Contacts of the helix formed by residues 396 - 400 (chain B) in PDB entry 6RQT
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 ALA 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B ASN* 3.5 15.7 + - + +
394B PRO 3.2 5.2 - - - +
395B ASP* 1.3 80.3 + - - +
397B THR* 1.3 64.9 + - - +
398B GLN* 3.1 18.0 + - + +
399B HIS 3.4 13.2 + - - -
400B GLN* 3.6 14.6 + - - +
521B LEU* 3.8 12.1 - - + -
523B GLU* 3.7 24.9 - - + +
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Residues in contact with THR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ALA* 1.3 72.8 - - - +
398B GLN* 1.3 64.0 - - - +
399B HIS 3.1 2.2 + - - -
400B GLN* 3.7 23.1 + - + +
521B LEU* 6.1 0.2 - - - +
523B GLU 2.8 32.7 + - - -
524B SER* 3.4 9.5 - - - -
527B PHE* 4.9 9.2 - - + -
528B LEU* 3.9 27.6 - - + -
649B MET* 5.0 4.5 - - + -
666B PRO* 3.3 33.5 - - - +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960A MET* 3.7 6.4 - - - +
961A VAL* 4.1 21.0 - - + +
210B ARG* 3.9 13.5 + - - -
393B ASN* 4.1 12.3 - - + +
396B ALA* 3.1 6.3 - - + -
397B THR* 1.3 80.5 + - - +
399B HIS* 1.3 90.0 + - + +
400B GLN 3.7 0.2 - - - -
523B GLU* 3.6 36.8 - - + +
636B GLN* 5.2 5.3 - - - +
666B PRO* 4.1 11.3 - - - +
667B PHE* 4.2 14.8 - - - +
669B GLN* 5.2 0.5 - - - +
670B VAL* 3.3 34.7 - - - +
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Residues in contact with HIS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL 4.0 0.3 - - - +
209B GLN* 3.3 20.9 - - - +
210B ARG* 3.5 31.2 - - + +
213B HIS* 3.7 25.0 - + - -
215B MET* 3.7 31.6 - - + -
392B ASP* 3.9 30.6 + - + -
393B ASN 3.5 19.4 + - - +
394B PRO* 4.0 7.1 - - + +
396B ALA 3.4 7.3 + - - +
397B THR 3.1 0.2 - - - -
398B GLN* 1.3 103.4 + - + +
400B GLN* 1.3 58.4 + - - +
636B GLN* 4.1 10.9 + - - -
667B PHE* 4.8 3.1 - + - -
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 3.2 41.0 - - + +
208B VAL 2.9 23.3 + - - +
210B ARG* 4.0 4.1 + - - +
394B PRO 5.0 2.6 + - - -
395B ASP 5.8 1.4 - - - -
396B ALA 3.6 18.0 + - - +
397B THR* 3.7 23.7 + - + +
398B GLN 3.7 2.0 - - - -
399B HIS* 1.3 76.8 + - - +
401B GLU* 1.3 95.9 + - - +
402B VAL* 5.9 1.1 - - + -
503B VAL* 5.7 3.6 - - + -
505B ARG* 4.5 5.1 - - - +
649B MET* 4.4 21.8 - - + +
666B PRO* 5.4 1.9 - - - +
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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
------------------------------------------------------------
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