Contacts of the helix formed by residues 488 - 508 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B CYS 4.4 2.9 - - - +
487B LEU* 1.3 90.7 - - + +
489B GLU* 1.3 67.9 + - - +
490B ASP* 3.2 19.6 + - - +
491B ARG* 3.2 17.1 + - + -
492B ALA* 2.9 20.9 + - - +
663B SER* 3.5 17.7 - - - +
670B LYS* 4.0 26.0 - - + +
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Residues in contact with GLU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU 4.0 0.2 + - - -
488B PRO* 1.3 72.5 - - - +
490B ASP* 1.3 61.4 + - - +
493B LEU* 3.1 37.2 + - + +
586B MET* 5.5 0.2 - - - +
590B LEU* 4.3 13.6 - - + +
621B SER* 4.5 4.3 + - - +
622B CYS* 3.3 46.2 + - - +
623B ALA 3.6 6.5 + - - -
626B THR* 3.1 25.4 + - + -
658B VAL* 4.2 25.2 - - + +
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B PRO* 3.3 12.6 - - - +
489B GLU* 1.3 74.7 - - - +
491B ARG* 1.3 65.8 + - - -
494B TYR* 3.0 30.2 + - - +
655B LEU* 3.6 17.6 - - + +
658B VAL* 4.2 13.1 - - + +
660B GLY 3.4 20.4 - - - +
661B LEU* 3.7 5.1 - - - +
662B LYS* 3.2 10.0 + - - +
663B SER* 2.7 45.1 + - - -
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Residues in contact with ARG 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 5.7 3.0 - - - +
487B LEU* 4.4 10.8 - - + -
488B PRO* 3.2 21.7 + - + +
490B ASP* 1.3 82.0 + - - +
492B ALA* 1.3 62.6 + - - +
494B TYR* 3.4 3.5 - - - +
495B TYR* 3.1 63.4 + - + -
526B ASP 4.7 0.4 + - - -
527B GLY* 4.0 12.9 + - - -
661B LEU* 3.6 28.9 - - + +
663B SER* 2.8 48.0 + - - -
664B PRO 3.8 8.3 + - - +
665B TRP* 3.3 31.7 - - - +
666B ARG 5.2 1.2 - - - +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 4.0 9.6 - - + -
488B PRO 2.9 17.3 + - - +
489B GLU 4.1 0.4 - - - +
491B ARG* 1.3 78.2 - - - +
493B LEU* 1.3 58.1 + - - +
495B TYR 3.5 1.2 + - - -
496B LEU* 3.1 18.9 + - - +
586B MET* 3.4 23.1 - - + -
589B MET* 3.3 39.3 - - + +
590B LEU* 3.8 11.2 - - + -
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B GLU* 3.1 31.3 + - + +
492B ALA* 1.3 73.0 - - - +
494B TYR* 1.3 63.3 + - - +
495B TYR 3.3 0.4 - - - -
496B LEU* 3.5 8.3 - - + -
497B GLY* 2.8 25.3 + - - -
586B MET* 4.3 13.2 - - + -
626B THR* 3.5 35.0 - - + +
651B VAL* 3.2 41.3 - - + +
654B ALA* 4.0 14.4 - - + +
655B LEU* 3.5 29.8 - - + -
658B VAL* 5.1 2.5 - - + -
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Residues in contact with TYR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP 3.0 23.4 + - - +
491B ARG* 3.4 4.7 - - - +
493B LEU* 1.3 82.3 - - - +
495B TYR* 1.3 81.6 + + - +
497B GLY* 3.7 1.0 + - - -
498B GLN* 3.2 45.0 + - + +
527B GLY 4.4 1.8 - - - -
528B SER* 2.7 35.6 + - - -
655B LEU* 4.1 23.8 - - + -
661B LEU* 3.8 38.8 - - + +
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU* 3.6 34.9 - - + +
480B LEU* 3.9 21.7 - - + +
487B LEU* 4.4 5.4 - - + -
491B ARG* 3.1 49.8 + - - -
492B ALA 3.8 4.9 - - - +
493B LEU 3.3 0.2 - - - -
