Contacts of the helix formed by residues 96 - 109 (chain B) in PDB entry 4I93
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 ASP 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B TRP* 3.2 4.5 - - - +
95B PRO* 1.3 78.0 - - - +
97B SER* 1.3 60.8 + - - +
98B ARG* 3.0 13.2 + - - +
99B GLN* 3.0 33.2 + - + +
100B PHE* 3.1 21.3 + - - +
207B ARG* 3.5 21.9 + - - +
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Residues in contact with SER 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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95B PRO 3.5 3.8 + - - -
96B ASP* 1.3 72.9 + - - +
98B ARG* 1.3 57.8 + - - +
100B PHE* 3.5 4.9 - - - +
101B LEU* 2.9 29.3 + - - +
123B TYR* 4.0 28.8 + - - -
128B ARG* 3.0 34.7 + - - +
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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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96B ASP* 3.0 10.0 + - - +
97B SER* 1.3 76.0 - - - +
99B GLN* 1.3 60.5 + - - +
101B LEU* 3.4 19.9 + - + +
102B GLU* 2.9 42.5 + - + +
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Residues in contact with GLN 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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94B TRP* 4.2 20.7 - - + -
95B PRO* 5.2 0.5 - - - +
96B ASP* 3.0 24.8 + - - +
98B ARG* 1.3 76.5 - - - +
100B PHE* 1.3 63.2 + - - +
102B GLU* 3.3 6.4 + - - +
103B GLU* 3.0 27.9 + - + +
207B ARG* 2.9 45.5 + - - +
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Residues in contact with PHE 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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89B PHE* 4.1 12.3 - + - -
94B TRP* 3.8 32.4 - + + -
96B ASP 3.1 13.0 + - - +
97B SER 3.5 7.6 - - - +
99B GLN* 1.3 77.5 - - - +
101B LEU* 1.3 59.3 + - - +
103B GLU* 3.3 4.8 + - - +
104B ALA* 2.9 28.8 + - - +
121B CYS* 4.1 12.1 - - + -
122B CYS 3.7 13.2 - - - -
123B TYR* 4.4 10.5 - - + -
128B ARG* 3.7 30.5 - - + -
129B LEU 3.6 36.8 - - - -
130B LEU* 3.8 12.3 - - + -
203B MSE 3.7 23.3 - - + -
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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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41B PHE* 4.1 9.0 - - + -
43B GLU* 3.9 38.1 - - + +
97B SER 2.9 18.0 + - - +
98B ARG* 3.4 22.9 + - + +
100B PHE* 1.3 78.7 - - - +
102B GLU* 1.3 63.5 + - - +
104B ALA* 3.3 4.0 + - - +
105B LYS* 2.9 46.7 + - + +
121B CYS* 3.6 23.1 - - - -
123B TYR* 4.1 17.7 - - + +
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Residues in contact with GLU 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 ARG* 2.9 33.0 + - + +
99B GLN* 3.3 5.8 + - - +
100B PHE 3.3 0.2 - - - -
101B LEU* 1.3 79.2 - - + +
103B GLU* 1.3 65.5 + - - +
105B LYS* 3.5 35.8 + - - +
106B ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 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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94B TRP* 4.3 21.7 - - + -
99B GLN* 3.0 20.1 + - + +
100B PHE* 3.6 5.2 - - - +
102B GLU* 1.3 75.1 - - - +
104B ALA* 1.3 65.9 + - - +
106B ALA* 3.1 6.5 + - - +
107B VAL* 3.0 25.6 + - - +
176B ARG* 3.4 36.4 + - - -
203B MSE 3.9 26.4 - - + +
204B LYS 5.4 0.2 + - - -
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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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41B PHE* 3.5 18.8 - - + -
100B PHE* 2.9 18.3 + - + +
101B LEU 3.3 4.0 + - - +
103B GLU* 1.3 77.0 - - - +
105B LYS* 1.3 56.9 + - - +
107B VAL 3.2 1.6 + - - +
108B GLY 2.8 24.9 + - - -
118B LEU* 3.3 11.4 - - + +
121B CYS* 3.9 11.9 - - + -
130B LEU* 3.8 24.9 - - + -
203B MSE 3.9 9.8 - - - -
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Residues in contact with LYS 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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41B PHE* 3.7 31.2 - - + -
43B GLU* 4.0 20.3 + - - -
101B LEU* 2.9 33.0 + - + +
102B GLU* 3.6 33.1 + - - +
103B GLU 3.3 0.2 - - - -
104B ALA* 1.3 72.0 - - - +
106B ALA* 1.3 62.4 + - - +
108B GLY* 3.1 10.9 + - - -
109B GLN* 3.1 21.5 + - - +
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Residues in contact with ALA 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 GLU 3.1 14.5 + - - +
103B GLU* 3.1 12.3 + - - +
105B LYS* 1.3 76.7 - - - +
107B VAL* 1.3 62.4 + - - +
109B GLN* 3.2 25.4 + - - +
110B LEU* 3.8 9.8 - - - +
176B ARG* 3.7 23.9 - - - +
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Residues in contact with VAL 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 GLU 3.0 12.5 + - - +
104B ALA 3.7 6.5 - - - +
106B ALA* 1.3 74.9 - - - +
108B GLY* 1.3 57.0 + - - +
109B GLN 3.1 0.2 - - - -
110B LEU* 3.1 32.2 + - - +
118B LEU* 3.7 25.6 - - + +
130B LEU* 6.2 1.3 - - + -
176B ARG* 3.8 18.8 - - - +
199B CYS* 4.0 16.2 - - + +
202B LEU* 3.8 29.8 - - + -
203B MSE 3.7 26.2 - - + -
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Residues in contact with GLY 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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41B PHE* 4.0 22.0 - - - +
104B ALA 2.8 15.7 + - - -
105B LYS 3.1 7.8 + - - -
107B VAL* 1.3 76.0 - - - +
109B GLN* 1.3 61.3 + - - +
110B LEU 3.3 7.4 - - - +
111B ARG* 5.1 8.5 + - - +
118B LEU* 3.8 18.7 - - - +
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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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41B PHE* 6.0 1.6 - - - +
105B LYS* 3.1 18.9 + - - +
106B ALA* 3.3 15.0 - - - +
107B VAL 3.1 0.8 - - - -
108B GLY* 1.3 75.6 - - - +
110B LEU* 1.3 68.4 + - + +
111B ARG* 3.5 5.4 + - - +
174B LYS* 4.9 9.5 + - - -
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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