Contacts of the helix formed by residues 546 - 563 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A GLY 2.8 28.8 + - - -
498A GLY* 3.7 1.6 - - - -
541A GLY 2.8 25.2 + - - +
542A ARG* 3.7 7.7 + - - +
543A ARG* 3.0 22.3 + - - +
544A GLU 3.4 0.6 - - - -
545A THR* 1.3 77.8 + - - +
547A VAL* 1.3 63.9 + - - +
549A THR* 3.0 28.0 + - - +
550A PHE* 3.7 15.2 - - + -
578A ASN* 4.6 4.3 - - - +
581A LEU* 5.3 4.3 - - + -
607A LEU* 6.1 2.2 - - + -
622A GLU* 2.9 23.0 + - - +
623A TYR* 4.3 28.5 - - + +
638A LEU* 3.8 18.2 - - + -
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Residues in contact with VAL 547 (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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544A GLU 4.7 7.5 + - - +
545A THR* 3.0 6.6 + - - +
546A LYS* 1.3 78.1 - - - +
548A ASN* 1.3 74.6 + - - +
550A PHE* 3.1 5.6 + - - -
551A ASP* 2.9 32.3 + - - +
589A ARG* 3.4 31.6 - - - +
638A LEU* 3.6 26.0 - - + +
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Residues in contact with ASN 548 (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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469A ASP* 4.4 7.7 + - - +
528A ARG* 3.6 32.8 + - - +
540A GLY* 2.8 30.6 + - - +
545A THR* 2.9 23.4 + - - +
547A VAL* 1.3 87.0 - - - +
549A THR* 1.3 54.0 + - - +
551A ASP* 4.3 10.7 - - - +
552A ASP* 2.7 41.0 + - - +
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Residues in contact with THR 549 (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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496A TYR 5.2 0.2 - - - +
497A GLY* 3.5 20.0 - - - +
527A ILE* 3.6 18.5 - - + +
528A ARG 2.8 26.2 + - - +
541A GLY* 3.5 19.6 + - - -
546A LYS* 3.0 22.2 + - - -
548A ASN* 1.3 76.9 - - - +
550A PHE* 1.3 60.9 + - + +
552A ASP* 3.3 6.3 + - - +
553A PHE* 3.0 27.7 + - - +
578A ASN* 5.6 0.2 - - - +
582A LEU* 3.8 12.8 - - + -
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Residues in contact with PHE 550 (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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546A LYS* 3.7 27.4 - - + -
547A VAL* 3.1 7.1 + - - +
549A THR* 1.3 79.8 - - + +
551A ASP* 1.4 65.9 + - - +
553A PHE* 3.2 5.3 + - - +
554A ILE* 2.9 33.1 + - + +
581A LEU* 3.5 32.1 - - + -
582A LEU* 3.5 26.5 - - + -
585A GLY* 3.5 20.2 - - - -
586A SER* 3.7 22.0 - - - -
589A ARG* 4.1 20.4 - - - +
607A LEU* 5.9 2.0 - - + -
638A LEU* 3.9 35.2 - - + -
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Residues in contact with ASP 551 (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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467A SER* 3.8 10.7 + - - +
468A LYS* 3.8 37.7 + - + +
528A ARG* 5.6 0.7 - - - +
547A VAL* 2.9 38.8 + - - +
548A ASN* 3.8 11.0 - - - +
550A PHE* 1.4 74.5 - - - +
552A ASP* 1.3 58.8 + - - +
554A ILE* 4.1 9.3 - - - +
555A ALA* 2.9 32.2 + - - +
589A ARG* 4.7 9.5 + - - -
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Residues in contact with ASP 552 (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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465A TYR* 2.7 24.1 + - - +
467A SER* 2.6 31.9 + - - -
473A ILE* 3.6 10.7 - - + +
527A ILE* 3.6 19.1 - - + -
528A ARG* 2.7 58.5 + - - +
548A ASN 2.7 23.2 + - - +
549A THR 3.6 2.5 - - - +
551A ASP* 1.3 74.7 - - - +
553A PHE* 1.3 56.7 + - - +
555A ALA* 4.6 0.7 - - - -
556A ALA 3.0 16.6 + - - -
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Residues in contact with PHE 553 (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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493A GLN* 3.0 56.7 + - + +
494A TYR 3.8 7.9 - - - -
495A GLY* 3.8 24.7 - - - -
525A PRO* 3.8 12.1 - - + -
527A ILE* 3.9 10.7 - - + +
549A THR 3.0 16.6 + - - +
550A PHE 3.2 4.0 + - - +
552A ASP* 1.3 76.2 - - - +
554A ILE* 1.3 61.8 + - - +
556A ALA* 3.2 7.3 + - - -
557A ALA* 3.3 3.3 + - - +
573A ILE* 3.5 37.2 - - + -
574A ASN 4.7 2.5 - - - -
582A LEU* 3.7 32.3 - - + -
583A VAL* 4.7 4.0 - - + -
586A SER* 3.4 21.5 - - - +
595A PHE* 4.9 2.0 - + - -
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Residues in contact with ILE 554 (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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550A PHE* 2.9 26.1 + - + +
551A ASP* 4.1 9.6 - - - +
553A PHE* 1.3 74.5 - - - +
555A ALA* 1.3 64.6 + - - +
