Contacts of the helix formed by residues 103 - 116 (chain B) in PDB entry 1ISA
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLY 4.3 6.7 - - - -
87B GLU* 3.9 42.0 - - + +
88B PRO* 3.8 26.2 - - + -
93B ALA* 6.5 1.8 - - + -
96B ILE* 4.0 16.9 - - + +
97B ALA* 5.2 1.4 - - - +
102B SER* 1.3 72.1 - - - +
104B ALA* 1.3 62.7 + - - +
106B PHE* 3.3 26.9 + + - -
107B LYS* 2.9 57.1 + - + +
178B TRP* 4.6 7.2 - + - -
183B TRP* 3.8 22.7 - + - -
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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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102B SER* 3.4 9.5 + - - +
103B PHE* 1.3 81.2 - - - +
105B ASP* 1.3 60.3 + - - +
107B LYS* 3.5 8.0 + - - +
108B ALA* 3.1 27.2 + - - +
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Residues in contact with ASP 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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100B PHE 3.3 24.1 - - - +
101B GLY* 4.4 3.3 - - - -
102B SER* 3.4 19.0 + - - +
103B PHE 3.2 0.6 - - - -
104B ALA* 1.3 78.8 - - - +
106B PHE* 1.3 65.2 + - - +
108B ALA* 3.3 6.5 + - - +
109B GLN* 3.0 38.1 + - - +
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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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96B ILE* 3.8 20.6 - - + -
100B PHE* 3.8 36.6 - + + +
102B SER 3.2 14.2 + - - +
103B PHE* 3.7 28.7 - + - +
105B ASP* 1.3 72.4 - - - +
107B LYS* 1.3 66.3 + - - +
109B GLN* 3.1 3.3 + - - +
110B PHE* 2.9 43.6 + + + +
125B LEU* 3.8 36.1 - - + -
135B ILE* 4.1 7.6 - - + -
153B LEU* 4.3 7.0 - - + -
178B TRP* 3.7 33.4 - + - -
183B TRP* 4.2 7.9 - + - -
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Residues in contact with LYS 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 PHE* 2.9 45.1 + - + +
104B ALA* 3.7 8.1 - - - +
106B PHE* 1.3 80.6 - - - +
108B ALA* 1.3 62.7 + - - +
110B PHE* 3.5 1.0 + - - +
111B THR* 2.8 32.8 + - - +
175B GLU 5.7 0.4 + - - -
178B TRP* 3.7 50.5 - - + +
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Residues in contact with ALA 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 ALA 3.1 15.2 + - - +
105B ASP* 3.5 11.9 - - - +
107B LYS* 1.3 76.9 - - - +
109B GLN* 1.3 64.0 + - + +
111B THR* 3.5 5.6 + - - -
112B ASP* 3.0 25.7 + - - +
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Residues in contact with GLN 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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100B PHE* 3.8 29.2 + - - +
105B ASP* 3.0 34.4 + - - +
106B PHE 3.7 0.9 - - - +
108B ALA* 1.3 77.4 - - + +
110B PHE* 1.3 62.7 + - - +
112B ASP* 3.4 6.2 + - - +
113B ALA* 3.0 24.6 + - - +
135B ILE* 3.7 15.5 - - + +
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Residues in contact with PHE 110 (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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106B PHE* 2.9 33.1 + + + +
107B LYS 3.9 3.1 - - - +
109B GLN* 1.3 76.3 - - - +
111B THR* 1.3 62.6 + - - +
113B ALA* 3.3 2.4 + - - +
114B ALA* 2.9 24.8 + - - +
123B THR* 3.5 28.1 - - + +
124B TRP 3.7 25.6 - - - -
125B LEU* 3.8 8.3 - - + -
135B ILE* 3.4 19.8 - - + +
153B LEU* 4.4 11.0 - - + -
154B THR 4.4 1.6 - - - -
155B VAL* 3.5 27.4 - - + -
174B LEU* 4.5 5.2 - - + -
177B PHE* 3.7 20.4 - + - -
178B TRP* 3.6 25.4 - + + -
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Residues in contact with THR 111 (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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107B LYS* 2.8 20.7 + - - +
108B ALA* 3.7 6.1 - - - -
110B PHE* 1.3 74.4 - - - +
112B ASP* 1.3 57.5 + - - +
114B ALA* 3.2 7.1 + - - +
115B ILE* 2.9 52.3 + - + +
171B PRO 5.9 0.7 - - - +
174B LEU* 4.4 17.3 - - + -
175B GLU* 5.9 0.7 - - - +
178B TRP* 3.1 23.9 + - - +
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Residues in contact with ASP 112 (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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108B ALA 3.0 18.5 + - - +
109B GLN* 3.7 6.5 - - - +
111B THR* 1.3 78.7 - - - +
113B ALA* 1.3 62.8 + - - +
115B ILE* 3.5 7.6 + - - +
116B LYS* 2.9 65.2 + - - +
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Residues in contact with ALA 113 (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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109B GLN 3.0 17.2 + - - +
110B PHE 3.7 3.8 - - - +
112B ASP* 1.3 77.2 + - - +
114B ALA* 1.3 61.1 + - - +
116B LYS* 3.5 4.7 + - - +
117B ASN* 3.2 22.9 + - - +
123B THR* 3.9 7.6 - - + -
135B ILE* 3.8 23.3 - - + -
137B SER* 3.7 11.3 + - - +
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Residues in contact with ALA 114 (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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110B PHE* 2.9 17.5 + - + +
111B THR 3.6 3.6 - - - +
113B ALA* 1.3 75.9 - - - +
115B ILE* 1.3 60.5 + - - +
117B ASN* 3.4 7.1 + - - +
123B THR* 3.3 17.9 + - - +
155B VAL* 4.0 13.2 - - + -
157B VAL* 3.8 6.6 - - + +
170B ARG* 2.9 25.4 + - - -
174B LEU* 3.9 30.7 - - + -
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Residues in contact with ILE 115 (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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111B THR* 2.9 38.4 + - + +
112B ASP* 3.8 7.9 - - - +
114B ALA* 1.3 76.8 - - - +
116B LYS* 1.3 69.2 + - + +
117B ASN 4.5 0.2 - - - +
170B ARG* 3.5 23.0 + - + +
171B PRO* 3.9 43.5 - - + -
174B LEU* 4.8 7.4 - - + -
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Residues in contact with LYS 116 (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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112B ASP* 2.9 52.5 + - - +
113B ALA* 3.8 5.2 - - - +
114B ALA 3.4 0.2 - - - -
115B ILE* 1.3 83.0 - - + +
117B ASN* 1.3 58.3 + - - +
118B PHE* 2.9 14.3 + - - +
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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