Contacts of the helix formed by residues 439 - 457 (chain A) in PDB entry 1G88
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 ASP 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A ASP* 3.2 11.9 - - - +
413A TYR* 3.7 31.9 - - + +
436A LYS* 3.1 19.8 + - - +
438A PHE* 1.3 76.3 - - - +
440A LEU* 1.3 67.8 + - - +
441A ARG* 3.6 10.6 + - - +
442A GLN* 2.9 33.3 + - + +
443A CYS* 3.1 21.8 + - - +
445A ARG* 4.4 3.8 + - - -
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Residues in contact with LEU 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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314A ILE* 3.7 17.0 - - + -
394A GLU* 3.5 48.2 - - + +
395A GLY 3.8 14.6 - - - +
396A ASP* 3.0 18.9 + - - +
438A PHE* 3.7 14.0 - - + -
439A ASP* 1.3 69.4 - - - +
441A ARG* 1.3 59.0 + - - +
443A CYS* 3.0 5.9 + - + +
444A HIS* 2.8 27.0 + - - +
531A ARG* 4.2 5.6 - - + -
532A ALA* 3.9 29.8 - - + +
535A LEU* 3.7 20.2 - - + -
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Residues in contact with ARG 441 (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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311A GLN* 3.1 52.1 + - - +
312A PRO* 3.4 18.3 + - - +
313A PRO 4.6 0.8 + - - -
314A ILE* 3.4 40.5 - - + +
396A ASP* 4.7 0.8 + - - -
439A ASP* 3.4 12.2 + - - +
440A LEU* 1.3 78.3 - - - +
442A GLN* 1.3 63.5 + - - +
444A HIS* 3.1 6.7 + - + +
445A ARG* 2.8 47.6 + - + +
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Residues in contact with GLN 442 (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 TYR 5.1 0.7 - - - +
413A TYR* 3.8 36.9 - - - +
416A ARG* 3.4 40.8 - - - +
417A GLU* 4.2 10.9 + - - -
439A ASP* 2.9 28.1 + - + +
440A LEU 3.3 0.4 - - - -
441A ARG* 1.3 71.7 - - - +
443A CYS* 1.3 55.4 + - - +
445A ARG* 2.9 30.8 + - + +
446A GLN* 2.7 39.0 + - + +
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Residues in contact with CYS 443 (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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438A PHE* 3.5 33.7 - - + -
439A ASP 3.1 9.7 + - - +
440A LEU* 3.0 10.5 + - + +
442A GLN* 1.3 80.7 + - - +
444A HIS* 1.3 55.4 + - - +
446A GLN* 3.0 7.5 + - - +
447A MET* 2.7 58.9 + - + +
498A LEU* 3.6 26.2 - - - +
499A CYS* 4.3 3.8 - - - -
532A ALA* 4.3 1.8 - - - -
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Residues in contact with HIS 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 3.4 34.3 + - + +
440A LEU 2.8 12.1 + - - +
441A ARG* 3.2 11.0 - - - +
443A CYS* 1.3 76.5 - - - +
445A ARG* 1.3 66.5 + - + +
447A MET* 3.1 28.1 - - - +
448A GLN* 3.2 48.2 + - - +
535A LEU* 3.6 31.4 - - + +
538A GLU* 4.8 8.5 - - - -
539A VAL* 4.4 14.6 - - + -
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Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 4.6 10.3 - - - +
439A ASP* 4.4 3.6 + - - -
441A ARG* 2.8 37.2 + - + +
442A GLN* 3.2 41.5 - - - +
444A HIS* 1.3 79.3 - - + +
446A GLN* 1.3 61.9 + - - +
448A GLN* 3.7 10.2 - - - +
449A GLN* 3.3 25.8 + - - +
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Residues in contact with GLN 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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416A ARG* 5.5 7.6 + - - -
442A GLN* 2.7 20.0 + - + +
443A CYS* 3.4 10.3 - - - +
445A ARG* 1.3 70.6 - - - +
447A MET* 1.3 65.9 + - - +
448A GLN 3.1 1.6 - - - -
449A GLN* 3.4 14.1 + - - +
450A GLN* 2.8 69.3 + - - +
498A LEU* 3.8 23.6 - - + -
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Residues in contact with MET 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 CYS* 2.7 49.8 + - - +
444A HIS* 3.1 21.5 - - + +
446A GLN* 1.3 73.2 - - - +
448A GLN* 1.3 65.9 + - - +
451A ALA* 3.0 27.2 + - - +
495A LEU* 3.8 5.9 - - + +
498A LEU* 3.8 18.4 - - + +
499A CYS* 4.2 8.1 - - - -
532A ALA* 3.9 18.4 - - + +
535A LEU* 3.9 14.6 - - + +
536A LEU* 3.7 43.9 - - + +
539A VAL* 4.3 8.2 - - + +
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Residues in contact with GLN 448 (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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444A HIS* 3.2 45.3 + - + +
