Contacts of the helix formed by residues 546 - 563 (chain B) in PDB entry 5N4D
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 LYS 546 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497B GLY 2.7 29.1 + - - -
498B GLY* 3.7 2.0 - - - -
541B GLY 2.7 25.0 + - - +
542B ARG* 3.7 8.3 + - - +
543B ARG* 3.0 22.0 + - - +
544B GLU 3.4 0.4 - - - -
545B THR* 1.3 78.0 - - - +
547B VAL* 1.3 62.8 + - - +
549B THR* 2.9 30.1 + - - +
550B PHE* 3.6 15.7 - - + -
578B ASN* 4.5 4.9 - - - +
581B LEU* 5.4 3.6 - - + -
607B LEU* 6.2 0.9 - - + -
622B GLU* 3.1 22.6 + - - +
623B TYR* 4.5 25.4 - - + +
638B LEU* 3.7 21.1 - - + -
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B GLU 4.6 8.7 + - - +
545B THR* 4.3 6.1 - - - +
546B LYS* 1.3 78.6 - - - +
548B ASN* 1.4 69.4 + - - +
550B PHE* 3.2 4.9 + - - +
551B ASP* 2.9 37.7 + - - +
589B ARG* 3.5 31.2 - - - +
638B LEU* 3.8 25.2 - - + +
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Residues in contact with ASN 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B ASP* 4.4 7.3 + - - +
528B ARG* 3.7 32.2 + - - +
540B GLY* 2.9 29.3 + - - +
545B THR* 2.9 25.0 + - - +
547B VAL* 1.4 83.1 - - - +
549B THR* 1.3 56.2 + - - +
551B ASP* 3.8 10.7 - - - +
552B ASP* 2.7 41.2 + - - +
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Residues in contact with THR 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B GLY* 3.5 20.0 - - - +
527B ILE* 3.5 23.1 - - + +
528B ARG 2.7 22.9 + - - +
541B GLY* 3.4 11.1 + - - -
546B LYS* 2.9 33.0 + - - -
548B ASN* 1.3 81.1 - - - +
550B PHE* 1.3 63.2 + - + +
552B ASP* 3.4 5.2 + - - +
553B PHE* 3.1 22.3 + - - +
582B LEU* 3.8 12.1 - - + -
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Residues in contact with PHE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B LYS* 3.6 28.0 - - + -
547B VAL* 3.2 7.7 + - - +
549B THR* 1.3 76.3 - - + +
551B ASP* 1.3 65.8 + - - +
553B PHE* 3.2 1.8 + - - +
554B ILE* 3.0 33.6 + - + +
581B LEU* 3.5 46.2 - - + -
582B LEU* 3.5 21.8 - - + -
585B GLY* 3.6 14.4 - - - -
586B SER* 3.7 22.2 - - - -
589B ARG* 4.0 20.2 - - - +
607B LEU* 6.1 1.3 - - + -
638B LEU* 3.8 35.2 - - + -
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Residues in contact with ASP 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B SER* 3.8 10.3 + - - +
468B LYS* 3.8 36.7 + - + +
528B ARG* 5.7 0.7 - - - +
547B VAL* 2.9 38.1 + - - +
548B ASN* 3.8 12.3 - - - +
550B PHE* 1.3 77.7 - - - +
552B ASP* 1.4 56.6 + - - +
554B ILE* 3.9 8.4 - - - +
555B ALA* 2.9 31.9 + - - +
589B ARG* 4.4 10.9 + - - -
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Residues in contact with ASP 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B TYR* 2.7 25.8 + - - +
467B SER* 2.6 34.0 + - - -
473B ILE* 3.7 11.5 - - + +
527B ILE* 3.6 18.6 - - + -
528B ARG* 2.9 58.1 + - - +
548B ASN 2.7 22.3 + - - +
549B THR 3.7 2.2 - - - +
551B ASP* 1.4 73.5 - - - +
553B PHE* 1.3 55.8 + - - +
555B ALA* 4.5 0.2 - - - -
556B ALA 3.0 16.6 + - - -
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Residues in contact with PHE 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B GLN* 2.9 57.6 + - + +
494B TYR 3.7 8.3 - - - -
495B GLY* 3.6 30.1 - - - -
525B PRO* 3.7 12.8 - - + -
527B ILE* 3.9 10.0 - - + +
549B THR 3.1 16.6 + - - +
550B PHE 3.2 3.8 + - - +
552B ASP* 1.3 73.6 - - - +
554B ILE* 1.3 67.1 + - - +
556B ALA* 3.3 7.7 + - - -
557B ALA* 3.3 2.9 + - - +
573B ILE* 3.6 30.1 - - + -
574B ASN 4.6 2.9 - - - -
582B LEU* 3.7 33.4 - - + -
583B VAL* 4.6 3.6 - - + -
586B SER* 3.5 20.9 - - - +
595B PHE* 5.0 1.3 - + - -
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Residues in contact with ILE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B PHE* 3.0 28.0 + - + +
551B ASP* 3.9 9.9 - - - +
553B PHE* 1.3 74.5 - - - +
555B ALA* 1.3 65.4 + - - +
