Contacts of the helix formed by residues 523 - 539 (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 ASP 523 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442R HIS* 3.5 21.4 - - - +
486R GLY* 6.2 0.4 - - - -
521R LEU 4.2 4.0 - - - +
522R GLU* 1.3 88.6 - - + +
524R ALA* 1.3 65.7 + - - +
525R SER* 3.0 34.3 + - - -
526R GLN* 3.2 35.8 + - - +
527R PHE* 3.7 7.4 + - - +
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Residues in contact with ALA 524 (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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523R ASP* 1.3 69.7 + - - +
525R SER* 1.3 67.6 + - - +
527R PHE* 2.9 19.9 + - - +
528R VAL* 3.0 23.9 + - + +
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Residues in contact with SER 525 (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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442R HIS 4.4 3.1 + - - -
443R GLN* 4.9 0.2 - - - -
444R PRO* 3.5 32.0 - - - +
523R ASP* 3.0 24.0 + - - -
524R ALA* 1.3 77.6 + - - +
526R GLN* 1.3 61.4 + - - +
528R VAL* 3.4 14.1 + - - +
529R GLN* 3.4 8.7 + - - +
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Residues in contact with GLN 526 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439R TRP* 4.5 4.7 - - + -
442R HIS* 3.7 6.7 - - - +
443R GLN 3.3 44.3 + - - +
444R PRO* 3.9 10.8 - - + -
486R GLY* 3.4 20.7 - - - +
487R ARG* 3.5 18.3 + - - +
490R THR* 2.7 35.3 + - + +
521R LEU* 5.6 1.7 - - + -
522R GLU 4.9 2.2 - - - +
523R ASP* 3.2 24.8 + - - +
524R ALA 3.2 0.2 - - - -
525R SER* 1.3 78.0 - - - +
527R PHE* 1.3 64.5 + - - +
529R GLN* 3.1 14.4 + - - +
530R LEU* 3.1 18.0 + - - +
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Residues in contact with PHE 527 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505R LEU* 3.5 47.3 - - + -
506R GLU* 4.2 8.7 - - + -
509R ARG* 3.8 47.1 - - + +
521R LEU* 4.6 15.8 - - + +
523R ASP 3.7 8.6 + - - +
524R ALA* 2.9 12.4 + - - +
526R GLN* 1.3 77.8 - - - +
528R VAL* 1.3 64.1 + - + +
530R LEU* 3.1 23.4 + - + +
531R LYS* 3.0 44.4 + - + +
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Residues in contact with VAL 528 (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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524R ALA* 3.0 25.8 + - + +
525R SER* 3.6 9.2 - - - +
526R GLN 3.2 0.2 - - - -
527R PHE* 1.3 79.4 - - + +
529R GLN* 1.3 61.0 + - - +
531R LYS* 3.3 17.0 + - + +
532R ALA* 3.0 21.8 + - + +
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Residues in contact with GLN 529 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439R TRP* 5.3 2.6 - - - -
444R PRO* 3.6 11.7 - - + +
445R LEU* 2.7 50.3 + - - +
447R SER* 3.4 24.6 + - - +
448R THR* 3.7 16.3 + - - +
451R LEU* 3.7 24.8 - - + +
490R THR* 5.3 1.6 - - - +
525R SER 3.4 7.6 + - - +
526R GLN* 3.1 10.5 + - - +
528R VAL* 1.3 77.5 - - - +
530R LEU* 1.3 61.8 + - - +
532R ALA* 3.2 7.4 + - - +
533R MET* 2.8 27.6 + - - +
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Residues in contact with LEU 530 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451R LEU* 4.1 10.5 - - + +
490R THR* 3.8 30.5 - - + +
493R ALA* 3.8 18.2 - - + -
494R ALA* 3.9 11.2 - - - +
497R LEU* 3.9 9.5 - - + +
505R LEU* 3.8 16.4 - - + -
521R LEU* 3.6 30.5 - - + -
526R GLN 3.1 18.2 + - - +
527R PHE* 3.3 21.5 - - + +
529R GLN* 1.3 74.0 - - - +
531R LYS* 1.3 67.4 + - - +
533R MET* 2.8 6.7 + - - +
534R GLN* 2.8 24.3 + - - +
