Contacts of the helix formed by residues 434 - 448 (chain A) in PDB entry 3AF5
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 GLY 434 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ILE* 3.9 11.2 - - - +
375A LEU* 5.0 2.9 - - - +
433A VAL* 1.3 78.2 - - - +
435A ARG* 1.3 77.0 + - - -
436A ALA 3.1 1.5 + - - -
437A GLN* 2.8 19.2 + - - +
438A GLU* 3.4 14.4 + - - +
469A HIS* 5.2 0.8 + - - -
654A SO4 3.4 14.4 - - - -
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Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A HIS 3.2 23.6 + - - -
345A ILE* 4.0 0.2 - - - +
373A THR* 5.6 2.8 - - - +
405A ARG* 5.0 0.4 - - - +
430A ALA* 4.1 10.5 - - + -
431A MET 4.7 1.0 + - - -
433A VAL 4.2 0.6 - - - -
434A GLY* 1.3 79.2 - - - -
436A ALA* 1.3 58.7 + - - +
438A GLU* 3.5 26.8 + - - +
439A VAL* 2.8 34.7 + - + +
548A VAL* 3.5 40.6 - - + +
549A SER* 3.9 8.7 - - - -
591A PHE* 2.8 39.7 + - - -
592A SER* 4.0 1.4 + - - +
593A GLY* 3.5 19.3 - - - +
654A SO4 2.8 49.4 + - - +
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA* 3.9 12.2 - - + +
431A MET 3.4 21.2 + - - +
432A ALA 3.7 7.2 - - - +
434A GLY 3.1 1.0 - - - -
435A ARG* 1.3 78.2 - - - +
437A GLN* 1.3 65.4 + - - +
439A VAL* 3.9 2.4 - - - +
440A MET* 2.9 35.2 + - - +
462A ILE* 3.8 30.7 - - + -
519A ILE* 4.6 6.9 - - + +
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Residues in contact with GLN 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.3 21.3 - - + -
432A ALA 3.0 18.6 + - - +
433A VAL* 3.5 3.8 - - - +
434A GLY 2.8 33.5 + - - +
436A ALA* 1.3 75.6 - - - +
438A GLU* 1.3 64.4 + - - +
440A MET* 3.1 11.3 + - - +
441A MET* 3.0 27.9 + - - +
462A ILE 3.7 3.8 - - - +
465A ALA* 3.7 6.4 - - - +
466A THR* 3.5 23.3 + - - +
469A HIS* 3.5 32.0 + - + +
492A PHE* 4.3 12.1 - - + -
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A THR* 3.6 16.0 + - - -
374A ARG* 3.0 45.3 + - - +
375A LEU* 3.5 19.0 + - + +
405A ARG* 3.8 12.5 + - - +
434A GLY 3.4 5.5 + - - +
435A ARG* 3.2 37.5 + - - +
437A GLN* 1.3 79.2 - - - +
439A VAL* 1.3 61.6 + - + +
441A MET* 3.2 8.8 + - - +
442A VAL* 3.2 25.7 + - + +
591A PHE* 4.1 18.3 - - + +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 4.5 8.5 - - + -
428A ILE* 4.3 16.2 - - + -
435A ARG* 2.8 24.4 + - + +
436A ALA* 3.9 3.8 - - - +
438A GLU* 1.3 69.3 - - - +
440A MET* 1.3 67.2 + - - +
442A VAL* 3.0 9.1 + - - +
443A LEU* 2.9 33.8 + - + +
519A ILE* 4.0 22.4 - - + -
548A VAL* 4.3 31.2 - - + -
591A PHE* 4.6 19.3 - - + -
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Residues in contact with MET 440 (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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436A ALA 2.9 23.5 + - - +
437A GLN* 3.1 13.2 + - - +
439A VAL* 1.3 78.3 - - - +
441A MET* 1.3 63.6 + - + +
443A LEU* 3.3 1.4 + - - -
444A GLU* 2.8 31.2 + - - +
458A LEU* 3.7 30.7 - - + -
462A ILE* 4.0 23.3 - - - -
463A TRP* 4.5 3.4 - - + -
466A THR* 3.8 27.6 - - + +
492A PHE* 4.4 7.2 - - + +
497A PHE* 3.3 43.2 - - + -
519A ILE* 4.3 7.2 - - + -
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Residues in contact with MET 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 3.6 31.9 + - + +
375A LEU* 3.3 31.0 - - + -
437A GLN 3.0 18.3 + - - +
