Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 1CKQ
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 ALA 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLN* 3.7 4.0 + - - +
141A ASN* 1.3 77.0 - - - +
143A ILE* 1.3 60.9 + - - +
144A GLU 3.1 1.9 + - - -
145A ARG* 3.3 30.8 + - - +
146A SER 4.8 0.2 + - - -
7B A 3.5 43.2 - - + +
8B T 3.0 28.2 + - + +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 3.5 34.3 - - + -
114A HIS 5.3 1.3 - - - +
115A GLN* 3.1 22.3 + - + +
141A ASN* 3.0 7.7 + - - +
142A ALA* 1.3 77.2 - - - +
144A GLU* 1.3 61.6 + - + +
145A ARG 3.1 0.2 - - - -
146A SER* 2.8 34.0 + - - +
169A LEU* 3.9 7.9 - - + -
174A PHE* 3.7 28.0 - - + -
200A ARG* 4.3 24.5 - - + +
203A ARG* 4.3 15.0 - - + -
204A LEU* 4.0 17.4 - - + +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASN* 3.0 35.0 + - + +
143A ILE* 1.3 74.6 - - + +
145A ARG* 1.3 63.1 + - - +
146A SER 3.0 3.6 + - - -
147A HIS* 3.1 30.9 + - + +
148A LYS 4.8 0.2 + - - -
203A ARG* 3.1 52.3 + - + +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 4.0 11.8 - - - +
142A ALA* 3.3 16.5 + - - +
143A ILE 3.1 0.4 - - - -
144A GLU* 1.3 77.0 - - - +
146A SER* 1.3 63.6 + - - +
147A HIS 3.0 0.2 - - - -
148A LYS* 3.0 23.9 + - + +
149A ASN* 4.4 1.2 + - - -
5B G 4.0 15.4 + - - +
6B A 2.8 43.4 + - - +
7B A 3.2 47.0 + - - +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 3.6 30.6 - - - +
142A ALA 4.8 0.2 + - - -
143A ILE* 2.8 33.0 + - - +
144A GLU 3.0 0.2 - - - -
145A ARG* 1.3 78.3 - - - +
147A HIS* 1.3 60.4 + - - +
148A LYS 3.3 0.9 + - - -
149A ASN* 3.6 6.3 + - - +
150A ILE* 3.4 23.8 + - - +
165A TYR* 4.7 1.9 + - - -
167A LEU* 4.3 12.9 - - - +
204A LEU* 4.0 16.9 - - - +
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Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 3.1 30.3 - - + +
145A ARG 3.0 0.6 + - - -
146A SER* 1.3 76.2 - - - +
148A LYS* 1.3 63.4 + - - +
150A ILE* 3.4 11.4 + - + +
151A SER* 3.0 24.8 + - - -
203A ARG 2.9 27.4 + - - -
204A LEU* 4.0 16.5 - - + +
206A ALA* 4.2 13.2 - - + +
207A ALA* 4.0 32.3 + - + +
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER 5.1 1.2 + - - -
88A ILE* 4.1 14.6 - - - +
145A ARG* 3.0 14.8 + - - +
147A HIS* 1.3 77.7 - - - +
149A ASN* 1.3 87.4 + - - +
151A SER* 3.1 7.7 + - - -
152A GLU* 3.0 42.6 + - + +
5B G 2.9 28.3 + - - -
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Residues in contact with ASN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 3.7 18.4 - - + +
89A LYS 4.8 0.4 + - - -
90A PRO* 4.4 13.2 - - + +
111A GLU* 3.2 22.8 + - - +
113A LYS* 5.4 3.8 - - - +
145A ARG 4.4 1.1 + - - +
146A SER* 3.6 6.7 + - - +
147A HIS 3.5 0.2 - - - -
148A LYS* 1.3 105.1 + - - +
