Contacts of the helix formed by residues 423 - 434 (chain A) in PDB entry 6AGF
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 TYR 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A LEU* 4.0 38.0 + - + +
272A PHE* 3.7 32.1 - + + -
416A LEU* 3.8 9.7 - - + +
419A ALA* 3.2 38.8 - - + -
420A GLY 3.3 8.0 + - - +
421A LYS 3.1 1.0 - - - -
422A THR* 1.3 86.5 + - - +
424A MET* 1.3 60.3 + - - +
425A ILE* 3.2 3.3 + - - +
426A PHE* 3.5 18.7 + - + +
427A PHE* 3.7 11.6 - - - -
1444A PRO 4.6 4.5 + - - -
1445A THR* 4.1 30.5 + - + +
1448A ARG* 5.5 1.6 - - - -
1449A VAL* 4.5 5.1 - - + +
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Residues in contact with MET 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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412A PHE* 4.4 17.5 - - + -
416A LEU* 3.9 10.3 - - + +
421A LYS 3.2 15.4 + - - +
422A THR 3.1 2.6 - - - -
423A TYR* 1.3 76.7 - - - +
425A ILE* 1.3 69.9 + - + +
426A PHE 3.1 0.9 - - - -
427A PHE* 2.9 23.1 + - - +
428A VAL* 3.0 34.0 + - + +
1526A ILE* 5.0 12.6 - - + +
1527A ILE* 3.6 31.9 - - + -
1530A PHE* 5.0 9.4 - - + -
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Residues in contact with ILE 425 (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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422A THR* 3.2 29.6 - - - +
423A TYR* 3.2 1.3 - - - -
424A MET* 1.3 86.2 - - + +
426A PHE* 1.3 60.5 + - - +
428A VAL* 4.0 7.9 - - + +
429A VAL* 3.3 31.9 + - + +
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Residues in contact with PHE 426 (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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264A PHE* 4.6 2.5 - + + -
267A VAL* 4.0 24.0 - - + -
268A GLY* 3.9 21.1 - - - -
271A LEU* 4.1 17.7 - - + -
272A PHE* 3.8 28.0 - + + -
389A TYR* 4.7 7.0 - - - -
399A LEU* 4.2 16.8 - - + -
402A LEU* 5.0 2.9 - - + -
423A TYR* 3.5 16.1 + - + +
424A MET 3.1 0.4 - - - -
425A ILE* 1.3 80.0 - - - +
427A PHE* 1.3 80.4 + + - +
429A VAL* 3.3 4.1 + - + +
430A ILE* 3.1 54.5 + - + +
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Residues in contact with PHE 427 (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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272A PHE* 5.1 2.2 - + - -
389A TYR* 4.3 3.6 - - - -
402A LEU* 4.1 38.6 - - + -
408A TRP* 4.7 3.4 - + + -
411A LEU* 3.9 20.6 - - + -
412A PHE* 3.6 40.6 - + + -
415A THR* 3.1 33.7 - - + -
416A LEU* 4.5 3.4 - - + -
423A TYR 3.7 17.7 - - - -
424A MET* 2.9 7.1 + - - +
426A PHE* 1.3 89.6 - + - +
428A VAL* 1.3 62.2 + - - +
430A ILE* 4.2 3.4 - - - +
431A ILE* 2.9 40.1 + - + +
1530A PHE* 4.7 4.0 - - + -
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Residues in contact with VAL 428 (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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424A MET* 3.0 42.6 + - + +
425A ILE* 4.2 7.6 - - - +
426A PHE 3.4 0.2 - - - -
427A PHE* 1.3 75.9 - - - +
429A VAL* 1.3 63.6 + - + +
431A ILE* 4.6 0.5 - - - +
432A PHE* 3.3 23.8 + - + +
1530A PHE* 4.1 30.4 - - + -
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Residues in contact with VAL 429 (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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264A PHE* 5.0 7.6 - - + -
425A ILE* 3.3 24.2 - - + +
426A PHE* 3.3 5.7 + - - +
427A PHE 3.2 0.4 - - - -
428A VAL* 1.3 80.4 - - + +
430A ILE* 1.3 66.5 + - + +
432A PHE* 4.7 3.6 - - + -
433A LEU* 2.7 43.8 + - + +
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Residues in contact with ILE 430 (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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264A PHE* 3.5 51.8 - - + -
399A LEU* 4.8 9.0 - - + +
402A LEU* 3.7 36.1 - - + -
403A MET 5.7 0.2 - - - +
426A PHE* 3.1 43.9 + - + +
427A PHE* 4.2 4.5 - - - +
429A VAL* 1.3 80.5 - - + +
431A ILE* 1.3 60.5 + - - +
434A GLY* 2.9 26.8 + - - +
435A SER* 2.9 10.5 + - - +
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Residues in contact with ILE 431 (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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402A LEU* 4.1 25.4 - - + +
405A GLN* 4.1 11.2 + - - +
408A TRP* 3.9 45.5 - - + -
427A PHE* 2.9 23.9 + - + +
428A VAL 4.6 0.7 - - - +
430A ILE* 1.3 74.9 - - + +
432A PHE* 1.3 59.6 + - - +
435A SER* 3.4 12.3 - - - -
436A PHE* 3.4 17.5 - - - +
1530A PHE* 4.2 17.3 - - + -
1534A THR* 4.0 23.6 - - + -
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Residues in contact with PHE 432 (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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428A VAL* 3.3 20.7 + - + +
429A VAL* 3.9 2.9 - - + +
430A ILE 3.2 0.2 - - - -
431A ILE* 1.3 77.9 - - - +
433A LEU* 1.3 89.2 + - + +
434A GLY 3.3 0.2 - - - -
436A PHE* 3.3 32.9 + + - +
437A TYR* 3.2 25.5 + + + +
1475A LEU* 5.6 4.7 - - + -
1479A LEU* 5.1 11.9 - - + -
1482A LEU* 3.8 29.4 - - + -
1592A MET* 4.8 8.7 - - + -
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Residues in contact with LEU 433 (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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260A CYS* 5.6 9.0 - - - -
264A PHE* 3.9 24.5 - - + -
429A VAL* 2.7 30.1 + - + +
432A PHE* 1.3 97.4 - - + +
434A GLY* 1.3 56.7 + - - +
437A TYR* 3.7 24.4 - - + +
438A LEU* 4.1 9.1 + - + +
1475A LEU* 4.5 22.7 - - + -
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Residues in contact with GLY 434 (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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264A PHE* 4.2 17.4 - - - -
403A MET* 3.8 13.4 - - - +
429A VAL 3.9 0.2 + - - -
430A ILE* 2.9 15.6 + - - +
433A LEU* 1.3 78.9 - - - +
435A SER* 1.3 59.4 + - - -
436A PHE 3.2 2.7 + - - -
438A LEU* 3.3 33.8 + - - +
439A ILE 4.2 0.2 + - - -
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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