Contacts of the helix formed by residues 194 - 201 (chain K) in PDB entry 6D6Q
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 CYS 194 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72K VAL* 3.3 37.9 - - - -
76K GLN* 2.8 41.7 - - - +
79K VAL* 5.7 2.9 - - + -
174K ILE* 3.4 15.5 - - - -
175K THR 3.3 5.6 + - - +
176K ASN* 5.1 2.2 - - - +
193K THR* 1.3 78.9 - - + +
195K GLU* 1.3 57.4 + - - +
197K TYR* 3.5 5.6 + - - +
198K VAL* 2.9 34.8 + - + +
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Residues in contact with GLU 195 (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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76K GLN* 5.1 1.4 - - - +
193K THR* 3.1 11.3 + - + +
194K CYS* 1.3 75.7 - - - +
196K GLU* 1.3 68.2 + - + +
198K VAL* 3.2 9.3 - - + +
199K LYS* 2.7 68.7 + - + +
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Residues in contact with GLU 196 (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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178K ARG* 5.5 4.5 - - - -
181K LYS* 4.2 19.9 + - - -
192K PHE* 3.8 26.2 - - + -
193K THR* 3.2 21.8 + - - +
195K GLU* 1.3 80.5 - - + +
197K TYR* 1.3 64.6 + - - +
199K LYS* 3.2 7.9 + - - +
200K SER* 2.9 23.5 + - - -
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Residues in contact with TYR 197 (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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54K ASP* 2.5 31.0 + - - -
64K HIS* 2.9 44.8 + + - -
66K LEU* 4.4 15.5 - - + +
79K VAL* 6.5 0.9 - - + -
85K ILE* 5.5 13.4 - - + +
174K ILE* 4.8 10.3 - - + -
192K PHE* 4.6 21.7 - + + +
193K THR 3.2 13.7 + - - +
194K CYS* 3.9 5.4 - - - +
196K GLU* 1.3 79.1 - - - +
198K VAL* 1.3 63.6 + - + +
200K SER* 2.8 23.1 + - - +
201K LEU* 3.3 38.8 - - + +
207K LEU* 6.6 0.2 - - + -
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Residues in contact with VAL 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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79K VAL* 4.9 18.4 - - + -
194K CYS* 2.9 29.9 + - + +
195K GLU* 3.2 18.2 - - + +
197K TYR* 1.3 80.5 - - + +
199K LYS* 1.3 61.4 + - + +
201K LEU* 4.6 4.3 + - - +
202K THR 5.1 1.7 + - - -
207K LEU* 3.4 47.8 - - + +
208K ILE* 3.7 29.4 - - + +
211K LEU* 6.5 1.1 - - + -
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Residues in contact with LYS 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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195K GLU* 2.7 57.1 + - + +
196K GLU* 3.5 7.2 - - - +
198K VAL* 1.3 81.2 - - + +
200K SER* 1.3 64.6 + - - +
201K LEU 3.2 3.7 + - - -
202K THR* 3.5 11.6 + - - -
208K ILE* 5.0 11.9 - - + -
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Residues in contact with SER 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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192K PHE* 6.5 1.8 - - - -
196K GLU 2.9 15.0 + - - -
197K TYR* 2.8 17.2 + - - -
199K LYS* 1.3 72.6 - - - +
201K LEU* 1.3 65.5 + - - +
202K THR* 3.4 6.5 + - - +
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Residues in contact with LEU 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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54K ASP* 3.2 47.9 - - + +
197K TYR* 3.3 49.1 + - + +
198K VAL* 5.0 4.9 - - - +
199K LYS 3.2 1.4 + - - -
200K SER* 1.3 80.5 - - - +
202K THR* 1.3 80.2 + - - +
203K ALA* 2.8 16.0 + - + +
207K LEU* 5.1 8.1 - - + -
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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