Contacts of the helix formed by residues 100 - 106 (chain B) in PDB entry 1IS2
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 LEU 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A LEU* 5.6 3.4 - - + -
64B VAL 5.5 0.4 - - - +
67B SER* 3.5 34.8 - - - +
68B ALA* 4.1 1.6 - - + +
70B MET* 5.0 0.4 - - + -
71B VAL* 4.2 9.4 - - + -
98B GLU* 2.6 23.2 + - - +
99B PRO* 1.3 74.5 - - + +
101B ASP* 1.3 57.4 + - - +
102B LEU 3.4 2.0 - - - -
103B HIS* 3.2 27.4 + - + +
104B LEU* 2.9 39.3 + - + +
130B LEU* 4.0 20.9 - - + -
133B THR* 4.5 12.3 - - + -
183B THR* 3.7 27.8 - - + -
184B SER* 6.1 0.4 - - - +
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Residues in contact with ASP 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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89B LYS* 3.5 19.9 + - - +
97B PRO* 6.4 0.2 - - - -
98B GLU* 2.8 30.2 + - + +
99B PRO 3.3 1.0 - - - -
100B LEU* 1.3 78.0 - - - +
102B LEU* 1.3 64.7 + - + +
104B LEU* 3.9 2.1 - - - +
105B GLY* 2.9 26.3 + - - -
235B MET* 4.0 16.2 - - + +
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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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99B PRO 5.0 0.8 + - - -
100B LEU 3.4 0.2 - - - -
101B ASP* 1.3 85.3 - - + +
103B HIS* 1.3 61.9 + - - +
105B GLY 5.8 0.2 - - - -
106B MET* 2.6 49.3 + - + +
107B PHE* 2.9 9.3 + - - -
134B GLY 4.3 0.9 - - - -
135B THR* 3.1 21.5 - - - +
136B TYR* 3.7 18.6 - - + +
178B GLY* 3.1 46.9 + - - +
235B MET* 6.1 0.9 - - + -
1699B FAD 3.4 20.2 - - + +
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Residues in contact with HIS 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 PRO 5.2 1.1 + - - +
100B LEU* 3.2 27.6 + - + +
102B LEU* 1.3 79.2 - - - +
104B LEU* 1.3 81.8 + - + +
107B PHE* 3.3 7.7 - + - +
108B LEU* 3.2 45.3 + - + +
127B ALA* 3.6 15.5 - - + +
130B LEU* 4.1 18.6 - - + +
132B ILE 3.3 16.8 + - - -
133B THR* 3.5 10.5 - - + -
134B GLY* 3.0 44.0 + - - +
184B SER* 5.5 0.2 - - - +
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Residues in contact with LEU 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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70B MET* 3.9 28.3 - - + -
71B VAL* 4.5 20.9 - - + -
74B MET* 4.6 10.3 - - + -
85B ILE* 5.7 6.7 - - + -
89B LYS* 6.2 1.6 - - + -
98B GLU* 4.8 3.4 - - - +
100B LEU* 2.9 22.2 + - + +
101B ASP* 4.3 2.2 - - - +
103B HIS* 1.3 102.3 - - + +
105B GLY* 1.3 57.7 + - - +
108B LEU* 3.8 15.6 - - + +
109B PRO* 3.1 19.1 - - - +
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Residues in contact with GLY 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 ASP* 2.9 17.4 + - - -
102B LEU* 4.8 0.4 - - - -
104B LEU* 1.3 79.6 - - - +
106B MET* 1.3 69.7 + - - +
109B PRO* 3.4 17.7 - - - +
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Residues in contact with MET 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 LEU* 2.6 37.0 + - + +
105B GLY* 1.3 82.4 - - - +
107B PHE* 1.3 61.2 + - - +
108B LEU 3.7 0.2 - - - -
109B PRO* 3.7 2.7 - - - -
110B THR* 2.6 49.1 + - - +
136B TYR* 3.4 56.3 - - + -
188B ILE* 4.5 0.3 - - - +
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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