Contacts of the helix formed by residues 504 - 519 (chain A) in PDB entry 4RG7
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 THR 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A HIS 3.9 7.8 + - - -
501A HIS 3.1 21.5 - - - +
502A TYR 3.5 0.5 - - - +
503A ASN* 1.3 79.2 - - - +
505A GLY* 1.3 65.4 + - - +
506A TRP* 3.5 7.1 + - - +
507A VAL* 3.5 17.0 - - + +
508A LEU* 3.4 17.2 + - - +
534A ILE* 5.8 0.7 - - - -
535A GLU* 5.1 1.6 + - - -
29B GLU* 4.4 8.9 + - - +
30B ARG* 3.1 41.3 + - - +
33B ALA* 5.1 4.0 - - - -
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Residues in contact with GLY 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ASN 3.5 3.4 + - - -
504A THR* 1.3 73.0 + - - +
506A TRP* 1.3 63.9 + - - +
508A LEU* 4.6 2.0 - - - -
509A CYS* 3.0 31.0 + - - +
531A VAL* 3.6 18.9 - - - +
534A ILE* 4.8 0.9 - - - -
535A GLU* 3.2 32.8 + - - +
538A ARG* 4.3 2.7 - - - -
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Residues in contact with TRP 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 3.5 37.6 - + - +
153A GLU* 4.9 6.8 + - - -
475A MET* 4.4 20.2 - - + -
479A TYR* 4.1 18.8 - + + -
504A THR* 3.2 6.6 + - - +
505A GLY* 1.3 73.8 - - - +
507A VAL* 1.3 97.4 + - + +
509A CYS* 3.3 2.1 + - - +
510A GLN* 3.1 64.7 + - + +
535A GLU* 4.1 1.0 + - - -
538A ARG* 3.9 24.1 - - - +
26B PHE* 3.6 31.8 - + - -
29B GLU* 3.9 19.7 + - - +
30B ARG* 4.4 6.3 - - - +
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Residues in contact with VAL 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU* 4.2 17.7 - - + +
497A LEU* 5.9 3.1 - - + -
501A HIS 3.2 22.0 - - - +
502A TYR* 3.7 25.8 - - + +
504A THR* 3.5 10.6 + - + +
505A GLY 3.4 0.2 - - - -
506A TRP* 1.3 99.6 - - + +
508A LEU* 1.3 66.2 + - - +
510A GLN* 2.9 16.5 + - - +
511A ILE* 2.9 32.2 + - + +
30B ARG* 5.2 2.2 - - - +
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A TYR* 3.1 48.7 - - + +
503A ASN* 3.6 19.7 - - - +
504A THR 3.4 13.8 + - - +
505A GLY 4.2 2.5 - - - +
506A TRP 3.4 0.2 - - - -
507A VAL* 1.3 80.2 - - - +
509A CYS* 1.3 53.3 + - - +
511A ILE* 3.4 9.1 + - + +
512A GLY* 2.7 31.0 + - - -
527A ILE* 3.9 27.5 - - + +
528A PHE* 4.7 0.3 - - - -
530A GLU* 3.5 32.3 - - + +
531A VAL* 4.3 15.7 - - + +
534A ILE* 4.6 2.5 - - + -
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Residues in contact with CYS 509 (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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505A GLY 3.0 17.4 + - - +
506A TRP 3.3 6.5 - - - +
508A LEU* 1.3 75.0 - - - +
510A GLN* 1.3 63.3 + - - +
512A GLY* 3.3 1.7 + - - -
513A ARG* 3.0 25.5 + - - +
528A PHE* 3.8 17.3 - - - -
531A VAL* 3.8 12.1 - - - -
538A ARG* 3.0 39.9 - - - +
541A GLY* 3.3 29.1 - - - -
542A MET 5.0 0.4 - - - -
544A ILE* 5.4 0.2 - - - +
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Residues in contact with GLN 510 (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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479A TYR* 3.2 31.3 + - + -
482A LEU* 5.4 11.2 - - + +
506A TRP* 3.1 66.7 + - + +
507A VAL* 2.9 7.6 + - - +
509A CYS* 1.3 79.7 + - - +
511A ILE* 1.3 55.9 + - + +
513A ARG* 3.1 11.7 + - - +
514A ALA* 2.8 33.5 + - - +
538A ARG* 4.3 3.6 + - - -
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Residues in contact with ILE 511 (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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490A ALA 5.4 0.4 - - - +
491A ILE* 4.5 15.5 - - + -
494A LEU* 4.1 20.0 - - + -
495A SER* 4.6 5.2 - - - +
502A TYR* 3.7 28.3 - - + +
507A VAL* 2.9 36.8 + - + +
508A LEU* 3.5 11.2 - - + +
510A GLN* 1.3 76.0 - - + +
512A GLY* 1.3 58.2 + - - +
514A ALA* 3.1 8.2 + - - +
515A TYR* 2.8 57.2 + - + -
527A ILE* 4.3 11.7 - - + -