557B ALA* 3.0 4.5 + - - +
558B GLN* 3.0 45.7 + - + +
586B SER* 4.2 13.9 - - - +
589B ARG* 4.1 15.3 - - + +
590B ALA* 4.0 42.8 - - + +
591B PRO* 4.5 4.0 - - + -
594B THR* 4.4 2.0 - - + -
595B PHE* 4.2 14.8 - - + -
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Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B TYR* 3.8 14.2 - - + -
466B GLU 4.0 15.7 - - - +
467B SER* 4.0 9.4 - - - -
468B LYS* 4.7 3.8 - - + +
551B ASP 2.9 19.2 + - - +
552B ASP 3.7 4.3 - - - +
554B ILE* 1.3 78.1 - - - +
556B ALA* 1.4 62.5 + - - +
558B GLN* 3.7 15.1 - - - +
559B PHE* 3.0 24.8 + - - +
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Residues in contact with ALA 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B TYR* 3.5 33.8 - - + +
475B MET* 3.9 7.0 - - - +
493B GLN* 3.7 11.7 - - - +
525B PRO* 3.8 18.4 - - + -
552B ASP 3.0 7.6 + - - +
553B PHE 3.4 9.4 - - - +
554B ILE 3.2 0.6 - - - -
555B ALA* 1.4 75.5 - - - +
557B ALA* 1.3 63.3 + - - +
559B PHE* 3.3 4.7 + - - +
560B LEU* 3.0 26.5 + - - +
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Residues in contact with ALA 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B GLN* 3.3 17.0 + - - +
553B PHE 3.3 3.8 + - - +
554B ILE 3.0 8.7 + - - +
556B ALA* 1.3 80.2 - - - +
558B GLN* 1.3 63.3 + - - +
560B LEU* 3.4 14.4 + - - +
561B VAL* 3.5 18.7 + - - +
571B VAL* 3.9 11.7 - - + +
594B THR* 4.0 11.9 - - + +
595B PHE* 3.6 29.4 - - + -
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Residues in contact with GLN 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B ILE* 3.0 32.3 + - - +
555B ALA* 3.7 18.4 - - - +
556B ALA 3.2 0.2 - - - -
557B ALA* 1.3 78.3 - - - +
559B PHE* 1.3 56.2 + - - +
561B VAL* 3.3 4.9 + - - +
562B LYS* 2.8 31.8 + - - +
591B PRO* 3.9 24.7 - - - +
594B THR* 4.3 14.4 + - + +
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Residues in contact with PHE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B VAL* 3.8 21.8 - - + -
464B TRP 3.8 18.6 - - - -
465B TYR* 3.4 28.5 - - + -
466B GLU 5.2 0.9 - - - -
475B MET* 3.7 17.3 - - + -
555B ALA 3.0 17.3 + - - +
556B ALA 3.6 3.4 - - - +
558B GLN* 1.3 74.5 - - - +
560B LEU* 1.3 70.5 + - - +
562B LYS* 4.3 5.2 - - - -
563B ASN* 3.0 54.8 + - - +
565B TYR* 3.5 27.8 - + - -
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B MET* 3.8 12.1 - - + -
477B ILE* 3.6 31.0 - - + -
491B ALA* 4.0 19.5 - - + -
493B GLN* 3.5 23.1 - - + +
521B ILE* 4.3 3.4 - - + -
523B ALA* 3.9 16.8 - - + -
556B ALA 3.0 17.0 + - - +
557B ALA 3.7 5.2 - - - +
558B GLN 3.3 0.6 - - - -
559B PHE* 1.3 77.6 - - - +
561B VAL* 1.3 60.5 + - - +
564B LYS 3.4 0.3 + - - -
565B TYR* 2.9 49.1 + - + -
566B ALA* 3.1 16.0 + - + -
571B VAL* 4.3 10.8 - - + -
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Residues in contact with VAL 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B ALA 3.5 5.8 + - - +
558B GLN* 3.3 7.1 + - - +
559B PHE 3.2 0.2 - - - -
560B LEU* 1.3 76.8 - - - +
562B LYS* 1.3 67.3 + - - +
564B LYS* 3.1 21.5 + - - +
566B ALA 3.5 7.4 - - - +
567B ALA 3.6 20.0 - - - +
568B PRO* 3.7 36.0 - - + +
569B GLY 4.8 2.7 - - - +
571B VAL* 3.7 23.6 - - + -
594B THR 5.5 3.6 - - - +
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Residues in contact with LYS 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558B GLN 2.8 20.5 + - - +
559B PHE* 4.0 4.3 - - - +
561B VAL* 1.3 80.7 - - - +
563B ASN* 1.3 69.2 + - - +
564B LYS* 3.5 18.5 + - - +
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Residues in contact with ASN 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B PHE* 5.3 1.9 - - - +
559B PHE* 3.0 45.4 + - - +
562B LYS* 1.3 90.0 - - - +
564B LYS* 1.3 71.2 + - - +
565B TYR* 3.3 25.3 + - + -
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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