Contacts of the helix formed by residues 488 - 509 (chain A) in PDB entry 4DN5
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 PRO 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLN* 6.4 0.4 - - + +
486A CYS 4.3 2.9 - - - +
487A LEU* 1.3 92.0 - - + +
489A GLU* 1.3 67.8 + - - +
490A ASP* 3.3 4.9 - - - +
491A ARG* 3.0 23.3 + - + -
492A ALA* 3.1 8.9 + - - +
663A SER* 3.3 32.5 - - - +
664A PRO* 6.0 1.1 - - + +
670A LYS* 3.8 25.1 - - + +
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Residues in contact with GLU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU 3.7 1.0 + - - -
488A PRO* 1.3 71.9 - - - +
490A ASP* 1.3 62.1 + - - +
492A ALA* 3.4 2.6 + - - +
493A LEU* 3.1 32.1 + - + +
586A MET* 4.6 0.2 - - - +
590A LEU* 4.0 19.6 - - + +
621A SER 4.2 4.2 - - - +
622A CYS* 3.5 14.6 - - - -
623A ALA* 2.7 34.4 + - - +
626A THR* 2.8 33.2 + - + +
658A VAL* 3.7 18.2 - - + +
670A LYS* 4.9 1.8 - - - +
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Residues in contact with ASP 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A PRO* 3.3 8.5 - - - +
489A GLU* 1.3 75.8 - - - +
491A ARG* 1.3 70.2 + - - -
493A LEU* 3.5 1.0 + - - -
494A TYR* 2.9 30.1 + - - +
655A LEU* 3.4 14.4 - - + +
658A VAL* 4.0 17.1 - - + +
660A GLY 3.5 18.9 - - - +
661A LEU* 4.5 3.1 - - - -
662A LYS* 2.9 14.9 + - - +
663A SER* 2.8 48.6 + - - -
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Residues in contact with ARG 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 6.0 1.1 - - - -
487A LEU* 4.1 12.3 - - + -
488A PRO* 3.0 23.5 + - + +
490A ASP* 1.3 77.8 + - - +
492A ALA* 1.3 65.1 + - - +
494A TYR* 3.3 7.1 + - - +
495A TYR* 3.0 66.2 + - - -
527A GLY 3.5 4.4 + - - -
661A LEU* 3.7 19.9 - - + +
663A SER* 3.1 37.1 + - - -
664A PRO 3.9 6.4 + - - +
665A TRP* 3.4 24.8 - - - +
1004A EDO 2.8 48.5 + - - -
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 4.2 6.2 - - + +
488A PRO 3.1 9.0 + - - +
489A GLU 3.7 5.2 - - - +
491A ARG* 1.3 77.5 - - - +
493A LEU* 1.3 57.5 + - - +
495A TYR* 3.3 1.7 + - - -
496A LEU* 3.0 29.3 + - - +
586A MET* 3.7 24.9 - - + -
589A MET* 3.7 35.7 - - + +
590A LEU* 4.0 11.4 - - + -
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU* 3.1 24.4 + - + +
490A ASP* 3.7 4.0 - - - +
492A ALA* 1.3 76.6 - - - +
494A TYR* 1.3 57.0 + - - +
496A LEU* 3.3 3.8 + - - +
497A GLY* 2.9 28.6 + - - -
586A MET* 3.9 19.3 - - + -
626A THR* 3.4 26.5 - - + +
629A ALA* 6.0 0.4 - - + -
651A VAL* 3.8 26.8 - - + +
654A ALA* 3.8 37.5 - - + +
655A LEU* 3.9 19.0 - - + +
658A VAL* 4.0 12.8 - - + -
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ASP 2.9 19.5 + - - +
491A ARG* 3.4 7.2 - - - +
493A LEU* 1.3 76.1 - - - +
495A TYR* 1.3 80.5 + + - +
497A GLY* 3.8 1.3 + - - -
498A GLN* 3.2 46.0 + - + +
527A GLY 4.4 1.1 - - - -
528A SER* 2.7 35.6 + - - -
655A LEU* 4.1 25.3 - - + +
661A LEU* 3.7 42.2 - - + +
