Contacts of the helix formed by residues 138 - 147 (chain A) in PDB entry 1K82
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 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ASP 3.0 24.7 + - - +
136A ASP* 3.5 9.5 + - - +
137A PHE* 1.3 76.8 - - - +
139A GLY* 1.3 59.2 + - - +
140A GLU* 3.1 11.6 + - - +
141A TYR* 2.7 35.6 + - - +
142A LEU* 2.9 28.9 + - - +
195A GLU* 5.5 2.9 - - - +
198A ALA* 3.9 11.9 - - - -
202A LYS* 5.1 2.0 - - - +
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Residues in contact with GLY 139 (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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138A ASN* 1.3 75.7 - - - +
140A GLU* 1.3 57.4 + - - +
142A LEU* 4.2 1.8 - - - -
143A HIS* 2.9 30.1 + - - +
191A LEU* 3.7 6.9 - - - +
194A CYS* 3.5 13.2 - - - +
195A GLU* 3.7 38.9 + - - -
198A ALA* 3.9 4.9 - - - +
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Residues in contact with GLU 140 (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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138A ASN* 3.1 9.2 + - - +
139A GLY* 1.3 72.4 - - - +
141A TYR* 1.3 67.7 + - - +
143A HIS* 3.5 8.1 + - - +
144A GLN* 3.0 40.1 + - - +
191A LEU* 4.0 29.6 - - + +
195A GLU* 4.7 4.4 + - - +
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Residues in contact with TYR 141 (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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130A PRO* 3.3 25.1 - - + +
136A ASP 3.9 19.1 - - - +
137A PHE* 3.8 21.8 - + - -
138A ASN* 2.7 22.9 + - - +
140A GLU* 1.3 73.4 - - - +
142A LEU* 1.3 65.6 + - - +
144A GLN* 3.1 19.4 + - - +
145A LYS* 2.9 59.9 + - + +
161A LYS 3.8 6.1 + - - -
162A LEU* 2.8 42.7 + - + -
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Residues in contact with LEU 142 (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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137A PHE* 4.3 17.0 - - + -
138A ASN 2.9 16.1 + - - +
139A GLY 3.8 4.3 - - - +
141A TYR* 1.3 81.2 - - - +
143A HIS* 1.3 63.8 + - - +
145A LYS* 3.3 3.6 + - - +
146A CYS* 3.0 40.0 + - - -
153A ILE* 5.1 2.5 - - + -
157A LEU* 4.7 6.5 - - + -
162A LEU* 3.8 30.7 - - + -
189A LEU* 5.7 0.2 - - + -
194A CYS* 3.4 39.7 - - + +
197A LEU* 3.9 23.1 - - + -
198A ALA* 4.3 7.9 - - + +
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Residues in contact with HIS 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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139A GLY 2.9 19.5 + - - +
140A GLU* 3.8 9.1 + - - +
141A TYR 3.2 0.2 - - - -
142A LEU* 1.3 76.9 - - - +
144A GLN* 1.3 63.2 + - - +
146A CYS* 3.2 12.6 + - + +
147A ALA* 3.3 17.7 + - + +
187A SER 5.7 1.0 + - - -
189A LEU 3.8 13.3 + - - -
190A SER* 3.7 6.0 - - - -
191A LEU* 3.4 50.1 + - + +
194A CYS* 3.6 12.1 - - - -
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Residues in contact with GLN 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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140A GLU* 3.0 38.4 + - - +
141A TYR* 3.1 19.3 + - - +
143A HIS* 1.3 79.4 + - - +
145A LYS* 1.3 80.4 + - + +
146A CYS 3.4 0.2 + - - -
147A ALA* 3.5 15.3 + - - +
148A LYS* 4.8 1.6 + - - +
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Residues in contact with LYS 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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141A TYR* 2.9 57.7 + - + +
142A LEU 3.8 1.6 - - - +
143A HIS 3.3 0.2 - - - -
144A GLN* 1.3 90.3 - - + +
146A CYS* 1.3 60.8 + - - +
147A ALA 3.4 0.4 + - - -
148A LYS* 4.3 4.4 + - - +
149A LYS* 3.5 15.9 - - - +
156A TRP* 3.7 8.4 - - + -
161A LYS* 5.9 6.5 - - - +
162A LEU* 3.4 26.0 - - + -
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Residues in contact with CYS 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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142A LEU* 3.0 38.3 + - - +
143A HIS* 3.2 7.1 + - + +
145A LYS* 1.3 75.7 - - - +
147A ALA* 1.3 58.6 + - - +
148A LYS 3.1 3.6 - - - -
149A LYS* 2.7 32.9 + - - +
153A ILE* 4.4 6.1 - - - -
156A TRP* 3.4 28.0 - - - -
186A ALA* 3.4 28.3 - - + +
187A SER* 3.6 10.3 - - - -
189A LEU* 5.6 0.4 - - - -
194A CYS* 4.8 6.5 - - - -
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Residues in contact with ALA 147 (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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143A HIS* 3.3 16.0 + - + +
144A GLN* 3.8 13.0 - - - +
145A LYS 3.4 1.6 - - - -
146A CYS* 1.3 77.1 - - - +
148A LYS* 1.3 63.1 + - + +
149A LYS 3.7 0.9 + - - +
187A SER* 4.1 16.5 - - - +
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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