Contacts of the helix formed by residues 209 - 215 (chain D) in PDB entry 1KLG
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 ASP 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLN* 4.0 16.4 + - - +
92D ASN* 5.5 2.0 - - - +
207D LYS* 3.5 6.1 + - - +
208D PHE* 1.3 74.8 - - - +
210D GLN* 1.3 61.7 + - - +
211D SER* 3.2 10.4 + - - -
212D LYS* 2.9 40.3 + - + +
213D TYR* 3.0 21.3 + - - +
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Residues in contact with GLN 210 (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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23D ASN* 3.0 32.1 + - + +
26D TYR* 3.5 27.7 - - - -
27D LEU* 3.8 17.7 - - + +
89D TYR* 4.4 13.4 - - + +
90D TYR 4.9 1.0 + - - -
91D VAL* 3.9 27.9 + - + +
208D PHE* 3.4 33.3 + - + +
209D ASP* 1.3 72.2 + - - +
211D SER* 1.3 57.6 + - - +
213D TYR* 3.3 1.6 + - - +
214D LEU* 2.9 36.4 + - - +
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Residues in contact with SER 211 (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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39A LYS* 3.6 10.7 + - - +
57A GLN* 4.3 10.8 + - - -
89D TYR* 3.3 41.9 + - - -
91D VAL 4.3 6.9 + - - -
92D ASN* 4.6 2.4 + - - -
112D TYR* 2.9 34.6 + - - -
209D ASP* 3.2 6.8 + - - -
210D GLN* 1.3 79.5 - - - +
212D LYS* 1.3 64.3 + - - +
215D MET 3.1 13.9 + - - -
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Residues in contact with LYS 212 (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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38A LYS 3.5 25.2 + - - -
39A LYS* 3.7 15.8 + - - +
40A GLU* 4.6 11.5 + - - +
57A GLN* 5.1 3.7 - - - +
209D ASP* 2.9 36.6 + - + +
211D SER* 1.3 76.6 - - - +
213D TYR* 1.3 63.6 + - - +
215D MET* 3.3 33.8 - - - +
216D MET 4.5 0.5 + - - -
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Residues in contact with TYR 213 (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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12D HIS* 5.6 4.3 - + - -
24D MET* 3.4 23.3 - - + -
27D LEU* 4.4 7.2 - - + -
28D TYR* 3.3 22.0 - + - -
164D ARG* 2.7 23.6 + - - -
199D ASP* 2.7 30.1 + - + -
200D MET* 3.5 2.6 - - - -
201D MET 4.0 11.9 - - - -
202D PRO* 5.0 2.0 - - + -
203D ALA 5.5 1.8 - - - -
208D PHE* 3.6 28.9 - + + -
209D ASP 3.0 16.8 + - - +
210D GLN 3.6 2.9 - - - +
212D LYS* 1.3 78.1 - - - +
214D LEU* 1.3 68.2 + - + +
215D MET 3.1 1.6 + - - -
216D MET* 3.3 39.3 + - + +
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Residues in contact with LEU 214 (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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27D LEU* 3.9 35.7 - - + -
28D TYR* 4.3 8.3 - - - +
87D SER* 3.5 37.5 - - - +
89D TYR* 4.0 21.3 - - + -
112D TYR* 3.5 21.9 - - + +
210D GLN 2.9 19.7 + - - +
213D TYR* 1.3 74.1 - - + +
215D MET* 1.3 61.9 + - - +
216D MET* 2.9 8.4 + - - -
217D TYR* 3.0 47.2 + - + +
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Residues in contact with MET 215 (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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37A ALA 3.5 26.2 - - - +
38A LYS* 4.0 9.6 - - - +
39A LYS* 3.8 16.6 - - + -
112D TYR* 3.4 42.8 - - + +
211D SER 3.1 8.5 + - - +
212D LYS* 3.3 41.7 - - + +
213D TYR 3.1 0.6 - - - -
214D LEU* 1.3 75.2 - - - +
216D MET* 1.3 52.2 + - - +
217D TYR 3.1 0.2 - - - -
218D ASN* 2.7 50.9 + - - +
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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