Contacts of the helix formed by residues 283 - 289 (chain H) in PDB entry 6KW5
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 283 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260H CYS* 3.0 36.3 - - - -
265H ASN* 4.3 11.9 - - - +
266H GLU 3.9 9.2 - - - -
267H SER* 3.7 26.0 - - - -
268H ILE* 6.4 0.4 - - - -
270H VAL 4.6 5.2 - - - -
272H TYR* 3.7 5.4 - - - -
282H LEU* 1.3 77.8 - - - +
284H SER* 1.3 65.7 + - - +
285H ARG* 3.4 9.0 - - + +
286H CYS* 4.2 9.0 - - - +
287H PHE* 3.6 20.4 + - - +
763L GLN* 5.9 1.1 - - - +
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Residues in contact with SER 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H VAL* 4.1 17.2 + - - +
272H TYR* 3.7 23.9 + - - -
283H CYS* 1.3 75.8 - - - +
285H ARG* 1.3 60.1 + - - +
287H PHE* 3.2 3.6 + - - +
288H GLN* 2.9 39.6 + - - +
303H ARG* 4.9 2.3 + - - -
230J LEU* 4.4 8.7 - - - +
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Residues in contact with ARG 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 3.1 21.5 + - - -
208A ILE* 3.0 28.1 + - - +
210A SER* 4.1 15.6 + - - -
283H CYS* 3.4 4.2 - - + +
284H SER* 1.3 76.4 - - - +
286H CYS* 1.3 63.9 + - - +
287H PHE 3.4 0.5 + - - -
288H GLN* 3.5 16.5 + - - +
289H GLU* 3.5 38.2 + - + +
291H HIS* 5.2 0.2 - - - -
761L VAL 4.5 7.2 + - - -
762L LEU 5.3 1.1 - - - -
763L GLN* 3.6 41.2 + - - +
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Residues in contact with CYS 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260H CYS* 4.1 11.4 - - - -
262H THR* 4.5 9.9 - - + -
263H CYS* 4.0 24.0 - - - -
282H LEU* 4.5 19.5 - - + +
283H CYS* 4.0 8.1 + - - +
284H SER 3.4 0.4 - - - -
285H ARG* 1.3 77.2 - - - +
287H PHE* 1.3 56.9 + - - +
289H GLU 4.3 0.9 - - - -
290H GLY* 3.4 2.6 + - - -
291H HIS* 3.1 41.6 + - + +
292H PHE* 4.2 3.6 - - - -
763L GLN* 3.8 21.8 - - - -
792L PHE* 4.5 11.2 - - - -
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Residues in contact with PHE 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A TYR* 2.6 33.4 + - - -
272H TYR* 3.9 33.4 - + + -
282H LEU* 4.2 18.1 - - + +
283H CYS 3.6 15.9 + - - +
284H SER 3.2 4.1 + - - +
285H ARG 3.2 0.4 - - - -
286H CYS* 1.3 76.9 - - - +
288H GLN* 1.3 57.0 + - - +
289H GLU 3.2 2.1 + - - -
290H GLY* 3.7 4.4 + - - +
292H PHE* 4.1 10.8 - + - -
298H SER* 3.5 35.0 - - - -
301H PHE* 3.7 37.2 - + + -
230J LEU* 4.1 13.0 - - + -
802L ARG* 4.4 12.3 - - - -
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Residues in contact with GLN 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A TYR* 4.0 5.0 + - - -
284H SER* 2.9 29.0 + - - +
285H ARG* 3.5 16.0 + - - +
287H PHE* 1.3 77.1 - - - +
289H GLU* 1.3 64.8 + - + +
228J ASP* 4.1 26.0 + - - +
229J ASP* 4.6 7.5 + - - +
230J LEU* 3.7 39.8 - - + +
797L VAL 3.6 10.2 - - - +
799L VAL* 5.2 2.4 + - - +
802L ARG* 3.5 21.4 + - - +
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Residues in contact with GLU 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 3.1 27.9 + - - -
208A ILE* 3.6 32.6 + - + +
483A TYR* 4.9 0.7 - - - -
285H ARG* 3.5 32.3 + - + +
288H GLN* 1.3 83.6 - - + +
290H GLY* 1.3 63.8 + - - +
291H HIS* 2.6 40.8 + - + +
763L GLN* 4.4 2.4 - - - +
796L SER* 3.4 9.5 - - - -
797L VAL* 2.6 38.3 + - - +
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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