Contacts of the strand formed by residues 91 - 96 (chain B) in PDB entry 3IKH
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 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 3.7 7.2 - - - -
11B VAL* 2.8 30.1 - - + +
13B GLU* 4.7 4.2 - - - +
63B ASP* 4.9 0.2 - - - +
65B ASN* 3.0 25.4 + - - +
89B HIS* 3.0 18.7 - - - +
90B SER* 1.3 75.8 - - - +
92B THR* 1.3 59.9 + - - +
107B THR* 3.5 4.8 - - - -
108B THR* 3.0 30.7 + - - -
15D TRP* 3.0 31.8 - - - -
31D LYS* 3.9 8.1 - - - +
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Residues in contact with THR 92 (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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10B THR* 5.4 0.7 - - - -
11B VAL 3.0 7.2 + - - +
12B ASP* 2.6 42.6 + - + +
13B GLU* 2.7 34.6 + - - +
91B ASP* 1.3 75.2 - - - +
93B SER* 1.3 56.1 + - - +
94B ILE* 4.3 10.1 - - + -
105B ILE* 2.8 24.1 - - + +
106B ILE 3.2 3.6 - - - -
107B THR* 2.8 26.5 + - - -
15D TRP* 4.7 2.0 - - - -
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Residues in contact with SER 93 (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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13B GLU* 3.6 7.4 - - - -
15B TRP* 4.1 8.9 - - - -
92B THR* 1.3 71.8 - - - +
94B ILE* 1.3 61.2 + - - +
95B ILE* 3.7 14.6 + - - +
104B ALA 3.5 2.3 - - - +
105B ILE* 3.4 6.1 - - - +
106B ILE* 2.8 43.5 + - - +
15D TRP* 4.2 19.7 - - - -
94D ILE* 3.8 23.9 - - - +
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Residues in contact with ILE 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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12B ASP* 4.2 23.6 - - + +
13B GLU 2.6 17.7 + - - +
14B THR* 3.7 26.5 - - + +
15B TRP* 2.8 34.0 + - - +
92B THR* 4.3 11.4 - - + -
93B SER* 1.3 73.6 + - - +
95B ILE* 1.3 60.1 + - - +
96B LEU* 5.0 1.1 - - + +
103B ASN* 3.7 34.8 - - + +
104B ALA 3.8 2.0 - - - -
105B ILE* 4.3 15.9 - - + -
228B THR* 5.8 7.0 - - + +
270B THR* 5.3 2.5 - - - +
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Residues in contact with ILE 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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15B TRP* 4.0 10.3 - - + -
17B ILE* 3.2 37.2 - - + -
20B ILE* 4.3 13.2 - - + -
93B SER* 4.1 14.8 - - - +
94B ILE* 1.3 72.5 - - - +
96B LEU* 1.3 59.0 + - - +
97B ASN* 3.6 9.3 + - - +
102B ASP 4.5 0.5 - - - +
103B ASN* 3.4 4.7 - - - -
104B ALA* 2.7 49.0 + - + +
106B ILE* 4.5 21.5 - - + -
21D PRO* 5.2 4.3 - - + -
94D ILE* 6.0 3.1 - - + -
96D LEU* 4.9 8.1 - - + -
106D ILE* 4.3 20.9 - - + -
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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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14B THR* 5.2 11.2 - - + -
15B TRP 2.9 19.7 + - - +
16B SER* 3.6 14.3 + - - +
17B ILE* 3.0 29.4 + - - +
32B VAL* 5.7 2.0 - - + -
94B ILE* 3.5 2.5 + - + +
95B ILE* 1.3 70.2 - - - +
97B ASN* 1.3 72.1 + - - +
102B ASP* 5.6 1.3 - - - -
103B ASN* 2.8 33.0 - - - +
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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