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Residues in contact with TYR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LEU* 3.6 39.4 - - + +
480A LEU* 4.4 6.1 - - + -
487A LEU* 3.8 15.0 - - + -
491A ARG* 3.0 48.8 + - - +
492A ALA 4.0 3.1 - - - +
494A TYR* 1.3 87.4 - + - +
496A LEU* 1.3 61.9 + - - +
497A GLY 3.2 0.2 - - - -
498A GLN* 3.3 6.1 + - - +
499A ALA* 2.9 30.6 + - - +
523A LEU* 4.0 17.0 - - + +
527A GLY 2.6 29.9 + - - -
529A HIS 5.1 1.1 - - - -
530A ALA* 3.9 25.1 - - + +
585A MET* 5.0 1.3 - - - +
589A MET* 4.3 2.2 - - - -
665A TRP* 3.2 16.3 - - - -
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ALA 3.0 17.3 + - - +
493A LEU* 3.6 4.7 - - - +
495A TYR* 1.3 75.4 - - - +
497A GLY* 1.3 53.8 + - - +
499A ALA* 3.1 5.2 + - + +
500A LEU* 2.7 54.4 + - + +
582A SER* 3.6 37.9 - - - +
583A CYS* 5.2 9.0 - - - -
585A MET* 4.3 9.9 - - + -
586A MET* 3.8 33.7 - - + -
589A MET* 4.4 4.5 - - + +
630A ILE* 5.6 2.9 - - + -
647A LEU* 5.3 1.3 - - + -
651A VAL* 3.7 26.9 - - + -
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Residues in contact with GLY 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU 2.9 14.5 + - - -
494A TYR* 4.1 2.0 - - - -
496A LEU* 1.3 75.6 - - - +
498A GLN* 1.3 57.4 - - - +
500A LEU* 3.3 5.4 + - - +
501A GLU* 3.0 37.2 + - - +
648A GLY* 5.2 2.3 - - - -
651A VAL* 3.7 23.0 - - - +
652A ASN* 4.7 9.6 + - - -
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Residues in contact with GLN 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ARG* 3.1 61.3 - - - +
494A TYR* 3.2 36.5 + - + +
495A TYR* 3.3 10.0 + - - +
497A GLY* 1.3 74.2 - - - +
499A ALA* 1.3 62.0 + - - +
501A GLU* 3.3 2.3 + - - +
502A GLY 3.2 16.3 + - - -
528A SER 2.9 21.2 + - - +
529A HIS* 3.7 6.7 - - - +
530A ALA* 2.9 42.0 + - + +
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR 2.9 17.2 + - - +
496A LEU* 3.5 6.1 - - + +
498A GLN* 1.3 75.4 - - - +
500A LEU* 1.3 57.4 + - - +
502A GLY* 3.1 3.3 + - - +
503A LEU* 2.9 34.6 + - + +
516A VAL* 5.9 1.3 - - + -
521A VAL* 5.2 8.5 - - + -
530A ALA* 5.4 1.1 - - - +
532A LEU* 3.8 27.4 - - + +
582A SER* 5.8 0.7 - - - -
585A MET* 4.1 21.8 - - + -
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU* 2.7 40.3 + - + +
497A GLY 3.6 4.5 - - - +
499A ALA* 1.3 70.4 - - - +
501A GLU* 1.3 60.4 + - - +
503A LEU* 3.8 11.0 - - + +
504A GLU* 3.2 27.7 + - - +
579A VAL* 5.0 2.0 - - + -
582A SER* 3.9 12.6 - - - +
644A ALA* 3.8 38.0 - - + +
647A LEU* 3.6 40.2 - - + -
648A GLY* 3.7 19.5 - - - +
651A VAL* 3.9 12.6 - - + -
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A SER* 5.0 1.0 + - - -
451A ARG* 2.4 43.9 + - + +
497A GLY 3.0 21.8 + - - +
498A GLN* 3.5 7.5 + - - +
499A ALA 3.2 0.2 - - - -
500A LEU* 1.3 76.0 - - - +
502A GLY* 1.3 62.1 + - - +
504A GLU* 3.7 9.8 + - - +
505A TYR* 3.3 21.3 + - - +
648A GLY* 6.2 2.9 - - - -
652A ASN* 4.6 17.1 + - - +
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Residues in contact with GLY 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A SER* 4.8 0.4 - - - -
