Contacts of the strand formed by residues 92 - 97 (chain D) 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 THR 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.6 24.6 - - - -
31B LYS* 4.8 13.5 + - + +
10D THR* 3.8 3.6 - - - -
11D VAL* 3.4 20.6 - - + +
13D GLU* 5.5 7.9 - - + -
65D ASN* 3.9 22.7 - - - +
90D SER 3.4 11.0 - - - +
91D ASP* 1.3 81.1 - - - +
93D SER* 1.3 63.5 + - - +
106D ILE 4.0 0.9 - - - +
107D THR* 3.6 1.7 - - - +
108D THR* 2.8 34.6 + - - +
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 3.8 2.6 + - - -
11D VAL 3.0 7.8 + - - +
12D ASP* 3.4 19.9 - - - -
13D GLU* 2.9 29.9 + - - +
92D THR* 1.3 74.5 - - - +
94D ILE* 1.3 63.1 + - - +
95D ILE* 3.7 2.1 + - - -
105D ILE* 4.3 6.1 - - - -
106D ILE 3.3 4.3 - - - -
107D THR* 2.8 33.3 + - - +
501D GOL 2.9 20.3 + - - -
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Residues in contact with ILE 94 (chain D).
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* 5.5 0.4 - - - +
15B TRP* 3.4 52.5 - - + +
93B SER* 3.8 20.4 - - - +
95B ILE* 6.0 3.6 - - + -
13D GLU* 3.7 17.0 - - - +
15D TRP* 4.2 16.4 - - + +
93D SER* 1.3 72.1 - - - +
95D ILE* 1.3 62.3 + - - +
96D LEU* 3.6 29.8 - - + +
104D ALA 3.7 0.9 - - - +
105D ILE* 3.4 5.5 - - - +
106D ILE* 2.9 43.9 + - + +
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASP* 3.7 33.2 - - + -
13D GLU 2.8 14.7 + - - +
14D THR* 3.4 21.4 - - + +
15D TRP 2.8 27.5 + - - -
93D SER* 4.4 6.3 - - - +
94D ILE* 1.3 76.3 - - - +
96D LEU* 1.3 60.3 + - - +
97D ASN 3.2 4.3 + - - -
103D ASN* 4.1 25.4 - - + -
104D ALA 3.7 2.7 - - - -
105D ILE* 4.3 21.3 - - + -
228D THR* 3.9 33.2 - - + +
270D THR* 4.8 0.9 - - - +
501D GOL 4.8 3.8 - - - -
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 5.8 0.7 - - + -
21B PRO* 5.3 5.4 - - + -
95B ILE* 4.9 11.7 - - + -
106B ILE* 3.8 31.9 - - + -
15D TRP* 3.6 19.3 - - + -
17D ILE* 3.9 20.2 - - + -
20D ILE* 5.0 9.4 - - + +
21D PRO* 4.9 6.1 - - + -
94D ILE* 3.6 25.8 - - + +
95D ILE* 1.3 67.7 - - - +
97D ASN* 1.3 60.6 + - - +
98D SER* 2.9 10.1 + - - -
102D ASP 4.7 0.2 - - - +
103D ASN* 3.4 2.0 - - - -
104D ALA* 2.8 48.4 + - + +
106D ILE* 5.2 9.6 - - + -
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 4.1 18.9 - - + +
15D TRP 2.6 17.9 + - - +
16D SER* 4.1 19.5 + - - -
17D ILE* 3.4 17.9 + - - +
32D VAL* 5.7 2.4 - - - +
95D ILE 3.2 3.0 + - - -
96D LEU* 1.3 67.7 - - - +
98D SER* 1.3 72.0 + - - +
99D ALA* 3.2 9.6 + - - +
101D GLY 5.4 0.5 - - - +
103D ASN* 2.9 26.8 + - - +
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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