445A ARG* 3.7 9.1 - - - +
446A GLN 3.1 0.6 - - - -
447A MET* 1.3 81.1 - - - +
449A GLN* 1.3 53.7 + - - +
451A ALA* 3.0 4.0 + - - +
452A ALA* 2.7 37.1 + - - +
539A VAL* 4.2 16.3 - - + +
543A MET* 3.5 30.5 - - + +
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 6.0 1.6 - - - +
445A ARG 3.3 16.6 + - - +
446A GLN* 4.0 14.9 + - - +
448A GLN* 1.3 78.7 - - - +
450A GLN* 1.3 58.4 + - - +
452A ALA* 3.1 7.9 + - + +
453A THR* 2.8 43.7 + - + +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLN* 2.8 42.9 + - - +
449A GLN* 1.3 74.5 - - - +
451A ALA* 1.3 56.9 + - - +
453A THR* 3.4 9.8 + - - +
454A ALA* 3.0 27.4 + - - +
490A ILE* 3.6 28.5 - - + +
494A ASP* 4.1 12.6 + - - +
495A LEU* 3.4 26.6 - - + +
498A LEU* 3.9 17.0 - - - +
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Residues in contact with ALA 451 (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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447A MET 3.0 18.8 + - - +
448A GLN 3.5 2.9 - - - +
450A GLN* 1.3 76.0 - - - +
452A ALA* 1.3 61.7 + - - +
453A THR 3.3 0.2 - - - -
454A ALA* 4.1 5.2 - - - -
455A GLN* 2.8 32.6 + - - +
495A LEU* 4.0 21.5 - - + -
539A VAL* 4.4 16.8 - - + -
540A LEU* 5.2 1.1 - - + -
543A MET* 4.7 10.5 - - + +
545A ILE* 3.5 12.0 - - + +
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Residues in contact with ALA 452 (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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448A GLN 2.7 15.8 + - - +
449A GLN* 3.4 11.0 - - + +
451A ALA* 1.3 77.5 - - - +
453A THR* 1.3 58.7 + - + +
455A GLN* 3.3 9.0 + - - +
456A ALA* 2.9 29.8 + - - +
543A MET* 4.0 17.9 - - - -
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Residues in contact with THR 453 (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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449A GLN* 2.8 29.9 + - + +
450A GLN* 3.4 13.4 + - - +
452A ALA* 1.3 75.7 - - + +
454A ALA* 1.3 64.4 + - - +
456A ALA* 3.9 5.8 - - - +
457A ALA* 3.0 30.1 + - - +
488A ALA* 4.0 5.7 + - - +
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Residues in contact with ALA 454 (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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450A GLN 3.0 18.4 + - - +
451A ALA* 3.7 5.4 - - - +
452A ALA 3.3 0.4 - - - -
453A THR* 1.3 81.0 + - - +
455A GLN* 1.3 60.7 + - - +
457A ALA* 3.9 5.2 - - - +
458A ALA* 5.2 1.0 - - - +
488A ALA 3.3 12.3 - - - +
489A GLY* 3.3 16.6 - - - -
490A ILE* 3.2 40.1 - - + +
545A ILE* 3.9 9.5 - - + +
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Residues in contact with GLN 455 (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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451A ALA 2.8 15.0 + - - +
452A ALA* 3.5 8.8 + - - +
453A THR 3.1 0.2 - - - -
454A ALA* 1.3 75.8 - - - +
456A ALA* 1.3 57.9 + - - +
457A ALA 2.9 4.0 - - - -
458A ALA* 2.8 35.1 + - + +
542A THR 5.0 0.5 - - - +
543A MET* 3.3 39.5 - - - +
544A PRO* 3.5 29.8 - - - +
545A ILE* 4.1 10.8 - - + +
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Residues in contact with ALA 456 (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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452A ALA 2.9 17.2 + - - +
453A THR* 4.1 6.5 - - - +
455A GLN* 1.3 70.8 - - - +
457A ALA* 1.3 56.6 + - - +
458A ALA 2.8 11.6 + - - -
459A ALA* 3.3 19.1 + - - +
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Residues in contact with ALA 457 (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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453A THR 3.0 20.1 + - - +
454A ALA 3.9 6.4 - - - +
455A GLN 2.9 2.5 - - - -
456A ALA* 1.3 74.5 - - - +
458A ALA* 1.3 58.1 + - - +
459A ALA 3.5 1.3 - - - +
460A ALA* 4.2 15.9 - - + +
488A ALA* 3.3 40.4 - - + -
489A GLY* 3.7 7.2 + - - +
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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
------------------------------------------------------------
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