451A ARG* 3.7 20.1 - - - +
452A ILE* 3.6 8.1 - - - +
498A GLN 3.2 6.9 + - - -
499A ALA 3.1 7.2 + - - -
501A GLU* 1.3 74.5 - - - +
503A LEU* 1.3 62.9 + - - +
505A TYR* 3.3 5.9 + - - +
506A LEU* 3.1 25.1 + - - +
532A LEU* 3.6 16.4 - - - -
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ALA* 2.9 20.9 + - + +
500A LEU* 3.9 15.9 - - + +
501A GLU 3.4 0.2 - - - -
502A GLY* 1.3 75.1 - - - +
504A GLU* 1.3 55.6 + - - +
506A LEU* 3.4 5.8 + - + +
507A HIS* 3.0 45.5 + - + +
513A HIS* 4.1 24.0 - - + -
516A VAL* 4.3 12.8 - - + -
532A LEU* 3.5 22.9 - - + -
578A ASP* 3.9 39.0 - - + +
579A VAL* 4.9 0.7 - - - +
582A SER* 4.1 16.8 - - - -
644A ALA* 4.0 4.9 - - + -
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LEU 3.2 19.0 + - - +
501A GLU* 3.9 10.7 - - - +
502A GLY 3.3 0.2 - - - -
503A LEU* 1.3 74.3 - - - +
505A TYR* 1.3 66.7 + - - +
507A HIS* 3.2 5.8 + - - +
508A SER* 3.0 27.1 + - - -
644A ALA* 3.9 12.3 - - + +
645A ALA* 3.4 35.9 - - + +
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Residues in contact with TYR 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 3.7 24.8 - - + -
448A THR* 2.8 43.3 + - - -
449A SER* 3.8 18.2 - - - +
452A ILE* 3.7 18.8 - - + -
501A GLU 3.3 12.5 + - - +
502A GLY 3.5 9.4 - - - +
504A GLU* 1.3 79.1 - - - +
506A LEU* 1.3 58.9 + - - +
508A SER* 2.8 19.9 + - - -
509A ARG* 3.1 60.7 + - - +
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ALA 3.3 25.8 - - - +
447A LEU* 3.9 14.4 - - + -
452A ILE* 3.6 12.6 - - + -
502A GLY 3.1 16.6 + - - +
503A LEU* 3.5 11.2 - - + +
505A TYR* 1.3 74.6 - - - +
507A HIS* 1.3 59.9 + - + +
509A ARG* 3.1 16.9 + - - +
510A ARG 3.2 0.3 + - - -
511A ILE* 2.9 51.5 + - + +
513A HIS* 4.4 15.3 - - + -
532A LEU* 4.3 11.4 - - + -
535A PHE* 3.7 27.1 - - + -
578A ASP* 5.6 0.2 - - - +
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Residues in contact with HIS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 3.0 45.4 + - + +
504A GLU* 3.2 5.1 + - - +
506A LEU* 1.3 77.0 - - + +
508A SER* 1.3 57.4 + - - +
510A ARG* 3.1 28.2 + - - +
511A ILE 3.4 20.9 - - - +
512A LEU* 4.6 0.4 - - - -
541A LEU* 4.8 2.4 - - - +
575A ALA* 3.5 43.3 + - + +
578A ASP* 3.0 28.7 + - + +
579A VAL* 4.5 3.1 - - + -
644A ALA* 3.7 19.4 + - + +
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Residues in contact with SER 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLU* 3.0 14.5 + - - -
505A TYR* 2.8 24.1 + - - -
507A HIS* 1.3 77.9 - - - +
509A ARG* 1.3 70.3 + - - +
510A ARG* 3.2 9.5 + - - +
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Residues in contact with ARG 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 3.8 31.1 - - + +
505A TYR* 3.1 55.0 + - - -
506A LEU* 3.1 10.7 + - - +
508A SER* 1.3 104.1 + - - +
510A ARG* 1.3 69.7 + - - +
511A ILE* 3.5 15.1 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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