Contacts of the helix formed by residues 93 - 104 (chain B) in PDB entry 1IXR
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 PRO 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B LEU 5.6 0.4 - - - +
91B ALA 3.9 3.6 - - - +
92B LEU* 1.3 90.6 - - + +
94B PRO* 1.3 78.4 - - + +
95B ARG* 4.7 3.1 - - + +
96B LEU* 3.3 23.0 + - + +
97B LEU* 2.8 17.8 + - - +
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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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64B ASP* 5.8 2.2 - - - +
66B GLU* 5.1 11.7 - - + -
67B ASN* 3.9 27.4 - - - +
70B LEU* 4.7 17.6 - - + +
89B LEU* 4.9 8.4 - - + +
92B LEU 3.7 1.5 - - - +
93B PRO* 1.3 83.9 - - + +
95B ARG* 1.3 62.9 + - + +
97B LEU* 2.5 30.9 + - + +
98B ALA* 2.6 16.3 + - - +
135B LEU* 5.8 1.3 - - + -
138B GLY* 6.5 0.4 - - - -
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Residues in contact with ARG 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 PRO* 3.4 4.0 - - + -
94B PRO* 1.3 85.9 - - + +
96B LEU* 1.3 58.5 + - - +
98B ALA* 2.9 20.2 + - - +
99B ARG* 3.0 21.4 + - - +
135B LEU* 5.2 1.5 - - - +
136B LEU 2.9 31.2 - - - +
137B ALA* 4.1 17.4 - - - +
138B GLY* 4.5 12.2 + - - +
140B LYS* 6.1 1.0 - - - +
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Residues in contact with LEU 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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92B LEU* 3.6 17.5 - - + -
93B PRO* 3.3 29.0 + - + +
94B PRO 3.2 0.8 - - - -
95B ARG* 1.3 78.9 - - - +
97B LEU* 1.3 56.8 + - - +
99B ARG* 3.7 6.8 - - + +
100B ALA* 3.0 22.7 + - - +
108B LEU* 3.0 36.3 - - + -
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Residues in contact with LEU 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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70B LEU* 4.8 6.1 - - + -
74B LEU* 4.8 7.6 - - + -
88B LEU* 4.0 28.3 - - + +
89B LEU* 3.2 35.0 - - + +
92B LEU* 3.5 25.1 - - + +
93B PRO 2.8 12.9 + - - +
94B PRO* 2.5 17.6 + - + +
96B LEU* 1.3 71.6 - - - +
98B ALA* 1.3 53.4 + - - +
100B ALA* 4.1 0.7 - - + -
101B LEU* 2.7 53.4 + - + +
109B LEU* 3.7 25.1 - - + -
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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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70B LEU* 4.3 21.0 - - + +
94B PRO 2.6 13.9 + - - +
95B ARG* 3.2 12.1 - - - +
97B LEU* 1.3 71.3 - - - +
99B ARG* 1.3 69.5 + - - +
101B LEU* 3.3 4.2 + - - +
102B LEU* 2.9 20.4 + - - +
131B VAL* 4.0 5.9 - - - +
132B PRO* 5.1 2.7 - - + -
135B LEU* 3.0 31.4 - - + +
136B LEU* 4.3 9.2 - - + -
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Residues in contact with ARG 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 ARG* 3.0 14.1 + - - +
96B LEU* 3.7 11.2 - - + +
98B ALA* 1.3 76.5 - - - +
100B ALA* 1.3 56.1 + - - +
102B LEU* 2.6 33.8 + - - +
103B GLU* 2.9 44.0 + - - +
136B LEU* 4.0 39.9 + - - +
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Residues in contact with ALA 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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96B LEU 3.0 17.2 + - - +
97B LEU* 3.5 8.1 - - - +
99B ARG* 1.3 80.2 - - - +
101B LEU* 1.3 54.0 + - - +
103B GLU* 4.8 2.2 - - - -
104B GLY* 2.6 31.9 + - - -
105B ASP* 3.1 32.3 + - + -
108B LEU* 4.3 20.0 - - + -
109B LEU* 4.5 10.7 - - + +
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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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70B LEU* 4.1 20.9 - - + -
73B LEU* 4.4 7.2 - - + -
74B LEU* 3.5 28.7 - - + -
88B LEU* 5.7 0.2 - - + -
97B LEU* 2.7 31.9 + - + +
98B ALA 3.4 5.4 - - - +
100B ALA* 1.3 73.0 - - - +
102B LEU* 1.3 65.4 + - - +
104B GLY* 4.0 4.8 + - - -
109B LEU* 4.4 16.6 - - + -
123B ILE* 3.9 32.1 - - + +
124B ALA* 4.6 3.1 - - - +
127B LEU* 3.5 36.1 - - + +
128B LYS* 3.9 1.2 + - - -
131B VAL* 4.1 10.3 - - + -
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Residues in contact with LEU 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 2.9 11.3 + - - +
99B ARG* 2.6 19.9 + - - +
101B LEU* 1.3 75.9 - - - +
103B GLU* 1.3 71.9 + - + +
128B LYS* 3.1 22.6 - - + +
129B GLY* 3.2 25.5 + - - +
131B VAL* 3.3 32.5 - - + +
132B PRO* 3.9 10.3 - - + -
136B LEU* 4.3 13.5 - - + -
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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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99B ARG* 2.9 45.1 + - + +
100B ALA* 4.1 2.8 + - - +
102B LEU* 1.3 87.7 - - + +
104B GLY* 1.3 59.6 + - - +
105B ASP* 4.8 15.7 - - - +
128B LYS* 3.4 25.5 + - - +
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Residues in contact with GLY 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 ALA 2.6 16.7 + - - -
101B LEU 4.3 4.3 - - - -
102B LEU 3.3 2.6 - - - -
103B GLU* 1.3 76.4 - - - +
105B ASP* 1.3 55.2 + - - +
106B ALA* 2.7 17.8 + - - +
109B LEU* 5.8 0.2 - - - -
124B ALA* 3.7 25.5 - - - +
128B LYS* 5.2 3.1 - - - -
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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