Contacts of the helix formed by residues 116 - 120 (chain C) in PDB entry 1KI1
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 GLN 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ALA 4.2 13.9 + - - +
14C VAL 4.0 8.1 + - - +
15C GLY* 4.5 6.3 - - - +
83C SER* 2.6 28.9 + - - +
84C VAL* 3.9 3.9 - - - +
85C VAL* 4.4 5.1 - - + +
115C THR* 1.3 89.8 + - + +
117C ILE* 1.3 59.2 + - - +
118C ASP* 3.1 14.4 - - - +
119C LEU* 3.0 48.5 + - + +
120C ARG 3.9 1.6 + - - -
157C CYS 3.4 6.4 + - - -
158C SER* 4.8 2.6 - - - +
159C ALA 5.5 1.9 - - - +
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 3.8 20.6 - - + -
114C GLY 4.5 0.2 - - - +
115C THR 4.2 1.8 - - - +
116C GLN* 1.3 70.4 - - - +
118C ASP* 1.3 68.7 + - - +
119C LEU 3.0 2.2 - - - -
120C ARG* 2.9 32.2 + - - +
121C ASP* 4.3 4.2 + - - +
156C GLU* 3.7 42.4 - - + +
157C CYS* 3.4 35.8 + - - +
158C SER* 3.7 7.2 - - - +
163C LYS* 4.0 34.8 - - + +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1300B ARG* 5.3 4.0 + - - -
116C GLN* 3.6 13.7 - - - +
117C ILE* 1.3 81.4 - - - +
119C LEU* 1.3 80.0 + - - +
120C ARG 3.7 0.3 + - - -
121C ASP* 4.1 7.8 + - - +
122C ASP* 4.3 6.1 + - - +
158C SER* 2.7 31.5 + - - +
159C ALA 4.7 0.9 + - - -
160C LEU* 3.4 31.8 - - + +
161C THR* 4.9 7.6 - - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C VAL* 3.9 20.2 - - + -
116C GLN* 3.0 41.2 + - + +
118C ASP* 1.3 94.0 - - - +
120C ARG* 1.3 63.0 + - - +
121C ASP 3.1 3.1 - - - -
122C ASP* 3.0 28.4 + - + +
125C THR* 3.7 27.6 - - + +
126C ILE* 5.0 0.3 - - - +
160C LEU* 6.1 0.4 - - + -
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304B LYS* 5.7 2.0 - - - +
84C VAL* 3.9 16.5 - - + +
85C VAL* 4.1 10.0 - - - +
116C GLN 3.9 1.4 + - - -
117C ILE* 2.9 31.9 + - - +
119C LEU* 1.3 77.5 - - - +
121C ASP* 1.3 68.0 + - - +
122C ASP 3.5 0.2 - - - -
126C ILE* 3.9 15.9 - - - +
136C PRO* 3.9 24.7 - - + +
137C ILE 2.9 30.8 + - - -
138C THR* 4.9 2.5 - - - +
139C PRO* 3.5 18.1 - - - +
156C GLU* 2.7 44.8 + - - -
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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