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Residues in contact with GLY 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU 2.7 14.9 + - - -
510A GLN 3.2 0.6 - - - -
511A ILE* 1.3 74.4 - - - +
513A ARG* 1.3 61.0 + - - +
515A TYR* 3.6 1.4 + - - -
516A PHE* 3.0 25.3 + - - +
524A ALA* 4.1 2.9 - - - +
527A ILE* 3.3 23.1 - - - +
528A PHE* 3.4 25.8 - - - -
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Residues in contact with ARG 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 6.3 2.7 - - + -
509A CYS 3.0 12.5 + - - +
510A GLN* 3.1 17.2 + - - +
512A GLY* 1.3 76.1 - - - +
514A ALA* 1.3 57.8 + - - +
516A PHE* 3.4 2.9 + - - +
517A GLU* 3.0 38.9 + - + +
528A PHE* 3.8 1.4 - - - -
544A ILE* 3.6 21.5 - - + -
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Residues in contact with ALA 514 (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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482A LEU* 5.8 4.7 - - + +
487A CYS* 4.1 16.3 - - + +
490A ALA* 4.9 8.7 - - + -
491A ILE* 3.5 25.8 - - + -
510A GLN 2.8 13.6 + - - +
511A ILE* 3.1 11.0 + - - +
513A ARG* 1.3 73.5 - - - +
515A TYR* 1.3 66.7 + - - +
517A GLU* 3.1 15.6 + - - +
518A LEU* 3.2 19.5 + - - +
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Residues in contact with TYR 515 (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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491A ILE* 3.9 30.7 - - + +
511A ILE* 2.8 49.1 + - + +
514A ALA* 1.3 73.8 - - - +
516A PHE* 1.3 57.4 + - - +
518A LEU* 3.6 11.2 + - + +
519A SER 3.1 5.4 + - - -
520A GLU* 3.0 38.2 + - + +
523A GLN* 3.7 36.6 - - + -
524A ALA* 3.7 20.9 - - + +
527A ILE* 4.3 9.4 - - + -
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Residues in contact with PHE 516 (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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512A GLY 3.0 20.4 + - - +
513A ARG* 3.5 4.3 - - - +
514A ALA 3.1 0.2 - - - -
515A TYR* 1.3 76.0 - - - +
517A GLU* 1.3 83.4 + - - +
519A SER* 2.9 20.7 + - - +
520A GLU 5.0 0.9 - - - -
521A TYR* 4.4 10.8 - + - -
524A ALA* 4.0 5.8 - - + +
544A ILE* 3.5 27.6 - - + -
547A THR* 3.3 34.5 - - + -
548A THR* 3.7 22.0 - - + -
551A HIS* 4.1 18.4 - + - -
608A TYR* 4.8 6.1 - + - -
641A TYR* 5.0 5.2 - - - -
642A ASN* 5.8 4.3 - - - -
677A LEU* 5.4 12.7 - - + +
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Residues in contact with GLU 517 (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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482A LEU 6.0 1.1 - - - +
485A TYR* 3.3 26.7 + - + -
487A CYS* 3.7 24.2 - - - -
513A ARG* 3.0 23.5 + - + +
514A ALA* 3.1 1.3 + - - +
516A PHE* 1.3 91.8 - - - +
518A LEU* 1.3 64.5 + - - +
519A SER* 3.3 3.6 + - - -
641A TYR* 2.6 39.3 + - - -
673A GLN* 4.6 14.6 - - - +
676A VAL* 4.6 2.9 - - - +
677A LEU* 5.7 2.4 - - - +
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Residues in contact with LEU 518 (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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487A CYS* 3.6 33.2 - - + -
488A LYS* 4.6 9.0 - - + +
491A ILE* 4.0 20.4 - - + -
514A ALA 3.2 10.0 + - - +
515A TYR* 3.6 15.9 - - + +
517A GLU* 1.3 75.1 - - - +
519A SER* 1.3 74.5 + - - +
520A GLU* 3.6 8.5 + - + +
673A GLN* 6.5 0.4 - - - -
676A VAL* 4.6 3.9 - - - +
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Residues in contact with SER 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A TYR 3.1 1.0 + - - -
516A PHE 2.9 19.4 + - - -
517A GLU 4.4 0.9 - - - -
518A LEU* 1.3 83.8 + - - +
520A GLU* 1.3 60.7 + - - +
521A TYR* 3.2 38.4 + - - -
676A VAL* 3.5 35.3 - - - +
677A LEU* 5.2 3.4 - - - -
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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
------------------------------------------------------------
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