494B TYR* 1.3 94.9 - + - +
496B LEU* 1.3 57.8 + - - +
498B GLN* 3.4 4.8 + - - +
499B ALA* 3.0 30.0 + - - +
521B VAL* 5.7 0.7 - - + -
523B LEU* 4.0 19.1 - - + +
527B GLY* 2.7 33.4 + - - -
528B SER 4.7 1.1 - - - -
530B ALA* 3.8 24.2 - - + +
585B MET* 5.5 0.9 - - - -
589B MET* 4.3 1.6 - - - -
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ALA 3.1 15.6 + - - +
493B LEU* 3.3 9.1 + - - +
495B TYR* 1.3 76.1 - - - +
497B GLY* 1.3 52.3 + - - +
499B ALA* 3.1 5.1 + - + +
500B LEU* 2.8 49.1 + - + +
582B SER* 3.8 35.7 - - - +
583B CYS* 5.3 7.9 - - - -
585B MET* 4.4 6.5 - - + -
586B MET* 3.4 35.0 - - + -
589B MET* 4.4 6.7 - - + +
629B ALA* 6.3 0.4 - - + -
630B ILE* 6.0 1.3 - - + -
647B LEU* 5.4 2.0 - - + -
651B VAL* 3.7 29.6 - - + -
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Residues in contact with GLY 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU 2.8 19.9 + - - -
494B TYR 4.1 2.0 - - - -
496B LEU* 1.3 73.3 - - - +
498B GLN* 1.3 55.3 + - - +
500B LEU* 3.2 10.9 + - - +
501B GLU* 2.9 35.3 + - - +
648B GLY* 5.1 4.7 - - - -
651B VAL* 3.9 13.2 - - - +
652B ASN* 5.0 12.1 + - - -
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Residues in contact with GLN 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ARG* 3.0 49.1 + - - +
494B TYR* 3.2 49.9 + - + +
495B TYR 3.8 7.0 - - - +
496B LEU 3.3 0.8 - - - -
497B GLY* 1.3 73.0 - - - +
499B ALA* 1.3 63.7 + - - +
501B GLU* 3.3 19.0 + - - +
502B GLY 3.1 16.5 + - - -
528B SER 3.5 3.7 - - - +
529B HIS 3.9 0.2 - - - -
530B ALA* 2.9 44.3 + - + +
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Residues in contact with ALA 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ARG* 5.5 0.2 - - - -
495B TYR 3.0 17.7 + - - +
496B LEU* 3.5 6.3 - - + +
498B GLN* 1.3 77.1 - - - +
500B LEU* 1.3 56.9 + - - +
502B GLY* 3.4 1.2 + - - -
503B LEU* 2.9 36.9 + - + +
516B VAL* 5.7 0.7 - - + -
521B VAL* 5.5 8.1 - - + -
530B ALA* 5.8 0.8 - - + +
532B LEU* 3.9 25.6 - - + +
585B MET* 4.1 22.9 - - + -
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Residues in contact with LEU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LEU* 2.8 37.7 + - + +
497B GLY* 3.4 7.6 - - - +
499B ALA* 1.3 74.5 - - - +
501B GLU* 1.3 55.8 + - - +
503B LEU* 3.6 11.1 - - + +
504B GLU* 2.8 35.8 + - - +
579B VAL* 4.4 6.1 - - + -
582B SER* 4.2 10.8 - - - +
644B ALA* 4.0 29.9 - - - +
647B LEU* 3.8 25.4 - - + -
648B GLY* 3.9 17.9 - - - +
651B VAL* 3.8 25.8 - - + -
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Residues in contact with GLU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B SER* 4.9 1.0 + - - -
450B PRO* 5.7 0.5 - - - +
451B ARG* 3.0 33.9 + - + +
497B GLY 2.9 21.8 + - - +
498B GLN* 3.3 21.6 + - - +
500B LEU* 1.3 76.1 - - - +
502B GLY* 1.3 56.5 + - - +
504B GLU* 3.4 13.4 + - - +
505B TYR* 3.1 27.0 + - - +
652B ASN* 5.0 12.8 + - - +
