Contacts of the helix formed by residues 296 - 306 (chain W) in PDB entry 6AH0
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 PRO 296 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228W ASN 5.5 2.2 - - - -
294W VAL 4.0 3.2 - - - -
295W SER* 1.3 68.8 - - - +
297W HIS* 1.3 62.3 + - - -
298W GLU 3.3 2.0 - - - -
299W MET* 3.0 8.0 + - - +
300W LEU* 3.0 21.3 + - - -
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Residues in contact with HIS 297 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W SER* 3.1 6.5 + - - +
296W PRO* 1.3 75.0 - - - +
298W GLU* 1.3 57.1 + - - +
300W LEU* 3.5 1.2 + - - +
301W GLN* 3.0 25.8 + - - -
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Residues in contact with GLU 298 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119W ASP 5.3 4.3 + - - -
120W PHE* 6.0 0.7 - - - +
121W GLU* 5.3 13.7 - - - +
295W SER 4.3 3.8 + - - -
296W PRO 3.3 0.4 - - - -
297W HIS* 1.3 71.1 - - - +
299W MET* 1.3 64.4 + - - +
301W GLN* 4.5 1.3 - - - +
302W ALA* 2.9 21.7 + - - -
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Residues in contact with MET 299 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W SER 5.4 0.2 + - - -
296W PRO* 3.0 10.4 + - - -
298W GLU* 1.3 75.9 - - - +
300W LEU* 1.3 56.9 + - - +
302W ALA* 3.4 2.3 + - - -
303W VAL* 3.0 24.1 + - - -
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Residues in contact with LEU 300 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296W PRO 3.0 11.6 + - - -
297W HIS* 3.9 3.1 - - - +
299W MET* 1.3 73.1 - - - +
301W GLN* 1.3 58.7 + - - +
303W VAL* 2.8 19.1 + - - +
304W VAL* 3.1 9.4 + - - -
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Residues in contact with GLN 301 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297W HIS 3.0 17.1 + - - -
298W GLU* 3.9 1.6 - - - +
300W LEU* 1.3 73.1 - - - +
302W ALA* 1.3 58.0 + - - +
304W VAL* 3.1 3.1 + - - +
305W LEU* 2.9 27.7 + - - -
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Residues in contact with ALA 302 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298W GLU 2.9 15.3 + - - -
299W MET 3.7 4.7 - - - -
301W GLN* 1.3 73.9 - - - +
303W VAL* 1.3 56.5 + - - +
304W VAL 3.3 0.2 - - - -
305W LEU* 4.6 1.8 - - - +
306W CYS* 3.1 30.2 + - - +
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Residues in contact with VAL 303 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299W MET 3.0 9.9 + - - -
300W LEU* 2.8 11.0 + - - +
302W ALA* 1.3 76.5 - - - +
304W VAL* 1.3 56.4 + - - +
309W LYS* 2.9 23.8 - - - +
311W PHE* 2.9 19.0 + - - +
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Residues in contact with VAL 304 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300W LEU 3.1 6.8 + - - -
301W GLN* 3.1 6.6 + - - +
303W VAL* 1.3 78.2 - - - +
305W LEU* 1.3 59.5 + - - +
306W CYS 3.4 0.8 + - - -
307W SER* 4.9 1.9 + - - -
309W LYS 4.2 5.8 - - - +
310W THR* 5.2 2.3 - - - -
311W PHE 3.4 19.2 + - - +
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Residues in contact with LEU 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C LYS* 5.3 13.5 - - - +
301W GLN 2.9 14.2 + - - -
302W ALA* 4.8 1.6 - - - +
304W VAL* 1.3 76.0 - - - +
306W CYS* 1.3 57.4 + - - +
307W SER 3.6 3.9 + - - -
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Residues in contact with CYS 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302W ALA* 3.1 21.0 + - - +
304W VAL 3.4 1.6 - - - -
305W LEU* 1.3 74.6 - - - +
307W SER* 1.3 49.3 + - - +
308W LYS* 2.7 18.5 + - - -
309W LYS* 2.9 16.8 + - - +
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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