Contacts of the helix formed by residues 189 - 199 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D ASN* 6.1 0.4 - - - -
187F THR* 3.1 14.3 + - - +
188F ARG* 1.3 78.3 - - - +
190F GLY* 1.3 61.0 + - - +
191F ASN* 3.2 3.1 - - - +
192F ASP* 2.1 55.4 - - + +
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Residues in contact with GLY 190 (chain F).
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* 3.9 9.4 + - - -
194D GLN* 5.9 1.3 - - - -
187F THR* 3.6 14.5 - - - +
188F ARG 3.6 4.8 + - - -
189F ALA* 1.3 74.4 - - - +
191F ASN* 1.3 56.6 + - - +
193F ALA* 3.4 4.2 + - - +
194F GLN* 2.9 35.9 + - - +
212F VAL* 4.1 3.9 - - - +
214F ASN* 3.6 21.4 + - - -
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Residues in contact with ASN 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ARG 4.7 11.9 + - - -
189D ALA* 5.8 0.4 - - - +
190D GLY 5.0 1.4 - - - +
191D ASN* 4.2 33.1 + - + +
214D ASN* 4.8 5.7 - - - +
216D TRP* 3.2 25.5 - - - -
189F ALA* 3.2 1.0 - - - -
190F GLY* 1.3 74.5 - - - +
192F ASP* 1.3 55.9 + - - +
194F GLN* 4.2 6.1 - - - +
195F LYS* 2.7 34.3 + - - +
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Residues in contact with ASP 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 4.3 5.2 - - - +
161F GLU* 2.8 27.0 - - - +
187F THR* 4.3 1.7 + - - -
189F ALA* 2.1 51.4 + - + +
191F ASN* 1.3 76.5 - - - +
193F ALA* 1.3 67.6 + - - +
195F LYS* 3.2 9.8 + - - +
196F PHE* 2.7 35.3 + - - +
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Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 4.5 7.4 - - + -
160F LEU* 4.3 14.5 - - + +
161F GLU* 4.1 6.5 - - - -
185F CYS* 4.6 2.9 - - - -
187F THR* 4.2 13.5 - - + -
189F ALA 3.8 3.6 - - - +
190F GLY 3.5 8.1 - - - +
191F ASN 3.2 0.4 - - - -
192F ASP* 1.3 91.6 + - - +
194F GLN* 1.3 60.5 + - - +
196F PHE* 3.1 5.8 + - - +
197F ILE* 2.9 35.5 + - - +
212F VAL* 4.3 13.5 - - + -
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Residues in contact with GLN 194 (chain F).
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* 5.0 9.6 - - - +
214D ASN* 3.1 24.3 + - - +
216D TRP* 3.9 14.4 - - + -
190F GLY 2.9 24.2 + - - +
191F ASN* 3.7 8.3 - - - +
193F ALA* 1.3 74.8 - - - +
195F LYS* 1.3 57.7 + - - +
197F ILE* 3.4 13.9 + - - +
198F TYR* 2.9 28.2 + - - +
212F VAL* 4.1 25.9 - - + +
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Residues in contact with LYS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D TRP* 3.5 30.9 - - + -
191F ASN* 2.7 23.8 + - - +
192F ASP* 3.5 9.0 - - - +
194F GLN* 1.3 74.3 - - - +
196F PHE* 1.3 57.6 + - - +
198F TYR* 3.1 4.5 + - + +
199F GLU* 2.9 57.5 + - - +
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Residues in contact with PHE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F LEU* 3.3 34.8 - - + -
161F GLU* 3.6 41.1 - - + -
163F PHE* 4.1 5.2 - - + -
164F ALA* 3.8 30.5 - - + -
192F ASP 2.7 21.5 + - - +
193F ALA* 3.1 5.4 + - - +
195F LYS* 1.3 72.8 - - - +
197F ILE* 1.3 62.8 + - - +
199F GLU* 3.3 17.7 + - + +
200F SER* 3.5 13.5 + - - -
203F LEU* 3.5 25.8 - - + -
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Residues in contact with ILE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F LEU* 4.3 15.3 - - + -
193F ALA 2.9 19.7 + - - +
194F GLN* 3.6 14.6 - - - +
196F PHE* 1.3 75.6 - - - +
198F TYR* 1.3 66.3 + - - +
200F SER 3.1 21.7 + - - +
203F LEU* 3.8 36.6 - - + +
204F TRP* 3.6 13.5 + - + +
207F ARG* 4.5 11.9 - - + -
210F ILE* 3.4 33.4 - - + +
212F VAL* 3.7 21.5 - - + -
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Residues in contact with TYR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LYS* 3.3 25.3 + - - +
228C ARG* 3.1 49.7 + - + +
232C ARG* 2.8 42.9 + - - -
234C GLN* 5.6 4.9 - - - -
216D TRP* 3.2 64.9 - + + +
217D ILE* 5.0 2.1 - - - +
194F GLN 2.9 17.9 + - - +
195F LYS* 3.6 6.5 - - - +
197F ILE* 1.3 76.3 - - - +
199F GLU* 1.3 70.7 + - + +
204F TRP* 3.8 21.1 - + + -
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Residues in contact with GLU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LYS* 5.9 1.6 - - - -
228C ARG* 4.2 29.8 + - - +
232C ARG* 4.2 2.3 + - - -
195F LYS* 2.9 51.2 + - - +
196F PHE* 3.3 10.9 + - + +
197F ILE 3.2 0.4 - - - -
198F TYR* 1.3 89.5 - - + +
200F SER* 1.3 58.6 + - - +
201F ASP* 4.1 1.4 + - - +
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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