Contacts of the helix formed by residues 198 - 204 (chain K) in PDB entry 6R1U
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 ASN 198 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K LEU 4.3 3.6 - - - +
195K GLU* 3.0 29.2 + - - +
196K VAL 3.9 2.4 - - - +
197K SER* 1.3 83.3 + - - +
199K HIS* 1.3 59.3 + - + +
200K TRP* 3.0 48.1 - - + +
201K TRP* 2.6 31.2 + - - +
202K TYR 4.0 1.0 + - - -
344K ARG* 4.4 2.7 + - - -
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Residues in contact with HIS 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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197K SER 4.0 2.6 + - - -
198K ASN* 1.3 72.9 - - - +
200K TRP* 1.3 81.9 + + + +
201K TRP 3.4 0.7 + - - -
202K TYR* 3.7 8.7 + - - +
203K SER* 4.0 7.1 + - - -
344K ARG* 4.2 16.2 + - - +
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Residues in contact with TRP 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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59K THR* 3.7 16.4 - - + -
87K CYS* 3.5 26.0 - - + -
195K GLU* 3.6 23.8 - - + -
198K ASN* 3.0 38.2 - - + +
199K HIS* 1.3 94.5 - + + +
201K TRP* 1.3 75.8 + + - +
203K SER* 2.5 30.9 + - - +
204K MET* 3.2 27.4 + - + +
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Residues in contact with TRP 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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86K SER* 3.7 30.9 - - - -
87K CYS* 4.1 25.7 + - + +
88K GLY* 4.7 3.2 - - - +
89K GLU* 4.9 0.7 - - - -
192K ARG 4.8 1.4 + - - -
195K GLU* 3.3 39.0 + - + +
196K VAL* 3.6 30.6 - - + +
198K ASN* 2.6 24.5 + - + +
200K TRP* 1.3 83.6 - + + +
202K TYR* 1.3 68.6 + - + +
204K MET* 3.2 14.2 + - - +
205K LEU* 3.4 27.2 + - + -
340K LEU* 3.7 21.6 - - + +
341K VAL* 3.8 33.9 - - + -
344K ARG* 4.5 7.6 - - + -
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Residues in contact with TYR 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 ASN 4.0 1.0 + - - -
199K HIS 3.7 5.1 + - - +
200K TRP 3.3 0.2 - - - -
201K TRP* 1.3 86.1 - + + +
203K SER* 1.3 61.2 + - - +
205K LEU* 2.9 49.2 + - + +
208K PRO* 3.9 25.4 - - + +
209K PRO* 4.0 7.3 - - + +
299K GLU 6.1 0.4 - - - -
300K TYR* 5.5 4.0 - + - -
303K ASP* 4.6 19.9 + - + -
306K MET* 3.6 39.8 + - + +
341K VAL* 5.0 0.4 - - + -
344K ARG* 3.8 35.4 - - + +
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Residues in contact with SER 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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55K LYS* 4.8 5.7 + - - -
199K HIS 4.0 4.1 + - - -
200K TRP* 2.5 35.0 + - - +
202K TYR* 1.3 83.8 - - - +
204K MET* 1.3 63.2 + - - +
205K LEU 3.3 5.2 + - - +
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Residues in contact with MET 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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55K LYS* 3.6 27.6 - - - +
56K ALA 4.1 5.8 - - - +
57K GLY* 3.3 38.4 - - - +
58K CYS* 3.7 9.4 - - - -
59K THR* 5.1 0.7 - - + +
84K HIS* 2.7 33.5 + - - +
86K SER* 3.9 4.2 - - - -
87K CYS* 3.5 17.3 - - - -
200K TRP* 3.4 39.9 - - + +
201K TRP 3.2 8.7 + - - +
202K TYR 3.1 0.6 - - - -
203K SER* 1.3 84.5 + - - +
205K LEU* 1.3 57.9 + - - +
206K ILE* 4.4 0.2 - - - +
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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