 2.8 23.9 + - + +
167B VAL* 3.8 25.6 - - + -
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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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100B GLN* 3.5 12.6 - - + +
101B LYS* 3.1 21.3 - - + +
103B VAL* 1.3 76.0 - - - +
105B GLU* 1.3 67.3 + - - +
107B LEU* 3.9 8.9 - - - -
108B LEU* 2.8 50.3 + - + +
160B ALA 5.1 0.4 - - - +
163B TYR* 3.9 11.5 - - + -
164B THR* 3.6 42.2 - - + +
167B VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 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 LYS* 2.8 33.0 - - + +
102B ALA* 3.0 13.2 - - - +
104B VAL* 1.3 85.0 - - - +
106B THR* 1.3 54.3 + - - +
108B LEU* 3.9 13.2 - - - +
109B GLN* 2.8 34.1 - - - +
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Residues in contact with THR 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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102B ALA* 2.8 15.0 + - - +
103B VAL* 2.7 20.9 + - - -
105B GLU* 1.3 68.4 - - - +
107B LEU* 1.3 58.4 + - + +
108B LEU 2.9 1.3 - - - -
109B GLN* 2.6 31.6 + - - +
110B GLU* 3.0 25.9 + - + +
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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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103B VAL* 2.8 32.3 + - + +
104B VAL* 4.1 6.3 - - - +
106B THR* 1.3 76.4 - - + +
108B LEU* 1.3 56.7 + - - +
109B GLN 2.9 5.7 + - - -
110B GLU* 2.9 32.0 + - + +
115B VAL* 3.5 31.1 - - + +
118B MET* 4.5 20.4 - - + -
159B ARG* 3.6 5.7 + - - -
163B TYR* 3.7 30.1 - - + -
166B TYR* 4.7 13.7 - - + -
167B VAL* 4.6 12.6 - - + -
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Residues in contact with LEU 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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104B VAL* 2.8 38.3 + - + +
105B GLU* 3.9 21.5 - - - +
106B THR 2.9 0.6 - - - -
107B LEU* 1.3 75.6 - - - +
109B GLN* 1.3 68.9 + - - +
156B THR* 3.9 32.0 + - + +
159B ARG* 3.6 21.0 + - + +
160B ALA* 3.9 29.4 - - + +
163B TYR* 3.5 22.9 - - + -
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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