Contacts of the helix formed by residues 422 - 428 (chain F) in PDB entry 6T8B
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 ARG 422 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322F ASP* 4.0 31.8 + - - +
323F PRO 4.0 20.3 + - - +
324F ALA* 5.0 1.1 - - - -
325F GLU* 5.1 9.6 + - - +
326F VAL* 4.7 18.5 - - + +
420F MET* 3.7 28.5 - - - +
421F VAL* 1.3 88.4 - - - +
423F PHE* 1.3 63.3 + - - +
424F SER 3.5 1.3 - - - +
425F GLU* 3.3 40.0 + - + +
426F VAL* 3.6 3.3 + - - +
694F ALA* 4.5 0.7 - - - -
695F PHE* 4.3 21.8 - - - -
700F GLU* 4.9 7.6 + - - +
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Residues in contact with PHE 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F LEU* 3.5 28.7 - - + -
322F ASP 5.4 0.2 + - - -
422F ARG* 1.3 71.6 - - - +
424F SER* 1.3 62.2 + - - +
425F GLU 3.1 1.8 - - - -
426F VAL* 3.0 6.4 + - + +
427F LEU* 3.0 48.7 + - + +
442F ALA* 3.8 17.5 - - + -
478F ALA* 3.4 37.5 - - + -
481F LEU* 3.7 22.7 - - + -
482F SER* 3.7 11.2 - - - -
485F PHE* 4.4 1.3 - + - -
694F ALA* 3.6 21.3 - - + -
695F PHE 3.9 7.1 + - - +
696F VAL* 3.6 25.1 - - + -
700F GLU* 4.2 9.3 + - - +
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Residues in contact with SER 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LEU* 4.9 5.8 - - - -
321F LEU* 3.7 28.9 - - - +
322F ASP 2.8 28.6 + - - -
323F PRO* 4.0 11.4 - - - +
324F ALA* 4.0 3.3 + - - +
422F ARG* 4.7 0.9 - - - +
423F PHE* 1.3 75.0 - - - +
425F GLU* 1.3 63.9 + - - +
427F LEU* 4.4 2.5 - - - +
428F SER* 3.0 30.8 + - - -
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Residues in contact with GLU 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F ALA* 3.4 40.1 - - + +
325F GLU 4.2 3.8 + - - -
326F VAL 4.7 4.0 + - - -
327F LYS* 5.0 6.8 + - - +
419F GLN* 5.4 5.6 + - - -
420F MET 4.2 7.6 - - - +
421F VAL* 3.9 7.3 - - - +
422F ARG* 3.3 34.3 + - + +
423F PHE 3.1 0.6 - - - -
424F SER* 1.3 78.4 + - - +
426F VAL* 1.3 61.3 + - - +
428F SER* 3.3 13.6 + - - -
429F SER* 4.4 5.5 + - - -
445F HIS* 3.5 27.1 + - + +
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Residues in contact with VAL 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F ARG 3.8 10.5 - - - +
423F PHE* 3.0 9.7 + - + +
425F GLU* 1.3 76.1 - - - +
427F LEU* 1.3 61.5 + - - +
428F SER 3.2 0.5 + - - -
429F SER* 2.8 28.1 + - - -
442F ALA* 3.5 31.2 - - + -
444F GLY* 3.8 32.5 - - - +
445F HIS* 3.4 28.0 - - + +
451F PRO* 4.7 4.5 - - + -
453F ILE* 4.2 9.8 - - + +
694F ALA* 4.0 12.6 - - + -
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Residues in contact with LEU 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F LEU* 3.7 31.1 - - + +
321F LEU* 3.6 19.1 - - + -
423F PHE* 3.0 45.3 + - + +
424F SER* 4.6 2.0 - - - +
426F VAL* 1.3 77.5 - - - +
428F SER* 1.3 56.5 + - - +
429F SER 3.0 6.9 + - - +
432F TYR* 3.4 54.8 - - + +
433F ASP* 4.9 0.7 + - - -
442F ALA* 3.7 22.2 - - + -
482F SER* 4.5 2.9 - - - +
485F PHE* 3.7 15.9 - - + -
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Residues in contact with SER 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F LEU* 4.9 10.1 - - - +
424F SER 3.0 20.0 + - - -
425F GLU* 3.3 12.5 + - - -
426F VAL 3.2 0.4 - - - -
427F LEU* 1.3 74.8 - - - +
429F SER* 1.3 59.8 + - - +
430F PRO* 4.1 1.7 - - - +
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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