Contacts of the helix formed by residues 109 - 116 (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 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B HIS* 4.5 24.5 - - + -
29B GLY 4.1 8.2 + - - +
30B VAL* 6.0 3.8 - - + -
91D ASP* 3.2 5.8 - - - -
108D THR* 1.3 75.1 + - - +
110D ALA* 1.3 69.4 + - - +
111D ALA 3.2 3.1 - - - -
112D ALA* 3.1 13.5 + - - +
113D ASP* 2.8 50.0 + - - +
138D ASN* 4.0 12.1 + - - -
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Residues in contact with ALA 110 (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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30B VAL* 6.5 0.7 - - + -
88D GLN* 2.7 32.2 + - - +
89D HIS* 4.8 10.1 - - + +
91D ASP* 3.1 2.7 + - - +
108D THR* 3.6 11.5 + - - +
109D THR* 1.3 80.0 - - - +
111D ALA* 1.3 58.8 + - - +
113D ASP* 3.5 9.0 + - - +
114D THR* 3.0 15.9 + - - -
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Residues in contact with ALA 111 (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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59D ALA* 3.5 34.4 - - + +
60D THR 5.0 3.8 - - - +
61D GLY* 5.4 0.7 - - - -
86D PHE* 5.0 4.6 - - + -
88D GLN* 3.8 8.0 - - + +
89D HIS 3.5 19.9 + - - +
90D SER* 4.5 2.7 - - - -
91D ASP* 3.1 22.8 + - - +
110D ALA* 1.3 74.7 - - - +
112D ALA* 1.3 66.8 + - - +
114D THR* 3.1 16.1 + - - -
115D PHE 3.5 3.5 + - - -
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Residues in contact with ALA 112 (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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7D GLY 5.3 1.1 - - - +
8D ASN* 4.6 15.5 - - + -
59D ALA* 4.3 10.2 + - - +
91D ASP* 3.1 13.5 + - - +
109D THR* 3.1 15.8 + - - +
111D ALA* 1.3 78.5 - - - +
113D ASP* 1.3 60.8 + - - +
114D THR 3.4 0.7 + - - -
115D PHE* 3.4 10.0 + - - +
120D MSE 4.2 1.4 - - - +
138D ASN* 5.1 3.6 - - + +
139D PHE* 4.0 22.4 - - + -
143D LYS* 2.8 24.2 + - - -
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D THR* 2.8 52.2 + - - +
110D ALA* 3.7 8.5 + - - +
112D ALA* 1.3 79.2 - - - +
114D THR* 1.3 59.0 + - - +
115D PHE 3.4 0.4 + - - -
116D SER* 4.3 6.2 + - - -
138D ASN 5.0 2.4 - - - +
139D PHE* 5.7 4.3 - - - -
140D SER 5.8 1.2 + - - -
143D LYS* 4.3 7.7 + - - +
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Residues in contact with THR 114 (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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86D PHE* 3.8 22.9 - - + -
87D ASN* 4.1 19.7 - - - +
88D GLN* 2.6 34.9 + - - +
110D ALA 3.0 3.6 + - - -
111D ALA 3.1 9.2 + - - -
113D ASP* 1.3 77.7 - - - +
115D PHE* 1.3 68.7 + - - +
116D SER* 4.0 4.8 - - - -
119D GLU* 4.2 2.1 - - - +
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Residues in contact with PHE 115 (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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57D ILE* 3.6 22.2 - - + -
58D ALA* 3.6 21.8 - - - -
59D ALA* 3.7 22.7 - - + -
82D PRO* 3.2 41.7 - - + -
86D PHE* 3.4 17.7 - + + -
111D ALA 3.5 3.0 + - - -
112D ALA* 3.4 8.2 + - - +
113D ASP 3.4 0.4 - - - -
114D THR* 1.3 77.4 - - - +
116D SER* 1.3 69.8 + - - +
119D GLU* 2.8 47.2 - - + +
120D MSE 3.4 39.9 - - + -
123D HIS* 4.2 1.6 - + - -
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Residues in contact with SER 116 (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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113D ASP 4.3 3.8 + - - -
114D THR 3.4 6.6 - - - -
115D PHE* 1.3 86.6 + - - +
117D LEU* 1.3 58.7 + - - +
118D ASP* 3.9 7.5 + - - +
119D GLU* 2.9 30.8 + - - +
120D MSE 3.1 16.5 + - - +
143D LYS* 3.6 13.9 - - - +
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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