Contacts of the helix formed by residues 200 - 206 (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 SER 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D PHE* 3.5 9.6 + - - -
197D ILE 3.1 5.9 + - - +
198D TYR 3.2 0.2 - - - -
199D GLU* 1.3 78.1 - - - +
201D ASP* 1.3 60.4 + - - +
202D VAL* 3.4 7.1 + - - +
203D LEU* 3.2 41.0 + - - +
204D TRP* 2.8 28.9 + - - +
232E ARG* 3.5 2.9 - - - -
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Residues in contact with ASP 201 (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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199D GLU 4.2 0.8 + - - -
200D SER* 1.3 71.5 + - - +
202D VAL* 1.3 64.8 + - + +
204D TRP* 3.8 1.2 - - - +
205D LYS* 2.9 27.3 + - - +
231E ARG* 2.7 47.5 + - - +
232E ARG* 2.9 34.9 + - - +
256E SER* 4.5 6.1 + - - -
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Residues in contact with VAL 202 (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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171D SER* 5.6 2.5 - - - +
174D ILE* 4.3 12.3 - - + -
175D THR* 3.6 45.1 - - + +
178D VAL* 4.2 10.1 - - + -
200D SER* 3.3 7.5 + - - +
201D ASP* 1.3 79.4 - - + +
203D LEU* 1.3 64.2 + - - +
205D LYS* 3.3 7.5 + - - -
206D HIS* 3.3 27.9 - - + -
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Residues in contact with LEU 203 (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* 4.0 11.0 - - + -
163D PHE* 4.2 19.1 - - + -
174D ILE* 4.2 10.1 - - + -
178D VAL* 3.6 31.6 - - + -
196D PHE* 3.5 39.5 - - + +
197D ILE* 4.0 17.9 - - + +
200D SER* 3.2 24.7 + - - +
202D VAL* 1.3 75.8 - - + +
204D TRP* 1.3 63.3 + - - +
206D HIS 3.2 3.5 + - - -
207D ARG* 2.9 22.7 + - - -
210D ILE* 3.6 12.2 - - + +
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Residues in contact with TRP 204 (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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197D ILE* 3.7 10.0 + - + +
198D TYR* 4.0 27.4 - + + -
200D SER 2.8 21.0 + - - +
201D ASP 3.8 1.8 - - - +
203D LEU* 1.3 72.6 - - - +
205D LYS* 1.3 68.8 + - - +
207D ARG* 2.9 82.2 + - - +
232E ARG* 3.2 60.5 - - + +
234E GLN* 3.4 26.8 - - - +
34F TYR* 6.4 2.0 - + - -
216F TRP* 4.9 9.2 - + - -
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Residues in contact with LYS 205 (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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201D ASP 2.9 18.4 + - - +
202D VAL* 3.5 7.6 - - - +
204D TRP* 1.3 84.3 - - - +
206D HIS* 1.3 84.7 + - + +
207D ARG* 3.4 8.2 + - - +
208D SER* 5.1 1.2 + - - -
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Residues in contact with HIS 206 (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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175D THR* 4.4 10.3 - - - +
178D VAL* 3.9 33.9 - - + +
179D ALA* 3.5 31.2 - - + +
202D VAL* 3.3 28.1 + - + +
203D LEU 3.2 5.3 + - - +
204D TRP 3.2 0.6 - - - -
205D LYS* 1.3 107.5 + - + +
207D ARG* 1.3 50.6 + - - +
208D SER* 2.8 10.0 + - - -
209D ASN* 2.6 33.0 + - + +
210D ILE* 3.7 5.2 - - - +
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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