Contacts of the helix formed by residues 189 - 199 (chain D) in PDB entry 1KQN
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 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D ALA* 5.1 5.5 - - + +
161D GLU* 5.8 0.2 - - - +
187D THR* 3.0 12.5 + - - +
188D ARG* 1.3 76.4 - - + +
190D GLY* 1.3 58.3 - - - +
191D ASN 3.4 2.0 - - - -
192D ASP* 3.3 27.5 + - + +
193D ALA* 2.9 28.1 + - - +
191F ASN* 5.8 0.4 - - - +
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Residues in contact with GLY 190 (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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187D THR* 3.8 11.9 - - - +
188D ARG 3.4 7.9 + - - -
189D ALA* 1.3 74.3 - - - +
191D ASN* 1.3 57.0 + - - +
193D ALA* 3.1 4.5 + - - +
194D GLN* 2.8 36.0 + - - +
212D VAL* 4.1 5.3 - - - +
214D ASN* 3.7 21.9 + - - -
191F ASN* 5.0 6.0 - - - +
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Residues in contact with ASN 191 (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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189D ALA 3.4 0.2 - - - -
190D GLY* 1.3 74.4 - - - +
192D ASP* 1.3 63.2 + - - +
194D GLN* 3.1 9.1 + - - +
195D LYS* 2.7 34.3 + - - +
188F ARG 5.0 6.4 + - - +
189F ALA* 6.1 0.2 - - - -
190F GLY* 3.9 23.6 + - - -
191F ASN* 4.2 25.9 + - + +
214F ASN* 4.3 5.9 - - - +
216F TRP* 3.9 26.5 - - - -
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Residues in contact with ASP 192 (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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161D GLU* 3.7 13.0 - - - +
189D ALA* 3.3 27.7 + - + +
190D GLY 3.2 0.6 - - - -
191D ASN* 1.3 81.2 - - - +
193D ALA* 1.3 56.4 + - - +
195D LYS* 3.6 11.8 - - - +
196D PHE* 2.8 31.4 + - - +
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Residues in contact with ALA 193 (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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157D ALA* 4.8 3.4 - - + -
160D LEU* 4.2 14.4 - - + +
161D GLU* 3.9 11.3 + - - +
185D CYS* 4.5 4.5 - - - -
187D THR* 4.1 16.2 - - + -
189D ALA 2.9 13.7 + - - +
190D GLY 3.4 8.3 - - - +
192D ASP* 1.3 76.3 - - - +
194D GLN* 1.3 57.6 + - - +
196D PHE* 3.3 4.2 + - - +
197D ILE* 3.0 34.0 + - - +
212D VAL* 4.1 15.5 - - + -
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Residues in contact with GLN 194 (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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190D GLY 2.8 21.9 + - - +
191D ASN* 3.4 11.4 - - - +
193D ALA* 1.3 78.1 - - - +
195D LYS* 1.3 57.0 + - - +
197D ILE* 3.2 11.9 + - - +
198D TYR* 2.8 28.6 + - - +
212D VAL* 4.2 24.5 - - + +
190F GLY* 5.9 1.0 - - - -
194F GLN* 5.0 9.5 - - - +
214F ASN* 3.2 26.1 + - - +
216F TRP* 3.6 15.2 - - + -
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Residues in contact with LYS 195 (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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191D ASN* 2.7 23.2 + - - +
192D ASP* 3.2 11.9 + - - +
194D GLN* 1.3 70.8 - - - +
196D PHE* 1.3 53.0 + - - +
198D TYR* 3.1 3.5 + - + +
199D GLU* 2.8 69.8 + - + +
225E LYS* 6.2 1.6 - - - +
216F TRP* 3.2 32.0 - - + -
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Residues in contact with PHE 196 (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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160D LEU* 3.4 32.8 - - + -
161D GLU* 3.4 49.4 - - + +
163D PHE* 4.1 3.6 - - + -
164D ALA* 3.9 24.0 - - + -
192D ASP 2.8 17.5 + - - +
193D ALA* 3.5 5.2 - - - +
195D LYS* 1.3 74.0 - - - +
197D ILE* 1.3 65.9 + - - +
199D GLU* 3.3 18.2 + - + +
200D SER* 3.5 14.7 + - - -
203D LEU* 3.5 26.5 - - + -
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Residues in contact with ILE 197 (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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160D LEU* 4.1 15.9 - - + -
193D ALA 3.0 19.7 + - - +
194D GLN* 3.6 9.9 - - - +
196D PHE* 1.3 75.7 - - - +
198D TYR* 1.3 66.5 + - - +
200D SER* 3.1 22.3 + - - +
203D LEU* 4.0 37.1 - - + +
204D TRP* 3.7 12.1 + - + +
207D ARG* 4.4 12.8 - - + -
210D ILE* 3.7 31.4 - - + +
212D VAL* 3.8 21.8 - - + -
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Residues in contact with TYR 198 (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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194D GLN 2.8 13.8 + - - +
195D LYS* 3.1 6.9 + - + +
197D ILE* 1.3 76.9 - - - +
199D GLU* 1.3 68.9 + - + +
204D TRP* 4.0 18.2 - + + -
225E LYS* 3.5 32.1 + - - +
228E ARG* 3.1 41.6 + - + +
232E ARG* 2.7 52.2 + - - -
234E GLN* 5.5 5.2 - - - -
216F TRP* 3.2 62.4 - + + +
217F ILE* 5.5 0.5 - - - +
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Residues in contact with GLU 199 (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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195D LYS* 2.8 54.2 + - - +
196D PHE* 4.0 11.2 - - + +
197D ILE 3.2 0.4 - - - -
198D TYR* 1.3 91.7 - - + +
200D SER* 1.3 56.1 + - - +
201D ASP 4.2 0.5 + - - -
225E LYS* 6.1 0.9 - - - -
228E ARG* 3.8 27.0 + - - +
232E ARG* 4.0 2.8 + - - -
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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