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B SER* 4.6 0.4 - - - -
451B ARG* 3.7 20.4 - - - +
452B ILE* 3.6 7.8 - - - +
498B GLN 3.1 7.5 + - - -
499B ALA 3.4 3.3 + - - -
500B LEU 3.3 0.2 - - - -
501B GLU* 1.3 77.5 - - - +
503B LEU* 1.3 62.3 + - - +
505B TYR* 3.3 6.5 + - - +
506B LEU* 3.1 26.7 + - - +
532B LEU* 3.7 15.9 - - - -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ALA* 2.9 24.6 + - + +
500B LEU* 3.6 15.3 - - + +
501B GLU 3.4 0.2 - - - -
502B GLY* 1.3 75.9 - - - +
504B GLU* 1.3 53.9 + - - +
506B LEU* 3.3 6.4 + - + +
507B HIS* 2.7 56.7 + - + +
513B HIS* 4.3 11.0 - - + -
516B VAL* 4.4 13.5 - - + -
532B LEU* 3.8 18.6 - - + -
578B ASP* 3.8 41.5 - - + +
579B VAL* 5.0 0.9 - - + +
582B SER* 4.3 15.3 - - - -
644B ALA* 4.1 4.0 - - + -
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B LEU 2.8 21.6 + - - +
501B GLU* 3.6 13.1 - - - +
503B LEU* 1.3 72.4 - - - +
505B TYR* 1.3 59.1 + - - +
507B HIS* 4.2 2.6 - - - +
508B SER* 3.0 30.7 + - - -
644B ALA* 3.8 10.1 - - + +
645B ALA* 3.4 39.5 - - + +
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Residues in contact with TYR 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 3.7 36.5 - - + -
448B THR* 2.7 30.4 + - - +
449B SER* 3.6 40.2 - - - +
450B PRO* 6.0 0.4 - - + -
452B ILE* 3.9 1.8 - - + -
501B GLU 3.1 13.3 + - - +
502B GLY 3.4 10.1 - - - +
504B GLU* 1.3 76.0 - - - +
506B LEU* 1.3 59.8 + - - +
508B SER* 3.0 17.2 + - - -
509B ARG* 3.3 58.3 + - - +
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ALA 3.6 23.8 - - - +
447B LEU* 3.8 14.1 - - + -
452B ILE* 3.7 7.6 - - + -
502B GLY 3.1 19.3 + - - +
503B LEU* 3.3 14.8 + - + +
505B TYR* 1.3 76.5 - - - +
507B HIS* 1.3 61.0 + - + +
509B ARG* 3.1 14.0 + - - +
510B ARG 3.2 0.2 + - - -
511B ILE* 2.8 55.1 + - + +
513B HIS* 4.5 10.1 - - + +
532B LEU* 3.9 17.0 - - + -
535B PHE* 3.7 26.5 - - + -
578B ASP* 5.6 0.2 - - - +
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Residues in contact with HIS 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 2.7 49.4 + - + +
504B GLU* 4.2 3.6 - - - +
506B LEU* 1.3 76.7 - - + +
508B SER* 1.3 62.2 + - - +
510B ARG* 3.1 15.2 + - - +
511B ILE 3.4 22.0 - - - +
512B LEU* 4.5 1.1 - - - -
541B LEU* 4.5 5.6 - - + +
575B ALA* 3.5 38.2 + - + +
578B ASP* 2.8 32.8 + - + +
579B VAL* 5.0 2.5 - - + -
644B ALA* 3.6 17.8 + - + +
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Residues in contact with SER 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B GLU* 3.0 21.6 + - - -
505B TYR* 3.0 14.4 + - - -
507B HIS* 1.3 76.0 - - - +
509B ARG* 1.3 66.1 + - - +
510B ARG* 3.3 4.7 + - - +
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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) + - + + + + + -
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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