Contacts of the helix formed by residues 540 - 555 (chain A) in PDB entry 1N54
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 ASN 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524A VAL* 5.9 3.8 + - - -
525A PRO 5.5 2.5 - - - +
526A ASN* 2.6 32.6 + - + +
539A PHE* 1.3 79.5 - - - +
541A PRO* 1.3 69.3 - - + +
542A LEU 3.2 1.8 + - - +
543A LYS* 3.5 44.7 - - + +
544A ILE* 3.1 29.5 + - + +
576A LEU* 5.4 2.5 + - + +
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Residues in contact with PRO 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASN* 3.3 27.6 - - - +
539A PHE* 3.5 30.9 - - + -
540A ASN* 1.3 85.5 - - - +
542A LEU* 1.3 62.5 + - + +
545A GLU* 3.3 15.5 + - - +
585A HIS* 3.2 37.4 + - + +
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Residues in contact with LEU 542 (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 TYR* 3.9 11.7 - - - +
496A PRO* 3.6 43.3 - - + +
497A GLY* 3.9 6.7 - - - +
524A VAL* 3.9 7.0 - - + -
525A PRO* 3.6 42.4 + - + +
526A ASN* 5.3 2.2 - - - +
540A ASN* 3.2 0.6 - - - +
541A PRO* 1.3 78.9 - - - +
543A LYS* 1.3 66.9 + - - +
544A ILE 3.1 2.4 + - - -
545A GLU* 3.2 9.3 + - - +
546A VAL* 3.1 39.0 + - + +
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Residues in contact with LYS 543 (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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518A PHE* 5.3 10.2 + - - -
521A LEU* 3.5 63.4 + - + +
522A LYS* 5.2 6.2 - - - +
524A VAL* 3.9 15.5 - - + +
540A ASN* 3.4 39.8 + - + +
542A LEU* 1.3 78.0 - - - +
544A ILE* 1.3 61.3 + - - +
546A VAL* 3.2 17.5 - - - +
547A PHE* 3.6 5.7 - - - +
575A THR* 5.9 3.0 + - - +
576A LEU* 3.7 27.3 - - + +
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Residues in contact with ILE 544 (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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539A PHE* 4.2 20.9 - - + -
540A ASN 3.1 24.2 - - - +
541A PRO 3.8 3.6 - - - +
543A LYS* 1.3 76.0 - - - +
545A GLU* 1.3 59.8 + - - +
547A PHE* 2.6 27.1 + - - +
548A VAL* 3.1 30.5 + - + +
576A LEU* 3.9 36.8 - - + +
582A GLY* 4.2 17.0 - - - +
585A HIS* 3.9 17.7 - - + -
586A VAL* 4.1 19.1 - - + -
589A VAL* 4.7 0.7 - - + -
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Residues in contact with GLU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LYS* 3.1 29.0 + - + +
487A TYR* 3.3 29.6 + - + +
541A PRO 3.3 12.2 + - - +
542A LEU* 3.2 17.0 + - - +
544A ILE* 1.3 81.4 - - - +
546A VAL* 1.3 59.7 + - - +
547A PHE 3.2 0.2 + - - -
549A GLN* 3.0 34.7 + - + +
585A HIS* 4.5 5.2 + - - +
589A VAL* 4.1 31.7 - - + +
592A GLU* 6.2 0.5 - - - +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TYR* 3.4 24.2 - - + -
497A GLY* 3.4 29.4 - - - +
500A VAL* 4.3 9.9 - - + -
501A ALA* 4.4 6.5 - - + +
504A LEU* 3.5 9.5 - - + +
521A LEU* 3.8 16.2 - - + -
524A VAL* 4.8 3.1 - - + -
542A LEU* 3.2 30.5 - - + +
543A LYS* 3.2 17.3 - - - +
545A GLU* 1.3 74.6 - - - +
547A PHE* 1.3 56.2 + - - +
549A GLN* 4.7 0.2 - - - -
550A THR* 2.4 30.9 + - - -
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Residues in contact with PHE 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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504A LEU* 4.6 5.4 - - + -
508A PHE* 3.8 26.5 - + - -
517A ILE* 4.0 13.7 - - + -
521A LEU* 4.4 6.7 - - + -
543A LYS 3.6 11.7 - - - +
544A ILE* 2.6 17.8 + - + +
546A VAL* 1.3 74.2 - - - +
548A VAL* 1.3 66.9 + - + +
549A GLN 3.3 0.2 - - - -
550A THR* 3.2 3.0 + - - -
551A LEU* 3.0 31.6 + - + +
569A PHE* 3.7 19.7 - - + -
572A VAL* 3.3 35.9 - - + -
573A PHE* 3.6 41.1 - + - -
576A LEU* 3.4 20.6 - - + -
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Residues in contact with VAL 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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544A ILE* 3.1 29.0 + - + +
