Contacts of the helix formed by residues 138 - 147 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D ASP 2.9 24.2 + - - +
136D ASP* 3.5 10.7 + - - +
137D PHE* 1.3 77.0 - - - +
139D GLY* 1.3 59.2 + - - +
140D GLU* 3.2 13.7 + - - +
141D TYR* 3.0 32.5 + - - +
142D LEU* 2.9 28.9 + - - +
195D GLU* 5.3 4.9 - - - +
198D ALA* 3.8 11.2 - - - +
202D LYS* 5.1 1.3 - - - +
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Residues in contact with GLY 139 (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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138D ASN* 1.3 73.9 - - - +
140D GLU* 1.3 56.2 + - - +
142D LEU* 4.2 1.8 - - - -
143D HIS* 2.7 36.9 + - - +
191D LEU* 4.2 6.7 - - - -
194D CYS* 3.6 12.3 - - - +
195D GLU* 3.7 37.0 + - - -
198D ALA* 3.8 4.2 - - - +
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Residues in contact with GLU 140 (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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138D ASN* 3.2 9.0 + - - +
139D GLY* 1.3 75.7 - - - +
141D TYR* 1.3 63.5 + - - +
143D HIS* 3.4 8.0 + - - +
144D GLN* 2.9 47.0 + - - +
191D LEU* 4.0 32.2 - - - +
195D GLU* 4.5 8.0 + - - +
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Residues in contact with TYR 141 (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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130D PRO* 3.3 20.7 - - + +
136D ASP 4.0 12.8 - - - +
137D PHE* 3.7 27.6 - + - -
138D ASN* 3.0 24.3 + - - +
140D GLU* 1.3 75.8 - - - +
142D LEU* 1.3 55.6 + - - +
144D GLN* 3.2 17.7 - - - +
145D LYS* 2.8 80.3 + - + +
161D LYS 3.9 6.1 + - - -
162D LEU* 2.7 37.8 + - + -
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Residues in contact with LEU 142 (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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137D PHE* 4.5 18.6 - - + -
138D ASN 2.9 17.1 + - - +
139D GLY* 3.6 4.7 - - - +
141D TYR* 1.3 81.8 - - - +
143D HIS* 1.3 63.0 + - - +
145D LYS* 3.2 2.6 + - - -
146D CYS* 2.9 44.6 + - - -
153D ILE* 5.1 2.0 - - + -
156D TRP* 5.0 0.4 - - + -
157D LEU* 4.9 6.3 - - + -
162D LEU* 3.9 28.3 - - + -
194D CYS* 3.6 34.8 - - + +
197D LEU* 4.0 26.9 - - + -
198D ALA* 4.2 5.6 - - + +
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Residues in contact with HIS 143 (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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139D GLY 2.7 21.6 + - - +
140D GLU* 3.8 9.8 + - - +
142D LEU* 1.3 75.5 - - - +
144D GLN* 1.3 62.5 + - - +
146D CYS* 3.3 10.9 + - + +
147D ALA* 3.4 17.0 + - + +
187D SER 5.7 1.0 + - - -
189D LEU 3.8 18.8 + - - -
190D SER* 3.9 2.6 - - - -
191D LEU* 3.6 43.1 + - + +
194D CYS* 3.6 13.2 - - - -
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Residues in contact with GLN 144 (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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140D GLU* 2.9 39.9 + - - +
141D TYR* 3.2 21.7 - - - +
143D HIS* 1.3 80.5 + - - +
145D LYS* 1.3 71.7 + - + +
146D CYS 3.4 0.9 + - - -
147D ALA* 3.5 16.9 + - - +
148D LYS 4.9 0.7 + - - -
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Residues in contact with LYS 145 (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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141D TYR* 2.8 65.1 + - + +
142D LEU 3.8 1.3 - - - +
144D GLN* 1.3 83.4 - - + +
146D CYS* 1.3 61.4 + - - +
147D ALA 3.4 0.2 - - - -
148D LYS* 4.5 2.5 + - - +
149D LYS* 3.6 6.4 - - - +
156D TRP* 3.6 18.1 - - + -
161D LYS* 5.9 4.0 - - - +
162D LEU* 3.4 25.8 - - + -
432K C 5.7 0.7 + - - -
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Residues in contact with CYS 146 (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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142D LEU* 2.9 38.4 + - - +
143D HIS* 3.8 6.7 - - + +
144D GLN 3.2 0.4 - - - -
145D LYS* 1.3 75.6 - - - +
147D ALA* 1.3 66.1 + - - +
148D LYS 3.1 3.4 - - - -
149D LYS* 2.8 22.7 + - - +
153D ILE* 4.4 6.1 - - - -
156D TRP* 3.4 28.5 - - - -
186D ALA* 3.4 27.8 - - - +
187D SER* 3.6 11.5 - - - -
189D LEU* 5.5 0.2 - - - -
194D CYS* 5.0 5.8 - - - -
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Residues in contact with ALA 147 (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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143D HIS* 3.4 13.2 + - + +
144D GLN* 3.6 15.3 - - - +
145D LYS 3.4 1.2 - - - -
146D CYS* 1.3 78.7 - - - +
148D LYS* 1.3 66.8 + - + +
149D LYS 3.7 0.3 + - - +
150D LYS* 5.9 0.5 + - - -
187D SER* 4.0 15.6 - - - +
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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