557A ALA* 3.1 5.0 + - - +
558A GLN* 3.1 42.2 + - - +
586A SER* 4.2 13.2 - - - +
589A ARG* 4.0 16.2 - - + +
590A ALA* 3.9 47.3 - - + +
591A PRO* 4.4 2.5 - - + -
594A THR* 4.3 4.3 - - + -
595A PHE* 4.2 14.1 - - + -
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Residues in contact with ALA 555 (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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465A TYR* 3.8 16.8 - - + -
466A GLU 3.9 15.7 - - - +
467A SER* 4.1 8.7 - - - -
468A LYS* 4.7 3.6 - - + +
551A ASP 2.9 23.1 + - - +
554A ILE* 1.3 73.5 - - - +
556A ALA* 1.3 63.6 + - - +
558A GLN* 3.6 15.3 + - - +
559A PHE* 2.9 25.5 + - - +
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Residues in contact with ALA 556 (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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465A TYR* 3.5 33.8 - - + +
475A MET* 3.9 6.9 - - - +
493A GLN* 3.7 11.9 - - - +
525A PRO* 3.8 18.6 - - + -
552A ASP 3.0 6.6 + - - +
553A PHE 3.4 10.1 - - - +
554A ILE 3.2 0.4 - - - -
555A ALA* 1.3 76.1 - - - +
557A ALA* 1.3 63.9 + - - +
559A PHE* 3.2 5.0 + - - +
560A LEU* 3.0 26.2 + - - +
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Residues in contact with ALA 557 (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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493A GLN* 3.3 19.5 + - - +
553A PHE 3.3 1.0 + - - +
554A ILE 3.1 7.9 + - - +
556A ALA* 1.3 80.1 - - - +
558A GLN* 1.3 62.5 + - - +
560A LEU* 3.4 15.8 + - - +
561A VAL* 3.4 17.7 + - - +
571A VAL* 3.9 13.4 - - + +
594A THR* 4.1 11.1 - - + +
595A PHE* 3.6 30.5 - - + -
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Residues in contact with GLN 558 (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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554A ILE* 3.1 18.8 + - - +
555A ALA* 3.6 19.4 + - - +
556A ALA 3.2 0.2 - - - -
557A ALA* 1.3 78.1 - - - +
559A PHE* 1.3 54.8 + - - +
561A VAL* 3.3 5.8 + - - +
562A LYS* 2.9 31.9 + - - +
591A PRO* 4.0 30.5 - - - +
594A THR* 4.2 15.0 + - + +
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Residues in contact with PHE 559 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A VAL* 3.9 21.3 - - + -
464A TRP 3.8 23.1 - - - -
465A TYR* 3.5 22.2 - - + -
466A GLU 5.3 0.7 - - - -
475A MET* 3.7 17.5 - - + -
555A ALA 2.9 18.6 + - - +
556A ALA 3.5 3.4 - - - +
558A GLN* 1.3 74.3 - - - +
560A LEU* 1.3 68.4 + - - +
562A LYS* 4.4 2.2 - - - -
563A ASN* 3.0 55.4 + - - +
565A TYR* 3.5 33.7 - + - -
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Residues in contact with LEU 560 (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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475A MET* 3.8 20.6 - - + -
477A ILE* 4.0 13.5 - - + -
491A ALA* 4.0 18.6 - - + -
493A GLN* 3.5 23.8 - - - +
521A ILE* 4.3 6.7 - - + -
523A ALA* 3.8 20.4 - - + -
556A ALA 3.0 15.5 + - - +
557A ALA* 3.4 6.0 + - - +
559A PHE* 1.3 76.6 - - - +
561A VAL* 1.3 61.2 + - - +
564A LYS 3.4 0.7 + - - -
565A TYR* 2.9 50.8 + - + -
566A ALA* 3.0 16.5 + - + -
571A VAL* 4.2 9.4 - - + -
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Residues in contact with VAL 561 (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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557A ALA 3.4 5.8 + - - +
558A GLN* 3.3 8.5 + - - +
559A PHE 3.2 0.4 - - - -
560A LEU* 1.3 76.1 - - - +
562A LYS* 1.3 67.7 + - - +
564A LYS* 3.0 18.2 + - - +
566A ALA 3.6 8.1 - - - +
567A ALA 3.6 20.2 - - - +
568A PRO* 3.8 34.2 - - + +
569A GLY 4.6 3.6 - - - +
571A VAL* 3.8 22.4 - - + -
594A THR 5.5 3.4 - - - +
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Residues in contact with LYS 562 (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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558A GLN 2.9 19.7 + - - +
559A PHE* 4.1 2.0 - - - +
561A VAL* 1.3 79.4 - - - +
563A ASN* 1.3 70.2 + - - +
564A LYS* 3.6 9.0 + - - +
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Residues in contact with ASN 563 (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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485A PHE* 5.1 1.7 - - - +
559A PHE* 3.0 44.3 + - - +
562A LYS* 1.3 89.7 - - - +
564A LYS* 1.3 68.0 + - - +
565A TYR* 3.2 25.9 + - + -
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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