547A PHE* 1.3 80.2 - - + +
549A GLN* 1.3 67.0 + - - +
551A LEU* 4.0 0.8 - - - +
552A LEU* 2.9 51.7 + - + +
573A PHE* 3.8 31.9 - - + -
586A VAL* 4.3 15.3 - - + +
589A VAL* 4.4 8.7 - - + -
590A MET* 4.2 23.1 - - + +
593A VAL* 5.2 0.2 - - + -
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Residues in contact with GLN 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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484A ILE* 3.3 20.1 + - - +
485A TYR* 3.4 21.9 - - + -
486A LYS* 3.1 39.4 - - + +
487A TYR* 5.1 4.9 - - + -
545A GLU* 3.0 26.4 + - + +
546A VAL* 4.7 2.0 - - - -
548A VAL* 1.3 80.1 - - - +
550A THR* 1.3 63.8 + - - +
552A LEU* 4.0 1.7 - - - +
553A HIS* 3.2 22.7 + - - +
589A VAL* 3.5 18.4 - - + +
592A GLU* 5.2 6.3 + - - +
593A VAL* 3.6 25.1 - - - +
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Residues in contact with THR 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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485A TYR* 3.3 23.5 + - + +
501A ALA* 3.6 31.5 - - - +
504A LEU* 4.1 2.0 - - + +
505A ALA* 3.7 20.2 - - - +
508A PHE* 3.7 15.5 - - + -
546A VAL 2.4 27.6 + - - -
547A PHE 3.2 3.7 + - - -
548A VAL 3.2 0.8 - - - -
549A GLN* 1.3 78.5 - - - +
551A LEU* 1.3 61.6 + - - +
553A HIS* 3.5 9.2 + - - +
554A LEU* 3.5 18.2 + - + +
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A PHE* 3.9 33.8 - - + -
547A PHE* 3.0 24.4 + - + +
548A VAL* 4.0 3.1 - - - +
550A THR* 1.3 74.7 - - - +
552A LEU* 1.3 67.7 + - + +
554A LEU* 3.6 5.1 + - + -
555A ALA* 3.2 27.4 + - + +
565A ALA* 3.9 28.5 - - + +
566A LEU* 4.7 0.7 - - + +
569A PHE* 3.5 39.7 - - + -
573A PHE* 4.1 20.0 - - + -
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Residues in contact with LEU 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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483A CYS* 4.8 1.6 - - - -
548A VAL* 2.9 38.6 + - + +
549A GLN 4.1 2.5 - - - +
551A LEU* 1.3 80.8 - - + +
553A HIS* 1.3 58.3 + - - +
554A LEU 3.4 0.2 - - - -
555A ALA* 3.4 1.5 - - + +
556A ALA* 2.8 31.7 + - - +
562A SER* 3.8 26.5 - - - +
565A ALA* 6.3 0.4 - - + -
566A LEU* 5.2 10.5 - - + -
573A PHE* 6.0 1.6 - - + -
590A MET* 4.0 19.1 - - + -
593A VAL* 4.6 11.0 - - + -
594A TRP* 3.5 34.6 - - + +
604A LEU* 4.6 12.8 - - + -
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Residues in contact with HIS 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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483A CYS* 4.5 17.5 - - + -
485A TYR* 3.5 53.0 - + + +
509A LYS* 5.9 1.1 - - - -
549A GLN 3.2 18.1 + - - +
550A THR 3.7 6.1 - - - +
551A LEU 3.2 0.8 - - - -
552A LEU* 1.3 81.0 - - - +
554A LEU* 1.3 78.3 + - + +
556A ALA* 3.4 16.3 + - + +
557A LYS 5.0 0.2 + - - -
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Residues in contact with LEU 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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505A ALA* 3.8 17.9 - - + +
508A PHE* 3.4 41.3 - - + -
509A LYS* 3.6 35.9 - - + +
550A THR* 3.5 12.6 + - + +
551A LEU* 3.6 6.2 + - + +
553A HIS* 1.3 94.0 - - + +
555A ALA* 1.3 57.8 + - - +
556A ALA 3.4 1.7 + - - -
557A LYS* 4.8 4.8 + - - +
561A HIS* 4.9 6.2 - - - +
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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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551A LEU* 3.2 20.5 + - + +
552A LEU* 3.4 3.8 - - + +
554A LEU* 1.3 77.4 - - - +
556A ALA* 1.3 62.7 + - - +
557A LYS 3.3 2.7 - - - -
558A SER 3.2 12.0 - - - +
561A HIS* 3.7 16.3 - - + +
562A SER* 2.9 44.1 + - - +
565A ALA* 4.0 10.1 - - + -
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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
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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