Contacts of the helix formed by residues 429 - 437 (chain A) in PDB entry 3QG2
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 ILE 429 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A TRP* 3.7 28.0 - - + -
386A PHE* 5.2 1.1 - - + -
390A GLU 5.1 0.7 - - - +
391A THR* 4.1 10.5 - - + -
404A TRP* 3.9 27.6 - - + -
426A LEU* 3.5 37.5 - - + +
427A GLY 2.7 16.8 + - - +
428A PRO* 1.3 72.8 - - - +
430A TYR* 1.3 76.4 + - + +
431A GLY 4.8 1.6 - - - +
432A PHE* 2.8 15.6 + - - +
433A GLN* 3.1 11.8 + - - -
485A MET* 3.8 25.6 - - + -
486A ALA 4.3 2.5 - - - +
487A LEU 4.3 8.5 - - - +
489A PRO* 6.5 0.4 - - + -
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Residues in contact with TYR 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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386A PHE* 3.4 43.3 - + + -
404A TRP* 3.8 29.6 - + - -
429A ILE* 1.3 74.0 - - + +
431A GLY* 1.3 55.4 + - - +
433A GLN* 3.0 7.4 + - - +
434A TRP* 2.7 52.7 + - - +
476A ALA* 3.7 14.9 - - + +
485A MET* 5.7 0.4 - - - -
489A PRO* 3.4 19.4 - - + +
490A CYS* 2.9 28.4 + - - +
491A HIS* 3.2 47.4 + + + -
525A TYR* 4.5 4.3 - - - -
611A UMP 5.3 1.2 + - - -
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Residues in contact with GLY 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 3.4 29.8 - - - -
389A GLY* 3.4 20.4 - - - -
390A GLU 3.9 12.4 + - - -
429A ILE* 3.0 4.0 + - - +
430A TYR* 1.3 77.0 - - - +
432A PHE* 1.3 61.6 + - - +
434A TRP* 3.3 2.8 + - - +
435A ARG* 3.1 20.4 + - - +
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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
----------------------------------------------------------
389A GLY 3.9 10.3 + - - -
391A THR* 3.7 19.8 - - + +
428A PRO* 3.3 28.9 - - + -
429A ILE 2.8 13.9 + - - +
431A GLY* 1.3 72.1 - - - -
433A GLN* 1.3 60.3 + - - +
436A HIS* 2.6 59.5 + + + +
438A GLY 5.4 0.7 - - - -
439A ALA* 3.7 36.8 - - + -
440A GLU 4.2 0.9 - - - -
441A TYR* 3.7 25.4 - + + -
448A TYR* 3.6 45.1 - + - -
481A ASP* 4.0 5.8 - - - -
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Residues in contact with GLN 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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428A PRO* 3.0 31.4 + - - +
429A ILE 3.1 9.0 + - - +
430A TYR 3.0 8.1 + - - +
432A PHE* 1.3 81.3 - - - +
434A TRP* 1.3 58.5 + - - +
437A PHE* 3.2 29.7 + - - +
455A GLN* 2.7 24.5 + - - +
475A CYS 4.3 2.5 - - - +
476A ALA* 3.6 34.3 - - - +
478A ASN* 2.9 32.2 + - - +
481A ASP* 3.0 28.9 + - - +
485A MET* 3.9 2.4 - - + +
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Residues in contact with TRP 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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383A LEU* 4.1 10.8 - - + -
386A PHE* 3.6 47.3 - + + -
387A ILE* 4.2 11.9 - - + -
430A TYR* 2.7 42.7 + + - +
431A GLY* 3.6 5.8 - - - +
433A GLN* 1.3 77.0 - - - +
435A ARG* 1.3 66.5 + - + +
455A GLN* 3.0 30.2 + - - +
456A LEU* 3.2 18.5 + - + -
474A LEU* 3.6 38.9 - - + +
475A CYS 4.9 0.7 - - - -
476A ALA* 4.4 12.3 - - + +
494A CYS* 5.8 0.4 - - - -
525A TYR* 4.0 24.5 - + - -
528A PHE* 3.8 33.9 - + - -
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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
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386A PHE 4.4 0.4 - - - +
387A ILE 2.8 30.6 + - - +
388A ARG* 4.6 5.4 + - - +
389A GLY* 3.7 15.9 - - - -
431A GLY 3.1 14.4 + - - +
434A TRP* 1.3 87.4 - - + +
436A HIS* 1.3 90.3 + - + +
451A LYS 4.1 0.9 - - - +
452A GLY 4.7 0.2 - - - -
453A VAL 3.4 6.9 - - - +
454A ASP* 2.8 58.6 + - - +
456A LEU* 3.8 25.5 - - - +
457A LYS* 5.0 3.8 - - - +
584A GLU* 2.9 35.6 + - - +
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Residues in contact with HIS 436 (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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388A ARG 5.9 0.4 + - - -
389A GLY* 5.1 7.4 + - - -
432A PHE* 2.6 48.6 + + + +
435A ARG* 1.3 99.0 + - + +
437A PHE* 1.3 66.5 + - - +
438A GLY 3.1 0.2 + - - -
439A ALA* 2.9 21.3 + - + +
448A TYR* 2.9 42.7 + + + +
449A GLU* 4.3 3.8 - - - -
450A ASN 4.7 2.7 - - - -
451A LYS 2.7 27.9 + - - +
452A GLY* 3.5 0.4 - - - -
453A VAL 3.7 5.2 - - - +
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Residues in contact with PHE 437 (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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432A PHE* 3.5 0.6 + - - -
433A GLN* 3.2 36.1 + - - +
436A HIS* 1.3 72.6 - - - +
438A GLY* 1.3 62.4 + - - +
452A GLY* 3.4 1.4 - - - -
453A VAL* 2.8 39.6 + - - +
455A GLN* 3.6 13.7 - - - +
475A CYS* 3.8 9.6 - - - -
477A TRP 4.6 3.6 - - - -
478A ASN* 3.2 43.5 - - + -
437B PHE* 4.2 8.3 - + - -
477B TRP 4.9 0.4 - - - -
478B ASN* 3.7 10.5 - - - -
479B VAL* 3.5 46.7 - - + -
480B LYS* 3.5 24.1 - - + +
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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