Contacts of the helix formed by residues 429 - 437 (chain B) in PDB entry 3QGT
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B TRP* 3.8 26.0 - - + -
390B GLU 5.0 1.1 - - - +
391B THR* 4.2 9.4 - - + -
404B TRP* 3.8 32.3 - - + -
426B LEU* 3.4 40.6 - - + +
427B GLY 2.8 16.7 + - - +
428B PRO* 1.3 73.9 - - - +
430B TYR* 1.3 74.2 + - + +
431B GLY 4.7 2.0 - - - +
432B PHE* 2.8 16.3 + - - +
433B GLN* 3.2 9.9 + - - -
485B MET* 4.0 24.2 - - + -
486B ALA 4.3 3.4 - - - +
487B LEU 4.3 8.1 - - - +
489B PRO* 6.4 0.7 - - + -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLU* 5.6 0.2 - - - -
386B PHE* 3.4 42.2 - + + -
404B TRP* 3.6 33.9 - + - -
429B ILE* 1.3 72.8 - - + +
431B GLY* 1.3 60.1 + - - +
433B GLN* 2.9 9.6 + - - +
434B TRP* 2.8 45.3 + - - +
476B ALA* 3.7 15.8 + - + +
489B PRO* 3.5 26.2 - - + +
490B CYS* 3.0 26.2 + - - +
491B HIS* 3.1 42.7 + + + -
525B TYR* 4.6 5.8 - - - -
611B UMP 5.7 0.9 - - - -
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Residues in contact with GLY 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 3.4 29.9 - - - -
389B GLY* 3.4 21.3 - - - -
390B GLU 3.9 11.5 + - - -
429B ILE* 3.0 3.8 + - - +
430B TYR* 1.3 77.1 - - - +
432B PHE* 1.3 61.4 + - - +
434B TRP* 3.2 3.2 + - - +
435B ARG* 3.2 20.3 + - - +
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLY 3.7 9.4 + - - -
391B THR* 3.6 18.7 - - + +
428B PRO* 3.3 28.5 - - + -
429B ILE 2.8 12.6 + - - +
431B GLY* 1.3 72.3 - - - -
433B GLN* 1.3 60.9 + - - +
436B HIS* 2.7 58.0 + + + -
438B GLY 5.2 0.7 - - - -
439B ALA* 3.6 37.5 - - + -
441B TYR* 3.7 28.9 - + + -
448B TYR* 3.7 41.7 - + - -
481B ASP* 4.0 6.3 - - - -
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B PRO* 3.0 29.8 + - - +
429B ILE 3.2 6.8 + - - +
430B TYR 2.9 8.1 + - - +
432B PHE* 1.3 79.3 - - - +
434B TRP* 1.3 60.7 + - + +
437B PHE* 3.2 31.1 + - - +
455B GLN* 2.7 23.3 + - - +
475B CYS 4.2 3.1 - - - +
476B ALA* 3.7 34.3 - - + +
478B ASN* 3.0 31.7 + - + +
481B ASP* 3.0 28.5 + - - +
485B MET* 3.8 1.5 - - + +
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Residues in contact with TRP 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B LEU* 4.2 9.0 - - + -
386B PHE* 3.7 49.4 - + + +
387B ILE* 4.2 13.2 - - + -
430B TYR* 2.8 37.7 + + + +
431B GLY* 3.2 6.5 + - - +
433B GLN* 1.3 77.4 - - + +
435B ARG* 1.3 66.3 + - + +
454B ASP* 3.6 0.7 - - - +
455B GLN* 3.0 30.1 + - - +
456B LEU* 3.0 21.7 + - + -
474B LEU* 3.7 37.7 + - + +
475B CYS 5.0 0.4 - - - -
476B ALA* 4.4 9.4 - - + +
494B CYS* 5.8 0.4 - - - -
525B TYR* 4.0 21.1 - + - -
528B PHE* 3.8 34.5 - + - -
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Residues in contact with ARG 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B PHE 4.5 0.2 - - - +
387B ILE 3.0 22.3 + - - +
388B ARG* 4.6 5.7 + - - +
389B GLY* 3.8 15.9 - - - +
431B GLY 3.2 13.2 + - - +
434B TRP* 1.3 86.8 - - + +
436B HIS* 1.3 90.7 + - + +
451B LYS 4.0 1.2 - - - +
452B GLY 4.5 0.3 - - - +
453B VAL 3.5 6.5 - - - +
454B ASP* 2.6 60.0 + - - +
456B LEU* 3.7 25.1 - - - +
457B LYS* 4.8 5.8 - - - +
583B ILE* 6.1 0.4 - - - +
584B GLU* 3.3 38.3 + - - +
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Residues in contact with HIS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ARG 5.8 0.8 + - - -
389B GLY* 5.1 7.2 + - - -
432B PHE* 2.7 52.0 + + + +
435B ARG* 1.3 97.0 + - + +
437B PHE* 1.3 66.0 + - - +
438B GLY 3.1 0.5 + - - -
439B ALA* 3.0 19.5 + - + +
448B TYR* 3.2 42.4 + + + +
449B GLU* 4.2 6.5 - - - -
450B ASN 4.6 2.9 - - - -
451B LYS 2.7 27.8 + - - +
452B GLY* 3.8 2.9 - - - -
453B VAL 3.8 1.8 - - - -
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Residues in contact with PHE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A PHE* 4.4 6.5 - + - -
477A TRP 4.8 2.0 - - - -
478A ASN* 3.6 11.0 - - - -
479A VAL* 3.6 37.7 - - + -
480A LYS* 3.5 23.8 - - + -
432B PHE 3.5 0.4 + - - -
433B GLN* 3.2 36.9 + - + +
436B HIS* 1.3 73.3 - - - +
438B GLY* 1.3 62.9 + - - +
452B GLY* 3.5 0.7 - - - -
453B VAL* 2.8 41.7 + - - +
455B GLN* 3.6 20.2 - - - +
475B CYS* 3.8 10.1 - - - -
477B TRP 4.7 2.5 - - - -
478B ASN* 3.3 42.0 - - + -
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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