Contacts of the helix formed by residues 407 - 424 (chain A) in PDB entry 2G47
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 GLN 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A TYR* 2.7 24.2 + - - +
337A LEU* 5.5 0.4 - - + -
404A GLU* 3.8 13.1 + - - +
405A GLY 3.0 19.9 + - - +
406A PRO* 1.3 72.2 - - - +
408A GLU* 1.3 64.0 - - - +
409A TRP* 2.9 37.9 - - + +
410A VAL* 3.2 25.8 + - + +
411A PHE 3.4 4.2 + - - -
459A PHE* 3.7 3.8 - - - -
524A LEU* 3.5 31.0 - - + +
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Residues in contact with GLU 408 (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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406A PRO 3.9 2.2 + - - -
407A GLN* 1.3 70.6 - - - +
409A TRP* 1.3 62.1 + - - +
411A PHE* 3.1 4.5 + - + +
412A GLN* 2.8 37.6 + - + +
459A PHE* 3.5 49.7 - - + +
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Residues in contact with TRP 409 (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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407A GLN* 2.9 42.0 - - + +
408A GLU* 1.3 78.8 - - - +
410A VAL* 1.3 79.3 + - + +
412A GLN* 3.6 7.8 - - - +
413A GLU* 2.8 45.5 + - - +
524A LEU* 5.1 6.7 - - + +
525A PRO* 3.1 33.0 - - + -
526A THR 3.8 11.9 - - - -
527A LYS* 3.8 39.7 - - + -
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Residues in contact with VAL 410 (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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333A TYR* 4.0 12.1 - - + -
336A HIS* 3.6 33.9 - - + +
337A LEU* 3.8 18.6 - - + -
407A GLN* 3.2 23.5 + - + +
408A GLU 3.1 0.4 - - - -
409A TRP* 1.3 114.6 - - + +
411A PHE* 1.3 63.8 + - - +
413A GLU* 3.2 7.6 + - - +
414A CYS* 3.1 24.1 + - - -
524A LEU* 5.7 1.8 - - + -
525A PRO* 5.4 5.4 - - + -
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Residues in contact with PHE 411 (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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328A SER* 3.7 24.0 - - - -
333A TYR* 4.4 14.3 - + + -
407A GLN 3.4 2.4 + - - +
408A GLU* 3.1 10.4 + - + +
410A VAL* 1.3 80.3 - - - +
412A GLN* 1.3 65.5 + - - +
414A CYS* 3.2 7.4 + - - +
415A LYS* 2.8 40.2 + - + +
456A LEU* 3.9 31.8 - - + +
457A GLU 3.9 13.7 - - - -
458A GLU 3.4 24.2 - - - -
459A PHE* 3.5 50.0 - + + -
464A ILE* 5.8 1.3 - - + -
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Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLU* 2.8 25.4 + - + +
409A TRP* 3.6 8.3 - - - +
411A PHE* 1.3 85.0 - - - +
413A GLU* 1.3 62.7 + - - +
415A LYS* 3.6 25.9 - - - +
416A ASP* 3.0 58.0 + - - +
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A HIS* 5.1 9.7 + - - -
409A TRP* 2.8 31.3 + - + +
410A VAL* 3.2 8.3 + - - +
412A GLN* 1.3 76.4 - - - +
414A CYS* 1.3 59.7 + - - +
416A ASP* 3.5 5.8 + - - +
417A LEU* 3.0 35.9 + - + +
526A THR 5.0 1.4 - - - +
527A LYS* 2.9 27.2 + - - +
528A ASN* 2.8 44.5 + - - +
531A ILE* 3.6 18.6 - - + +
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Residues in contact with CYS 414 (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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336A HIS* 3.9 39.0 - - - -
410A VAL* 3.1 18.1 + - - -
411A PHE* 3.6 9.2 - - - +
413A GLU* 1.3 78.6 - - - +
415A LYS* 1.3 55.0 + - - +
417A LEU* 3.1 9.8 + - - +
418A ASN* 2.7 43.9 + - - +
456A LEU* 3.9 15.3 - - + -
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Residues in contact with LYS 415 (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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411A PHE* 2.8 28.9 + - + +
412A GLN* 3.3 26.4 + - - +
414A CYS* 1.3 76.5 - - - +
416A ASP* 1.3 61.5 + - - +
418A ASN* 3.3 3.6 + - - +
419A ALA* 2.9 28.6 + - + +
455A LEU* 5.4 0.7 - - - +
456A LEU* 3.5 43.6 + - + +
457A GLU* 2.7 35.6 + - - +
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Residues in contact with ASP 416 (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 GLN* 3.0 47.2 + - - +
