Contacts of the helix formed by residues 197 - 206 (chain K) in PDB entry 1KN0
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 GLU 197 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.3 21.6 - - - +
45A GLN* 2.8 27.2 + - - +
77A GLU* 4.5 7.9 + - + +
78A MET* 4.4 21.1 - - + -
192K LYS* 2.4 34.2 + - - +
194K GLN* 5.1 0.7 + - - -
195K ASP 3.7 3.1 - - - +
196K LEU* 1.3 85.1 - - - +
198K PRO* 1.3 59.0 - - - +
199K SER* 3.3 5.9 - - - -
200K VAL* 3.0 19.2 + - + +
201K GLU* 2.7 32.6 + - - +
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Residues in contact with PRO 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K GLN* 5.6 2.9 - - - +
196K LEU* 3.9 19.2 - - + +
197K GLU* 1.3 86.0 - - - +
199K SER* 1.3 65.1 + - - +
201K GLU* 3.7 7.3 - - + +
202K GLU* 2.9 27.4 + - - +
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Residues in contact with SER 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.8 17.6 - - - +
197K GLU* 3.3 4.9 - - - -
198K PRO* 1.3 80.9 - - - +
200K VAL* 1.3 67.1 + - - +
202K GLU* 3.6 8.6 - - - +
203K ALA* 3.3 18.5 + - - +
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Residues in contact with VAL 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 5.0 3.1 - - + +
38A ALA* 3.7 36.1 - - + +
39A ILE* 3.4 20.9 - - + +
42A ALA* 3.9 13.0 - - + -
77A GLU 4.5 1.6 - - - +
78A MET* 3.4 6.1 - - + +
197K GLU* 3.0 24.8 + - + +
199K SER* 1.3 74.4 - - - +
201K GLU* 1.3 66.8 + - - +
202K GLU 2.9 2.9 + - - -
203K ALA* 3.0 4.0 + - - +
204K ARG* 3.0 51.7 + - - +
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Residues in contact with GLU 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 4.3 3.1 + - - +
36B TYR* 3.6 23.0 + - - -
37B GLN* 4.9 8.3 - - - +
40B GLN* 3.5 23.0 + - - +
41B LYS* 5.5 6.2 + - - +
44B ARG* 4.3 14.2 + - - +
196K LEU* 4.3 13.7 - - + -
197K GLU 2.7 19.8 + - - +
198K PRO* 3.8 8.5 - - + +
200K VAL* 1.3 74.4 - - - +
202K GLU* 1.3 63.2 + - - +
204K ARG* 3.5 23.4 + - - +
205K TYR* 3.2 21.5 + - + +
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Residues in contact with GLU 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198K PRO 2.9 17.9 + - - +
199K SER* 3.6 8.3 - - - +
200K VAL 2.9 1.0 + - - -
201K GLU* 1.3 75.9 - - - +
203K ALA* 1.3 66.9 + - - +
205K TYR* 3.0 16.7 + - - +
206K ASN* 2.9 29.3 + - - +
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Residues in contact with ALA 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 4.5 4.2 + - - -
34A GLU* 3.6 22.1 - - + +
35A GLU* 3.5 31.6 - - - +
38A ALA* 4.4 3.4 - - + -
199K SER 3.3 9.2 + - - +
200K VAL 3.0 6.8 + - - +
202K GLU* 1.3 81.1 - - - +
204K ARG* 1.3 60.6 + - - +
206K ASN* 3.4 11.5 + - - +
207K SER* 3.2 19.1 + - - -
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Residues in contact with ARG 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.1 33.6 + - - +
39A ILE* 4.0 0.2 - - - +
77A GLU 3.2 13.9 + - - -
78A MET 2.3 38.4 + - - -
79A PHE* 3.2 20.5 + - - +
80A GLY 3.8 4.0 - - - +
82A ASN* 5.7 0.4 - - - -
116A LYS* 4.8 6.1 - - - +
36B TYR* 2.8 45.9 + - + +
40B GLN* 3.9 1.6 - - - +
200K VAL* 3.0 32.1 + - - +
201K GLU* 3.5 24.6 + - - +
203K ALA* 1.3 74.7 - - - +
205K TYR* 1.3 61.8 + - - +
207K SER* 2.8 25.3 + - - -
208K CYS* 3.7 9.5 + - - -
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Residues in contact with TYR 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 3.6 37.5 + - + +
34B GLU* 4.9 5.4 + - - +
36B TYR* 4.6 9.8 - + - -
37B GLN* 2.9 54.4 + - + +
201K GLU* 3.2 16.8 + - + +
202K GLU* 3.0 10.8 + - - +
204K ARG* 1.3 80.2 - - - +
206K ASN* 1.3 69.8 + - - +
207K SER 3.1 3.8 + - - -
208K CYS* 3.3 17.4 + - - +
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Residues in contact with ASN 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 4.8 12.1 - - + +
202K GLU* 2.9 39.3 + - - +
203K ALA* 3.7 10.0 - - - +
205K TYR* 1.3 87.3 - - - +
207K SER* 1.3 55.8 + - - +
208K CYS 3.3 8.4 - - - +
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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