438A GLU 3.4 6.5 - - - +
439A VAL 3.2 0.2 - - - -
440A MET* 1.3 83.7 - - + +
442A VAL* 1.3 63.8 + - - +
444A GLU* 3.7 7.6 - - + +
445A GLU* 3.0 21.1 + - - +
480A LEU* 4.2 11.9 - - - -
483A GLN* 6.0 0.2 - - - -
491A PRO* 4.0 29.2 - - + +
492A PHE* 3.6 34.5 - - + +
497A PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 3.6 29.4 + - + +
409A GLU* 3.6 33.4 - - + +
412A LEU* 4.3 21.1 - - + -
413A ILE* 5.7 2.2 - - + -
438A GLU* 3.2 15.5 + - - +
439A VAL* 3.0 10.9 + - - +
441A MET* 1.3 78.0 - - - +
443A LEU* 1.3 63.3 + - + +
445A GLU 3.8 0.2 + - - -
446A TYR* 3.3 22.0 + - + +
591A PHE* 3.9 24.9 - - + -
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 3.9 15.5 - - + -
413A ILE* 4.5 10.8 - - + -
416A ILE* 3.8 25.4 - - + -
428A ILE* 5.0 2.0 - - + -
439A VAL* 2.9 34.4 + - + +
440A MET* 3.9 4.0 - - - +
442A VAL* 1.3 75.9 - - - +
444A GLU* 1.3 59.7 + - - +
446A TYR* 3.3 4.8 + - - +
447A ALA* 2.8 27.2 + - - +
452A ILE* 3.5 14.5 - - + +
456A ILE* 3.6 30.3 - - + -
496A ILE* 4.3 1.8 - - - -
497A PHE* 4.8 2.0 - - + -
517A ILE* 4.3 14.1 - - + -
519A ILE* 4.2 13.9 - - + -
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A MET 2.8 19.3 + - - +
441A MET* 3.7 10.0 - - + +
443A LEU* 1.3 73.4 - - - +
445A GLU* 1.3 60.6 + - - +
446A TYR 3.0 1.3 - - - -
447A ALA* 2.9 17.2 + - + +
448A ARG* 3.0 38.5 + - - +
489A TYR* 2.7 25.4 + - - -
491A PRO* 3.2 42.2 - - - +
494A SER* 3.8 19.0 + - - +
496A ILE* 3.8 8.2 - - - +
497A PHE* 4.2 6.3 - - + -
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 2.5 49.2 + - - +
441A MET 3.0 7.7 + - - +
444A GLU* 1.3 77.7 - - - +
446A TYR* 1.3 61.5 + - - +
447A ALA 3.5 0.3 + - - -
448A ARG* 3.5 41.4 + - - +
449A ILE* 3.8 15.0 + - + +
479A ARG* 3.6 22.6 + - - -
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Residues in contact with TYR 446 (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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409A GLU* 5.8 4.7 - - - +
413A ILE* 3.3 46.0 - - + +
416A ILE* 6.5 0.4 - - + -
417A HIS* 3.1 32.9 + + - -
442A VAL* 3.3 18.6 + - + +
443A LEU* 3.4 5.6 - - - +
444A GLU 3.0 0.4 - - - -
445A GLU* 1.3 78.8 - - - +
447A ALA* 1.3 61.7 + - - +
449A ILE* 3.2 30.5 - - + +
451A GLY* 3.0 50.6 + - - -
452A ILE* 3.6 18.4 - - + -
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Residues in contact with ALA 447 (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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443A LEU 2.8 14.3 + - - +
444A GLU* 2.9 10.5 + - + +
446A TYR* 1.3 74.0 - - - +
448A ARG* 1.3 53.9 + - + +
449A ILE 3.0 4.3 - - - -
450A GLY* 2.6 28.1 + - - -
451A GLY 3.7 0.2 + - - -
452A ILE* 3.6 26.6 + - + +
494A SER* 5.2 1.1 - - - +
496A ILE* 3.8 25.1 - - + -
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 5.4 0.8 - - - +
444A GLU* 3.0 33.9 + - - +
445A GLU* 3.8 40.1 + - - +
446A TYR 3.4 0.2 - - - -
447A ALA* 1.3 74.7 - - + +
449A ILE* 1.3 60.6 + - + +
450A GLY 3.3 1.1 - - - -
479A ARG* 5.4 3.6 - - - +
483A GLN* 3.7 20.0 + - - +
489A TYR* 3.1 41.4 + - + +
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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
------------------------------------------------------------
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