Contacts of the helix formed by residues 549 - 560 (chain A) in PDB entry 5A7R
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 ARG 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A THR* 1.3 97.1 + - - +
550A PRO* 1.3 80.1 - - + +
551A GLN* 3.2 7.0 - - + +
552A ASN* 2.9 38.7 + - - +
553A LEU 3.8 0.2 + - - -
577A TRP* 3.5 17.4 - - - +
578A ASP* 2.7 42.0 + - - -
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Residues in contact with PRO 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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549A ARG* 1.3 107.3 - - + +
551A GLN* 1.3 62.5 + - - +
553A LEU* 3.0 14.6 + - + +
554A LYS* 3.1 12.0 + - - +
573A LEU* 4.4 7.7 - - + +
574A ILE* 3.9 33.6 - - + +
577A TRP* 3.6 41.1 - - + +
578A ASP* 3.7 20.9 - - - +
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Residues in contact with GLN 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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549A ARG* 3.2 5.7 + - + +
550A PRO* 1.3 80.7 - - - +
552A ASN* 1.3 61.5 + - - +
554A LYS* 3.4 18.8 + - - +
555A ASP* 2.9 58.3 + - - +
574A ILE* 4.5 7.0 - - - +
1984A GOL 2.8 36.2 + - - -
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Residues in contact with ASN 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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546A LYS 4.2 6.1 - - - +
547A PHE* 3.8 21.8 - - + -
548A THR* 2.9 32.2 + - - -
549A ARG* 2.9 25.9 + - - +
551A GLN* 1.3 80.2 - - - +
553A LEU* 1.3 59.2 + - - +
555A ASP* 3.5 7.1 + - - +
556A ALA* 3.1 27.9 + - - +
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Residues in contact with LEU 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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547A PHE* 4.0 25.5 - - + -
549A ARG 3.8 0.4 + - - -
550A PRO 3.0 8.9 + - - +
552A ASN* 1.3 77.1 - - - +
554A LYS* 1.3 66.2 + - - +
556A ALA* 3.3 2.7 + - + +
557A ILE* 3.1 42.7 + - + +
573A LEU* 3.7 31.2 - - + -
577A TRP* 4.3 13.9 - - + -
594A LEU* 4.2 27.6 - - + -
638A PHE* 4.3 9.9 - - + -
639A PHE* 3.8 22.7 - - + -
665A PHE* 5.8 0.2 - - + -
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Residues in contact with LYS 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 PRO 3.1 12.3 + - - +
551A GLN* 3.7 21.9 - - - +
553A LEU* 1.3 79.3 - - - +
555A ASP* 1.3 64.5 + - - +
557A ILE* 3.4 2.1 + - - +
558A LEU* 3.1 40.6 + - + +
565A SER 5.3 3.8 + - - -
568A TRP 5.2 3.9 + - - -
569A ASP* 6.2 0.2 - - - +
570A PHE* 3.5 58.8 - - + +
573A LEU* 4.9 1.7 - - + +
574A ILE* 4.7 3.8 - - + +
1984A GOL 3.0 44.3 + - - +
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Residues in contact with ASP 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 GLN* 2.9 52.2 + - - +
552A ASN* 3.9 6.8 + - - +
553A LEU 3.3 0.2 - - - -
554A LYS* 1.3 80.4 - - - +
556A ALA* 1.3 61.8 + - - +
558A LEU* 3.4 7.9 + - - +
559A LYS* 3.2 35.1 + - - +
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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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542A ALA* 3.6 29.5 - - - +
543A LEU* 4.3 8.5 - - + -
547A PHE* 4.0 15.5 - - + -
552A ASN 3.1 18.1 + - - +
553A LEU* 3.6 5.6 - - + +
555A ASP* 1.3 75.6 - - - +
557A ILE* 1.3 62.1 + - - +
559A LYS* 3.1 21.6 + - - +
560A TYR* 3.3 17.4 - - - -
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Residues in contact with ILE 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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543A LEU* 5.0 0.9 - - + -
553A LEU* 3.1 41.6 + - + +
554A LYS 3.9 3.8 - - - +
556A ALA* 1.3 74.5 - - - +
558A LEU* 1.3 61.7 + - - +
559A LYS 3.4 0.7 + - - -
560A TYR* 3.6 14.8 + - - +
561A ASN* 3.0 34.9 + - - +
568A TRP* 4.1 11.4 - - + -
570A PHE* 4.2 24.5 - - + -
573A LEU* 5.3 0.2 - - + -
638A PHE* 4.4 10.5 - - + +
639A PHE* 3.8 26.9 - - + +
640A CYS* 4.1 10.3 - - + -
665A PHE* 4.3 16.4 - - + -
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Residues in contact with LEU 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 LYS* 3.1 47.4 + - + +
555A ASP* 3.4 8.0 + - - +
556A ALA 3.2 0.2 - - - -
557A ILE* 1.3 72.5 - - - +
559A LYS* 1.3 64.3 + - - +
560A TYR 3.2 2.7 - - - -
561A ASN* 3.1 20.7 + - + +
562A VAL* 3.3 17.7 + - - +
564A TYR 4.2 2.2 - - - +
565A SER* 3.8 42.3 - - - +
568A TRP* 4.0 26.5 - - + +
570A PHE* 4.0 12.6 - - + -
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Residues in contact with LYS 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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538A LEU* 3.6 25.7 - - + +
541A THR 5.6 0.2 + - - -
542A ALA* 3.9 26.5 + - + +
545A ASN* 4.5 16.4 - - - +
555A ASP* 3.2 24.9 + - - +
556A ALA* 3.1 12.6 + - - +
558A LEU* 1.3 77.1 - - - +
560A TYR* 1.3 57.3 + - + +
561A ASN 3.4 0.2 - - - -
562A VAL* 3.7 15.9 - - - +
1985A PPI 3.8 2.6 - - - +
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Residues in contact with TYR 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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535A ARG* 4.0 16.4 + - + -
538A LEU* 4.0 15.3 - - + -
539A ILE* 3.6 38.6 - - + -
542A ALA* 3.9 15.7 - - + -
543A LEU* 3.7 13.3 - - + +
556A ALA 3.3 19.3 - - - -
557A ILE* 3.7 12.4 - - - -
558A LEU 3.2 0.4 - - - -
559A LYS* 1.3 75.1 - - + +
561A ASN* 1.3 93.1 + - - +
639A PHE* 2.5 41.6 + - - +
640A CYS 3.7 7.0 - - - -
641A THR* 3.9 16.5 - - + +
1985A PPI 3.3 20.0 - - - +
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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