150A ILE* 1.3 56.9 + - - +
152A GLU* 3.6 5.6 - - - +
153A ILE* 3.0 35.0 + - + +
165A TYR* 3.4 19.1 - - + +
5B G 3.7 16.5 + - - -
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 3.4 22.9 + - - +
147A HIS* 3.4 12.5 + - + +
148A LYS 3.2 0.2 - - - -
149A ASN* 1.3 76.8 - - - +
151A SER* 1.3 58.6 + - - +
154A ALA* 3.1 28.4 + - + +
163A PHE* 3.5 23.7 - - + -
165A TYR* 3.7 31.2 - - + -
167A LEU* 4.6 15.5 - - + -
204A LEU* 5.6 1.1 - - + -
207A ALA* 4.0 31.2 - - + +
233A GLN 5.6 1.6 - - - +
235A ALA* 4.3 13.2 - - + -
237A ILE* 6.1 0.2 - - + -
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A HIS 3.0 18.1 + - - -
148A LYS* 3.1 6.5 + - - -
150A ILE* 1.3 75.9 - - - +
152A GLU* 1.3 60.0 + - - +
154A ALA* 3.4 5.5 + - - +
155A ASN* 3.1 40.4 + - - +
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 4.6 19.2 - - - +
66A ILE* 3.8 29.3 - - + +
88A ILE* 4.0 35.7 - - + +
148A LYS* 3.0 35.3 + - + +
149A ASN* 3.3 6.9 + - - +
151A SER* 1.3 75.0 - - - +
153A ILE* 1.3 59.7 + - - +
155A ASN* 3.3 12.0 + - - +
156A PHE* 3.0 26.6 + - - +
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.0 26.9 - - + -
66A ILE* 6.1 0.4 - - + -
88A ILE* 4.1 16.2 - - + -
90A PRO* 5.4 2.9 - - + -
94A ILE* 5.1 0.9 - - + -
106A VAL* 6.2 0.4 - - + -
109A VAL* 4.2 23.6 - - + -
149A ASN 3.0 20.5 + - - +
150A ILE 4.2 0.2 - - - +
152A GLU* 1.3 72.0 - - - +
154A ALA* 1.3 61.0 + - - +
156A PHE* 3.2 11.9 + - + +
157A MET* 2.9 45.6 + - + +
163A PHE* 3.6 17.9 - - + -
164A PRO* 6.1 0.4 - - + -
165A TYR* 4.0 26.2 - - + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.1 21.0 + - + +
151A SER* 3.6 9.0 - - - +
152A GLU 3.2 0.2 - - - -
153A ILE* 1.3 76.9 - - - +
155A ASN* 1.3 60.8 + - - +
158A LEU* 3.0 18.1 + - - +
163A PHE* 3.6 13.6 - - + -
233A GLN* 3.0 46.5 + - + +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 4.4 5.8 - - + +
69A ALA* 5.0 2.3 - - - +
70A LEU* 3.2 48.8 - - + +
73A ILE* 4.6 2.1 - - - +
151A SER* 3.1 28.2 + - - +
152A GLU* 3.6 11.3 + - - +
153A ILE 3.2 0.2 - - - -
154A ALA* 1.3 79.9 - - - +
156A PHE* 1.3 62.2 + - - +
157A MET 3.5 0.2 + - - -
158A LEU* 3.5 19.5 + - - +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 4.4 15.5 - - - -
61A ILE* 4.0 28.5 - - + -
65A GLU* 3.8 30.7 - - + -
66A ILE* 3.8 29.8 - - + +
69A ALA* 3.9 21.5 - - + +
73A ILE* 6.1 0.3 - - - +
94A ILE* 6.3 0.2 - - + -
96A GLU* 5.2 3.4 - - - -
106A VAL* 4.4 16.4 - - + -
152A GLU 3.0 13.3 + - - +
153A ILE* 3.2 16.4 + - + +
155A ASN* 1.3 79.0 - - - +
157A MET* 1.3 67.1 + - + +
158A LEU 3.5 0.7 + - - -
159A SER* 5.2 3.6 + - - -
160A GLU* 5.3 0.9 - - - +
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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