Contacts of the helix formed by residues 149 - 156 (chain B) in PDB entry 1I7K
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 ASN 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B CYS 5.5 0.4 + - - -
103B TYR* 3.7 28.7 - - - +
104B HIS 3.5 22.8 + - - +
105B PRO* 3.0 6.7 + - - +
107B VAL 3.9 10.1 + - - +
108B ASP* 5.8 0.2 - - - -
147B PRO* 4.4 1.3 - - - -
148B LEU* 1.3 77.9 - - - +
150B THR* 1.3 62.1 + - - +
151B HIS* 3.2 13.2 + - - +
152B ALA* 3.0 21.8 + - - +
153B ALA* 3.0 20.8 + - - +
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Residues in contact with THR 150 (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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147B PRO* 4.3 21.8 - - + +
148B LEU 4.0 2.0 - - - -
149B ASN* 1.3 69.6 + - - +
151B HIS* 1.3 67.2 + - - +
153B ALA* 3.3 9.0 + - - +
154B GLU* 3.1 35.7 + - - +
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Residues in contact with HIS 151 (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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103B TYR* 2.5 36.4 + + + -
149B ASN* 3.2 10.0 + - - +
150B THR* 1.3 82.4 + - - +
152B ALA* 1.3 61.0 + - - +
154B GLU* 3.4 5.1 + - - +
155B LEU* 3.2 31.6 + - + +
165B TYR* 4.2 24.6 + + - -
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Residues in contact with ALA 152 (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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103B TYR* 3.4 28.6 + - + -
104B HIS 3.8 4.0 - - - +
105B PRO* 3.7 21.3 - - - +
149B ASN* 3.0 27.9 + - - +
151B HIS* 1.3 77.1 - - - +
153B ALA* 1.3 64.7 + - - +
155B LEU 3.3 0.2 + - - -
156B TRP* 2.9 25.1 + - - +
162B PHE* 3.5 10.2 - - + -
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Residues in contact with ALA 153 (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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105B PRO* 3.7 3.9 - - + +
144B ILE* 3.5 44.1 - - + +
147B PRO* 3.9 21.8 - - + -
149B ASN 3.0 13.3 + - - +
150B THR* 3.3 9.4 + - - +
152B ALA* 1.3 77.4 - - - +
154B GLU* 1.3 63.0 + - + +
156B TRP* 3.5 12.3 - - - +
157B LYS* 4.5 2.3 + - - +
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Residues in contact with GLU 154 (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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150B THR* 3.1 25.1 + - - +
151B HIS* 3.9 5.8 - - - +
152B ALA 3.2 0.2 - - - -
153B ALA* 1.3 77.3 - - + +
155B LEU* 1.3 62.9 + - - +
156B TRP 3.4 0.3 + - - -
157B LYS* 3.7 21.3 + - - +
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Residues in contact with LEU 155 (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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103B TYR* 3.6 18.8 - - + +
151B HIS* 3.2 23.8 + - + +
152B ALA 3.9 0.7 - - - +
154B GLU* 1.3 72.0 - - - +
156B TRP* 1.3 66.8 + - - +
157B LYS 2.9 4.6 + - - -
158B ASN* 2.9 26.9 + - + +
161B ALA* 3.5 29.6 - - + +
162B PHE* 3.5 31.8 - - + +
165B TYR* 3.8 23.3 - - + -
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Residues in contact with TRP 156 (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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72B THR* 6.3 0.2 - - - -
73B VAL* 3.8 29.8 - - + -
74B TYR* 3.9 8.1 - + - -
105B PRO* 4.5 5.4 - - + -
139B LEU 3.4 25.6 - - - -
140B GLY* 3.5 14.8 - - - -
142B PRO* 3.3 30.0 - - + +
144B ILE* 4.0 22.0 - - + +
152B ALA 2.9 16.7 + - - +
153B ALA 3.5 11.7 - - - +
154B GLU 3.2 0.4 - - - -
155B LEU* 1.3 76.5 - - - +
157B LYS* 1.3 63.3 + - - +
158B ASN 3.2 0.9 + - - -
159B PRO* 3.9 15.7 - - + +
162B PHE* 3.6 30.0 - + - +
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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