Contacts of the helix formed by residues 447 - 460 (chain R) in PDB entry 1G4W
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 SER 447 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445R LEU* 3.9 1.6 - - - +
446R PRO* 1.3 80.7 - - - +
448R THR* 1.3 65.0 + - - +
449R ASP* 3.6 12.5 + - - +
450R GLN* 3.0 41.6 + - - +
451R LEU 3.6 3.5 + - - -
529R GLN* 3.4 12.2 + - - +
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Residues in contact with THR 448 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447R SER* 1.3 73.1 - - - +
449R ASP* 1.3 60.8 + - - +
451R LEU* 3.3 4.3 + - - +
452R GLU* 3.2 20.1 + - - +
529R GLN* 3.7 21.2 + - + +
532R ALA* 3.5 18.9 - - + +
533R MET* 3.6 38.5 - - + +
536R GLN* 3.7 24.5 - - - +
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Residues in contact with ASP 449 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447R SER* 3.0 12.0 + - - +
448R THR* 1.3 77.8 + - - +
450R GLN* 1.3 60.1 + - + +
452R GLU* 3.5 10.5 + - - +
453R TYR* 2.9 29.3 + - - +
536R GLN* 3.7 23.4 + - - +
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Residues in contact with GLN 450 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413R GLU 5.3 1.0 + - - -
414R ALA* 4.3 10.1 - - - +
438R ASN* 2.8 27.1 - - - +
445R LEU* 3.7 12.0 - - + +
446R PRO* 2.9 45.7 - - - +
447R SER* 3.0 19.9 + - - +
449R ASP* 1.3 75.4 - - - +
451R LEU* 1.3 61.1 + - - +
453R TYR* 3.6 12.5 - - + +
454R LEU* 2.8 30.3 + - - +
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Residues in contact with LEU 451 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439R TRP* 4.1 22.2 - - + -
445R LEU* 3.4 20.5 - - + +
447R SER 3.6 1.6 + - - -
448R THR 3.3 9.1 + - - +
449R ASP 3.2 0.4 - - - -
450R GLN* 1.3 76.9 - - - +
452R GLU* 1.3 62.3 + - - +
454R LEU* 3.0 8.7 + - + +
455R ALA* 2.8 28.9 + - - +
490R THR* 4.2 8.7 - - + +
491R MET* 5.1 3.1 - - - -
494R ALA* 4.1 12.8 - - + -
529R GLN* 3.7 38.1 - - + +
530R LEU* 4.1 19.7 - - + -
533R MET* 3.8 22.9 - - + -
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Residues in contact with GLU 452 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448R THR 3.2 8.9 + - - +
449R ASP* 3.7 12.7 - - - +
451R LEU* 1.3 80.3 - - - +
453R TYR* 1.3 55.6 + - - +
455R ALA* 3.2 5.0 + - - +
456R ASP* 2.9 32.6 + - - +
498R LYS* 3.1 32.7 + - - +
533R MET* 4.1 17.8 - - + +
536R GLN* 3.3 27.3 - - - +
537R LEU* 3.6 17.3 - - + +
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Residues in contact with TYR 453 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414R ALA* 5.8 5.2 - - + -
415R ILE* 3.7 17.7 - - + -
449R ASP 2.9 18.7 + - - +
450R GLN* 3.6 12.3 - - + +
452R GLU* 1.3 74.9 - - - +
454R LEU* 1.3 65.7 + - + +
456R ASP* 3.1 14.8 + - + +
457R ARG* 3.0 64.0 + - + +
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Residues in contact with LEU 454 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373R VAL* 5.0 1.8 - - + -
415R ILE* 4.7 14.4 - - + -
434R LEU* 5.6 4.3 - - + -
436R VAL* 3.5 34.5 - - + -
439R TRP* 3.8 24.9 - - + -
445R LEU* 3.5 26.2 - - + -
450R GLN 2.8 11.6 + - - +
451R LEU* 3.2 10.5 - - + +
453R TYR* 1.3 82.3 - - + +
455R ALA* 1.3 62.4 + - - +
457R ARG* 3.4 4.2 + - + +
458R VAL* 3.0 35.6 + - + +
491R MET* 4.0 19.7 - - + -
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Residues in contact with ALA 455 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451R LEU 2.8 12.1 + - - +
452R GLU 3.4 8.7 - - - +
454R LEU* 1.3 76.6 - - - +
456R ASP* 1.3 60.6 - - - +
458R VAL* 3.5 1.3 + - - -
459R LYS* 3.0 24.4 + - - +
491R MET* 5.0 3.3 - - - -
494R ALA* 4.0 22.4 - - + +
495R LEU* 3.7 15.8 - - + +
498R LYS* 3.8 24.1 - - + +
533R MET* 4.0 7.6 - - + -
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Residues in contact with ASP 456 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452R GLU* 2.9 23.1 + - - +
453R TYR* 3.1 14.9 + - + +
455R ALA* 1.3 75.9 - - - +
457R ARG* 1.3 53.9 + - + +
459R LYS* 3.0 6.6 + - - +
460R ASN* 2.6 54.9 + - - +
498R LYS* 3.0 35.1 + - - +
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Residues in contact with ARG 457 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409R ALA* 3.3 28.2 + - - +
412R GLY* 6.3 0.8 - - - -
415R ILE* 3.5 39.3 - - + +
417R GLN* 2.5 38.2 - - - +
434R LEU* 3.6 13.9 - - + +
453R TYR* 3.0 60.3 + - + +
454R LEU* 4.0 3.8 - - + +
456R ASP* 1.3 77.1 - - + +
458R VAL* 1.3 61.6 + - - +
460R ASN* 3.4 12.8 - - - +
461R SER* 3.4 21.0 - - - -
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Residues in contact with VAL 458 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370R SER* 6.0 0.7 - - - -
371R CYS* 3.8 22.1 - - - -
373R VAL* 4.1 11.7 - - + -
434R LEU* 3.7 19.5 - - + -
454R LEU* 3.0 23.9 + - + +
455R ALA* 3.7 5.2 - - - +
457R ARG* 1.3 77.3 - - - +
459R LYS* 1.3 60.6 + - - +
461R SER* 2.9 18.1 + - - -
462R ASN* 4.7 1.2 + - - +
463R GLN 5.2 2.1 + - - -
477R PRO* 4.2 5.8 - - + -
491R MET* 3.5 24.7 - - + -
495R LEU* 3.8 27.1 - - + -
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Residues in contact with LYS 459 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455R ALA 3.0 16.7 + - - +
456R ASP* 3.0 7.9 + - - +
458R VAL* 1.3 80.2 - - - +
460R ASN* 1.3 63.5 + - - +
461R SER 3.4 1.4 + - - -
463R GLN* 2.8 80.9 + - + +
495R LEU* 4.6 15.7 - - + +
498R LYS* 5.6 11.0 - - + -
499R ASP* 5.7 11.2 - - + +
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Residues in contact with ASN 460 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456R ASP* 2.6 43.9 + - - +
457R ARG* 3.4 9.7 - - - +
458R VAL 3.2 0.2 - - - -
459R LYS* 1.3 80.5 - - - +
461R SER* 1.3 58.0 + - - +
463R GLN* 3.7 19.8 + - - +
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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