413A GLU* 3.9 5.5 - - - +
415A LYS* 1.3 78.8 - - - +
417A LEU* 1.3 64.5 + - + +
419A ALA* 3.3 9.1 + - - +
420A VAL* 3.1 27.7 + - + +
531A ILE* 6.4 2.0 - - + -
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Residues in contact with LEU 417 (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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413A GLU* 3.0 29.6 + - + +
414A CYS* 3.1 10.3 + - - +
416A ASP* 1.3 77.0 - - + +
418A ASN* 1.3 62.1 + - - +
420A VAL* 3.1 11.7 + - + +
421A ALA* 2.9 29.3 + - - +
528A ASN* 4.6 7.0 - - - +
531A ILE* 3.7 44.6 - - + -
532A PRO* 4.4 10.8 - - + -
613A LEU* 3.9 31.0 - - + +
614A ALA* 4.4 6.3 - - - -
634A TYR* 4.9 1.3 + - + -
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Residues in contact with ASN 418 (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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414A CYS* 2.7 27.1 + - - +
415A LYS* 3.5 5.8 - - - +
417A LEU* 1.3 74.6 - - - +
419A ALA* 1.3 57.6 + - - +
421A ALA* 3.7 7.4 - - - +
422A PHE* 2.8 31.7 + - - +
453A GLU 5.7 0.4 + - - -
454A TYR* 3.0 32.3 + - - +
455A LEU* 4.0 5.3 - - - +
456A LEU* 3.8 23.8 - - - +
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Residues in contact with ALA 419 (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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415A LYS* 2.9 14.8 + - + +
416A ASP* 3.5 13.7 - - - +
418A ASN* 1.3 78.2 - - - +
420A VAL* 1.3 61.4 + - + +
422A PHE* 3.5 2.4 + - - +
423A ARG* 3.0 25.3 + - - +
455A LEU* 3.8 17.7 - - + +
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Residues in contact with VAL 420 (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 ASP* 3.1 15.0 + - + +
417A LEU* 3.1 15.7 + - + +
419A ALA* 1.3 78.8 - - + +
421A ALA* 1.3 61.7 + - - +
423A ARG* 3.2 6.0 + - - +
424A PHE* 3.0 31.8 + - + -
531A ILE* 6.0 2.0 - - + -
532A PRO* 4.5 5.2 - - + +
535A PHE* 3.7 35.7 - - + -
634A TYR* 3.1 30.4 + - + +
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Residues in contact with ALA 421 (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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417A LEU 2.9 15.9 + - - +
418A ASN* 3.7 7.9 - - - +
420A VAL* 1.3 77.2 - - - +
422A PHE* 1.3 57.5 + - - +
424A PHE 3.6 0.5 - - - -
425A LYS* 2.9 30.8 + - - +
454A TYR* 3.9 17.8 + - + +
634A TYR* 3.4 15.2 + - - +
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Residues in contact with PHE 422 (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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55A THR* 5.4 1.1 - - + -
56A LYS* 3.9 8.3 - - - -
57A SER* 3.4 43.5 - - - -
58A PRO* 5.5 1.3 - - + -
418A ASN 2.8 21.8 + - - +
419A ALA 3.9 3.6 - - - +
421A ALA* 1.3 72.6 - - - +
423A ARG* 1.3 66.0 + - - +
425A LYS* 3.3 33.9 - - + +
450A LEU* 3.2 27.1 - - + -
451A THR* 3.6 26.9 - - + -
454A TYR* 3.6 35.8 - + + -
455A LEU* 3.9 20.2 - - + -
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Residues in contact with ARG 423 (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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57A SER* 2.8 22.5 + - - -
58A PRO* 3.2 37.8 - - + +
59A GLU* 2.9 37.4 + - + +
419A ALA 3.0 18.3 + - - +
420A VAL* 3.5 6.7 - - - +
422A PHE* 1.3 81.4 - - + +
424A PHE* 1.3 93.3 + - + +
425A LYS 3.6 1.7 + - - +
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Residues in contact with PHE 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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59A GLU* 4.1 7.9 - - + -
420A VAL* 3.0 36.8 + - + +
421A ALA* 3.6 2.7 - - - -
423A ARG* 1.3 120.2 - - - +
425A LYS* 1.3 58.7 + - - +
535A PHE* 3.4 48.5 - + + -
537A ILE* 6.1 0.2 - - + -
568A PHE 6.1 0.2 - - - -
569A LEU* 3.6 19.7 - - + +
570A PRO* 3.4 28.9 - - + -
571A LYS* 2.7 33.5 + - - -
634A TYR* 4.2 15.0 - + + +
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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