Contacts of the helix formed by residues 558 - 569 (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 SER 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A ALA 3.2 17.0 - - - +
557A LYS* 1.3 79.5 - - - +
559A PHE* 1.3 67.7 + - - +
560A SER* 3.3 7.1 + - - -
561A HIS* 2.8 43.1 + - - -
562A SER* 3.5 7.8 + - - -
600A MET* 4.1 4.3 - - - +
53B GLU* 4.1 6.1 - - - -
54B GLU* 3.3 12.3 - - - -
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Residues in contact with PHE 559 (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 SER* 1.3 74.2 - - - +
560A SER* 1.3 64.4 + - - +
561A HIS 3.4 0.2 - - - -
562A SER* 4.1 3.9 - - - -
563A PHE* 3.2 42.0 + + + -
597A HIS* 4.1 7.2 - - - -
599A GLN* 3.5 30.1 - - + -
600A MET* 3.4 43.1 - - + -
603A VAL* 3.5 36.1 - - + -
53B GLU* 2.9 18.6 + - - +
54B GLU* 3.1 48.4 + - + +
57B TYR* 4.2 14.6 - + + -
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Residues in contact with SER 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A SER* 3.6 8.5 - - - -
559A PHE* 1.3 77.4 - - - +
561A HIS* 1.3 66.4 + - - +
563A PHE* 3.8 4.6 - - - +
564A SER* 3.0 26.2 + - - -
53B GLU* 2.6 28.1 + - - -
68B LYS* 5.8 3.6 - - - -
69B ILE 5.7 0.2 + - - -
71B MET* 6.5 0.4 - - - -
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Residues in contact with HIS 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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554A LEU 4.9 3.6 - - - +
555A ALA* 3.7 22.9 - - + +
557A LYS* 3.5 22.8 + - + +
558A SER* 2.8 36.5 + - - +
560A SER* 1.3 81.2 + - - +
562A SER* 1.3 58.2 + - - +
564A SER* 3.0 8.2 + - - -
565A ALA* 2.8 35.3 + - - +
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Residues in contact with SER 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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552A LEU* 3.8 19.1 - - - +
555A ALA* 2.9 29.9 + - - -
556A ALA* 4.7 0.7 - - - -
558A SER 3.5 8.4 + - - -
559A PHE* 4.1 4.7 - - - -
561A HIS* 1.3 78.0 - - - +
563A PHE* 1.3 60.7 + - - +
565A ALA* 3.5 2.3 - - - +
566A LEU* 3.0 33.2 + - - +
594A TRP* 4.9 0.5 + - - -
600A MET* 3.6 18.7 - - - +
604A LEU* 4.1 17.3 - - - +
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Residues in contact with PHE 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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559A PHE* 3.2 24.3 + - + +
560A SER* 3.8 5.6 - - - +
561A HIS 3.0 1.6 + - - -
562A SER* 1.3 76.9 - - - +
564A SER* 1.3 59.5 + - - +
565A ALA 2.9 0.9 - - - -
566A LEU* 2.7 33.8 + - + +
567A ALA* 2.8 11.9 + - - +
603A VAL* 3.4 48.7 - - + -
604A LEU* 4.4 8.3 - - + -
606A ASP* 6.1 0.2 - - - -
607A LYS* 3.6 42.7 - - + +
53B GLU* 5.4 1.3 - - - -
57B TYR* 3.3 35.0 - + - -
68B LYS* 6.5 0.9 - - + -
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Residues in contact with SER 564 (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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560A SER 3.0 12.8 + - - -
561A HIS* 3.0 18.9 + - - -
563A PHE* 1.3 76.0 - - - +
565A ALA* 1.3 55.9 + - - +
567A ALA* 3.3 10.0 - - - +
568A LYS* 2.7 32.5 + - - +
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Residues in contact with ALA 565 (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* 3.9 31.5 - - + +
552A LEU* 6.3 0.7 - - + -
555A ALA* 4.0 13.0 - - + -
561A HIS 2.8 19.0 + - - +
562A SER 3.5 5.6 - - - +
563A PHE 2.8 0.4 + - - -
564A SER* 1.3 78.6 + - - +
566A LEU* 1.3 63.1 + - - +
567A ALA 3.0 0.9 + - - -
568A LYS* 3.2 2.2 + - - -
569A PHE* 3.1 34.2 + - + +
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Residues in contact with LEU 566 (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* 4.7 1.1 - - + +
552A LEU* 5.2 10.5 - - + -
562A SER 3.0 19.3 + - - +
563A PHE* 2.7 21.2 + - + +
565A ALA* 1.3 75.3 - - - +
567A ALA* 1.3 56.5 + - - +
569A PHE 3.8 0.9 - - - -
570A HIS* 3.1 28.6 + - - +
573A PHE* 3.2 41.4 - - + -
604A LEU* 3.9 26.7 - - + +
607A LYS* 4.7 9.9 - - + -
608A MET* 4.3 25.6 - - + +
613A ILE* 3.9 18.5 - - + +
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Residues in contact with ALA 567 (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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563A PHE 2.8 9.4 + - - +
564A SER* 3.3 14.6 - - - +
566A LEU* 1.3 77.2 - - - +
568A LYS* 1.3 62.7 + - - +
570A HIS* 2.9 24.8 - - - +
611A THR* 6.1 6.1 - - + -
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Residues in contact with LYS 568 (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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508A PHE 5.8 0.6 + - - -
511A LYS* 3.9 32.1 + - - +
512A ALA 3.7 23.3 + - - -
513A THR* 5.1 9.2 - - - +
514A ASN* 3.5 18.9 + - - +
564A SER 2.7 20.0 + - - +
565A ALA* 4.6 0.7 - - - -
567A ALA* 1.3 74.8 - - - +
569A PHE* 1.3 86.0 + - + +
570A HIS* 3.1 4.9 + - - +
571A GLU* 4.4 1.0 + - - +
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Residues in contact with PHE 569 (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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508A PHE* 3.4 34.8 - + - -
512A ALA 3.4 23.8 - - - -
513A THR 4.6 1.8 - - - -
514A ASN* 3.5 12.3 - - - +
517A ILE* 3.9 15.9 - - + -
547A PHE* 3.7 18.2 - + + -
551A LEU* 3.5 27.6 - - + -
565A ALA* 3.1 19.8 + - - +
566A LEU 3.8 3.4 - - - -
568A LYS* 1.3 104.8 - - + +
570A HIS* 1.3 63.2 + - - +
571A GLU 3.2 2.9 - - - -
572A VAL* 2.9 21.1 + - + +
573A PHE* 3.1 13.9 + - - -
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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