Contacts of the helix formed by residues 423 - 428 (chain A) in PDB entry 6T8O
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 PHE 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A LEU* 3.7 22.0 - - + -
422A ARG* 1.3 71.6 - - - +
424A SER* 1.3 60.6 + - - +
425A GLU 3.1 1.8 - - - -
426A VAL* 3.0 8.7 + - + +
427A LEU* 3.0 53.7 + - + +
442A ALA* 3.7 26.9 - - + -
478A ALA* 3.8 20.4 - - + -
481A LEU* 4.4 10.1 - - + -
482A SER* 3.4 23.1 - - - -
485A PHE* 4.2 13.9 - + - -
694A ALA* 3.6 20.9 - - + -
695A PHE 3.8 16.7 + - - +
696A VAL* 4.6 9.6 - - + -
700A GLU* 4.7 7.7 + - - +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LEU 5.2 4.0 - - - -
321A LEU* 4.1 22.2 - - - +
322A ASP 3.2 24.3 + - - -
323A PRO* 5.5 0.7 - - - -
324A ALA* 3.8 20.4 + - - +
422A ARG* 4.4 3.3 - - - +
423A PHE* 1.3 77.2 - - - +
425A GLU* 1.3 60.8 + - - +
426A VAL 3.1 0.7 - - - -
427A LEU* 4.4 4.3 - - - +
428A SER* 3.0 30.1 + - - -
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 3.7 29.4 - - + +
325A GLU 3.9 13.5 + - - +
327A LYS* 5.7 3.3 - - - +
420A MET 4.4 3.2 - - - +
421A VAL* 4.2 7.3 - - - +
422A ARG* 3.3 41.6 + - + +
423A PHE 3.1 0.6 - - - -
424A SER* 1.3 75.6 + - - +
426A VAL* 1.3 59.2 + - - +
428A SER* 4.2 9.1 + - - -
429A SER 5.2 0.5 + - - -
445A HIS* 3.6 26.6 + - - +
451A PRO* 4.4 5.2 - - - +
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 3.7 20.2 - - + -
422A ARG 3.6 15.7 - - - +
423A PHE* 3.0 12.4 + - + +
425A GLU* 1.3 80.5 - - - +
427A LEU* 1.3 63.1 + - - +
428A SER 3.3 1.7 + - - -
429A SER* 3.4 19.1 + - - -
442A ALA* 3.7 24.9 - - + -
444A GLY* 4.0 27.6 - - - +
445A HIS* 4.2 6.1 - - + +
451A PRO* 4.2 8.0 - - + +
453A ILE* 4.2 13.8 - - + +
694A ALA* 4.0 11.4 - - + -
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 3.8 27.3 - - + +
321A LEU* 3.7 16.6 - - + -
423A PHE* 3.0 52.4 + - + +
424A SER* 3.7 4.2 + - - +
426A VAL* 1.3 77.9 - - - +
428A SER* 1.3 58.5 + - - +
429A SER 3.1 7.3 + - - +
432A TYR* 3.4 54.0 - - + +
433A ASP* 4.6 2.6 + - - +
442A ALA* 3.9 11.7 - - + -
482A SER* 4.9 1.1 - - - +
485A PHE* 3.7 22.0 - - + -
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 5.7 5.6 - - - -
424A SER 3.0 19.4 + - - -
425A GLU* 4.2 9.9 + - - -
426A VAL 3.3 0.4 - - - -
427A LEU* 1.3 75.7 - - - +
429A SER* 1.3 63.6 + - - +
430A PRO* 3.8 2.4 - - - +
433A ASP* 5.9 1.1 - - - +
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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