Contacts of the helix formed by residues 93 - 101 (chain B) in PDB entry 1II7
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.5 7.2 - - - +
82B GLU* 2.9 41.6 + - - -
86B ASP 4.0 11.9 - - - -
88B THR* 3.5 16.3 + - - -
91B GLY 3.6 0.2 + - - -
92B PRO* 1.3 76.1 - - - +
94B VAL* 1.3 65.7 + - - +
95B LEU* 3.2 11.8 + - - +
96B ASN* 2.9 23.0 + - - +
97B LEU* 3.2 8.8 + - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.5 18.6 - - + +
51B PHE* 3.2 46.4 - - + -
53B SER 4.9 0.2 - - - +
54B SER 4.8 1.5 + - - +
56B PRO* 3.9 15.5 - - + -
61B LEU* 3.3 34.1 - - + -
86B ASP* 4.3 18.3 + - + +
93B SER* 1.3 73.3 - - - +
95B LEU* 1.3 59.7 + - + +
97B LEU* 3.3 7.5 + - + +
98B LEU* 2.9 29.7 + - + +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.8 35.4 - - + -
51B PHE* 4.6 3.4 - - + -
80B ALA* 4.0 20.0 - - + +
81B ILE* 3.3 38.4 - - - +
82B GLU* 3.5 18.4 - - + +
86B ASP* 4.4 9.2 - - - +
93B SER* 3.1 7.8 + - - +
94B VAL* 1.3 77.7 - - + +
96B ASN* 1.3 59.8 + - - +
98B LEU* 3.1 11.7 + - + +
99B GLU 2.8 24.8 + - - -
104B VAL* 3.6 11.6 - - + +
106B VAL* 3.6 18.2 - - + +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 5.1 5.2 - - - -
82B GLU* 4.1 4.6 + - - +
91B GLY 4.8 0.2 - - - +
92B PRO* 3.4 21.2 - - + +
93B SER* 2.9 32.8 + - - +
95B LEU* 1.3 76.5 - - - +
97B LEU* 1.3 63.7 + - - +
99B GLU* 3.1 16.0 + - - +
100B ASP* 3.1 20.4 + - - +
106B VAL* 4.2 23.8 - - - +
110B ARG* 5.3 11.3 - - - +
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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
----------------------------------------------------------
58A PRO* 4.3 12.8 - - + +
61A LEU* 4.1 27.4 - - + -
62A LYS* 4.1 38.4 - - + +
65A ILE* 4.3 6.5 - - + -
97A LEU* 6.3 0.7 - - + -
101A PHE* 6.3 0.2 - - + -
61B LEU* 4.7 17.7 - - + -
92B PRO* 5.3 1.2 - - + +
93B SER 3.2 9.1 + - - +
94B VAL* 3.4 10.8 - - + +
96B ASN* 1.3 79.2 - - - +
98B LEU* 1.3 64.4 + - + +
100B ASP* 3.1 21.6 + - - +
101B PHE* 3.3 48.0 + - + -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.1 7.6 - - + -
51B PHE* 3.8 33.0 - - + -
61B LEU* 5.3 4.5 - - + -
64B ALA* 5.0 0.7 - - + -
65B ILE* 4.1 27.1 - - + +
68B LEU* 3.6 29.6 - - + -
94B VAL* 2.9 22.6 + - + +
95B LEU* 3.1 13.0 + - + +
97B LEU* 1.3 77.7 - - + +
99B GLU* 1.3 62.2 + - - +
101B PHE* 3.0 22.8 + - + +
102B GLY 3.2 0.2 + - - -
103B LEU* 3.1 24.7 + - + +
104B VAL* 3.9 13.7 - - + -
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Residues in contact with GLU 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 LEU 2.8 13.0 + - - +
96B ASN* 3.1 10.9 + - - +
98B LEU* 1.3 70.9 - - - +
100B ASP* 1.3 60.5 + - - +
101B PHE 3.0 1.8 - - - -
102B GLY* 2.7 23.8 + - - +
104B VAL* 3.2 24.8 - - - +
105B TYR* 4.3 4.9 - - + -
106B VAL* 3.0 24.5 + - + +
110B ARG* 2.7 44.7 + - - -
114B VAL* 4.7 5.0 - - - +
116B ASN* 5.2 1.9 + - - -
119B LEU* 3.9 13.1 - - - +
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 2.8 45.1 + - - +
96B ASN* 3.1 14.3 + - - +
97B LEU* 3.1 13.7 + - + +
99B GLU* 1.3 77.8 - - - +
101B PHE* 1.3 70.9 + - + +
102B GLY 3.4 0.7 + - - -
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Residues in contact with PHE 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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65A ILE* 3.8 28.5 - - + -
101A PHE* 3.8 16.2 - + - -
65B ILE* 3.8 35.7 - - + -
72B LYS* 4.9 3.8 + - - -
97B LEU* 3.5 45.8 - - + -
98B LEU* 3.0 18.1 + - + +
99B GLU 3.0 1.4 - - - -
100B ASP* 1.3 87.4 - - + +
102B GLY* 1.3 60.2 + - - +
103B LEU* 3.5 18.7 + - + +
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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