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Residues in contact with LYS 531 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505R LEU* 3.7 19.5 - - + +
527R PHE* 3.0 36.1 + - + +
528R VAL* 3.5 16.8 - - + +
530R LEU* 1.3 77.6 - - - +
532R ALA* 1.3 63.3 + - - +
534R GLN* 3.2 6.5 + - - +
535R ALA* 2.9 22.6 + - - +
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Residues in contact with ALA 532 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448R THR* 3.5 23.1 - - + +
528R VAL* 3.0 15.1 + - + +
529R GLN* 3.4 9.9 - - - +
530R LEU 3.1 0.2 - - - -
531R LYS* 1.3 75.5 - - - +
533R MET* 1.3 62.9 + - - +
535R ALA* 3.1 17.6 + - - +
536R GLN* 3.2 18.3 + - + +
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Residues in contact with MET 533 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448R THR* 3.6 15.9 - - + +
451R LEU* 3.8 29.6 - - + -
452R GLU* 4.1 21.4 - - + +
455R ALA* 4.0 6.7 - - + -
494R ALA* 3.1 39.5 - - + +
497R LEU* 4.1 7.2 - - + -
498R LYS* 4.0 13.0 - - + -
529R GLN 2.8 16.1 + - - +
530R LEU* 2.8 11.8 + - - +
532R ALA* 1.3 73.7 - - - +
534R GLN* 1.3 64.3 + - - +
536R GLN* 3.2 6.9 + - - +
537R LEU* 3.0 43.0 + - + +
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Residues in contact with GLN 534 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497R LEU* 3.4 32.0 - - + +
501R PRO 5.2 0.9 - - - -
502R HIS* 3.8 15.2 + - - +
503R SER 2.7 29.7 + - - -
505R LEU* 3.5 18.8 + - + +
530R LEU 2.8 14.8 + - - +
531R LYS* 3.5 10.2 - - - +
533R MET* 1.3 72.9 - - - +
535R ALA* 1.3 53.1 + - - +
537R LEU* 3.0 7.3 + - - +
538R LEU* 2.7 57.9 + - + +
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Residues in contact with ALA 535 (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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531R LYS 2.9 11.6 + - - +
532R ALA* 3.2 15.0 - - - +
534R GLN* 1.3 76.2 - - - +
536R GLN* 1.3 58.4 + - + +
538R LEU* 3.1 11.2 + - - +
539R MET* 2.8 38.4 + - + +
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Residues in contact with GLN 536 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448R THR* 3.7 27.2 - - - +
449R ASP* 3.7 21.0 + - - +
452R GLU* 3.3 23.4 - - - +
532R ALA* 3.3 15.0 - - - +
533R MET* 3.2 5.7 + - - +
535R ALA* 1.3 77.0 - - + +
537R LEU* 1.3 63.8 + - - +
539R MET* 3.2 25.1 + - - +
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Residues in contact with LEU 537 (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* 3.6 26.2 - - - +
497R LEU* 3.6 43.7 - - + +
498R LYS* 3.9 18.8 - - + +
501R PRO* 3.6 24.8 - - + +
533R MET* 3.0 34.7 + - + +
534R GLN* 3.5 7.4 - - - +
536R GLN* 1.3 77.9 - - - +
538R LEU* 1.3 61.1 + - - +
539R MET 4.5 2.1 - - - -
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Residues in contact with LEU 538 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501R PRO* 3.2 27.8 - - + +
502R HIS* 3.9 22.2 - - + +
534R GLN* 2.7 41.0 + - + +
535R ALA* 3.5 7.6 - - - +
537R LEU* 1.3 76.0 - - - +
539R MET* 1.3 68.9 + - + +
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Residues in contact with MET 539 (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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535R ALA* 2.8 28.2 + - + +
536R GLN* 3.2 18.1 + - - +
537R LEU 4.5 2.2 - - - -
538R LEU* 1.3 82.3 - - + +
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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