Contacts of the helix formed by residues 570 - 580 (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 PHE 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A LYS* 3.5 50.1 - - + +
557A ILE* 4.2 25.6 - - + -
558A LEU* 4.0 23.6 - - + -
568A TRP* 3.8 34.8 - + + -
569A ASP* 1.3 77.7 + - - +
571A THR* 1.3 63.9 + - - +
573A LEU* 3.0 28.7 + - + +
574A ILE* 3.0 29.2 + - + +
662A ASN* 5.6 0.7 - - + -
665A PHE* 2.9 40.6 - + + -
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Residues in contact with THR 571 (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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569A ASP* 2.6 29.1 + - - -
570A PHE* 1.3 78.2 - - - +
572A ALA* 1.3 59.4 + - - +
574A ILE* 3.4 8.3 + - + +
575A ASP* 2.8 45.6 + - - +
665A PHE 3.1 1.6 + - - -
667A GLY* 3.7 13.0 - - - +
668A ARG* 3.8 28.4 + - + +
1984A GOL 6.1 1.0 - - - -
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Residues in contact with ALA 572 (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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571A THR* 1.3 74.1 - - - +
573A LEU* 1.3 54.8 + - - +
575A ASP* 4.0 5.0 - - - +
576A PHE* 2.9 31.0 + - - +
664A LEU 4.0 4.9 - - - +
665A PHE 2.8 22.2 + - - +
666A GLU 3.6 10.5 - - - +
667A GLY 3.3 17.9 + - - +
668A ARG* 5.6 0.2 - - - -
672A LYS* 4.0 24.9 - - + +
673A PRO* 6.1 0.3 - - - +
676A LEU* 4.2 4.4 - - + +
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Residues in contact with LEU 573 (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* 4.8 10.3 - - + +
553A LEU* 3.7 38.4 - - + -
554A LYS* 4.9 3.4 - - + +
557A ILE* 5.3 0.2 - - + -
570A PHE* 3.0 32.1 + - + +
572A ALA* 1.3 77.2 - - - +
574A ILE* 1.3 65.8 + - + +
576A PHE* 3.4 9.8 + - + +
577A TRP* 3.1 32.8 + - + +
589A LEU* 5.9 1.8 - - + -
638A PHE* 5.1 4.7 - - + -
665A PHE* 3.5 37.6 + - + +
676A LEU* 4.9 9.4 - - + -
680A PHE* 5.4 6.7 - - + -
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Residues in contact with ILE 574 (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* 3.9 28.3 - - + +
551A GLN* 4.5 7.6 - - - +
554A LYS* 4.7 5.4 - - + -
570A PHE* 3.0 37.4 + - + +
571A THR* 3.9 7.9 - - + +
573A LEU* 1.3 78.3 - - + +
575A ASP* 1.3 64.9 + - - +
577A TRP* 3.9 0.5 - - - +
578A ASP* 2.9 44.6 + - - +
579A LYS* 4.6 7.2 - - - +
1984A GOL 3.8 25.8 - - - +
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Residues in contact with ASP 575 (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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571A THR* 2.8 29.9 + - - +
572A ALA* 4.0 5.2 - - - +
574A ILE* 1.3 73.4 - - - +
576A PHE* 1.3 62.6 + - - +
579A LYS* 2.7 65.5 + - + +
580A VAL* 3.0 12.5 + - + +
667A GLY 4.8 1.0 - - - +
668A ARG* 2.9 37.0 + - - +
673A PRO* 6.5 0.4 - - + -
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Residues in contact with PHE 576 (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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572A ALA 2.9 20.3 + - - +
573A LEU* 3.7 9.2 - - + +
575A ASP* 1.3 77.0 - - - +
577A TRP* 1.3 62.5 + - + +
580A VAL* 3.5 10.7 - - + +
581A LEU* 2.9 63.8 + - + +
589A LEU* 4.6 6.5 - - + -
673A PRO* 3.6 43.4 - - + +
676A LEU* 3.8 23.8 - - + -
677A LYS* 3.8 16.2 - - + -
680A PHE* 3.8 24.5 - + - -
1982A GOL 3.7 20.9 - - - -
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Residues in contact with TRP 577 (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 14.4 - - + -
548A THR 4.0 4.9 + - - -
549A ARG* 3.5 33.5 - - - +
550A PRO* 3.6 39.1 - - + +
553A LEU* 4.3 12.8 - - + -
573A LEU* 3.1 23.5 + - + +
574A ILE 3.9 2.0 - - - +
576A PHE* 1.3 85.1 - - + +
578A ASP* 1.3 64.7 + - - +
581A LEU* 3.9 24.5 - - - +
586A ALA* 4.1 16.3 - - + +
589A LEU* 4.0 18.6 - - + -
590A TYR* 3.6 46.2 - + + -
594A LEU* 3.6 19.7 - - + -
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Residues in contact with ASP 578 (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* 2.7 45.2 + - - -
550A PRO* 3.7 13.4 - - - +
574A ILE* 2.9 29.4 + - + +
577A TRP* 1.3 76.7 - - - +
579A LYS* 1.3 75.0 + - + +
580A VAL 3.8 0.2 - - - -
581A LEU 4.7 5.3 - - - +
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Residues in contact with LYS 579 (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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574A ILE* 4.6 12.1 - - - +
575A ASP* 2.7 47.9 + - + +
578A ASP* 1.3 86.4 + - + +
580A VAL* 1.3 62.0 + - + +
581A LEU 5.0 0.7 - - - -
668A ARG* 4.8 7.4 - - - +
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Residues in contact with VAL 580 (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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575A ASP* 3.0 15.4 + - + +
576A PHE* 3.5 18.6 - - + +
579A LYS* 1.3 84.3 - - + +
581A LEU* 1.3 67.6 + - - +
582A GLU* 3.5 3.5 + - - +
585A GLU* 4.7 1.0 - - - +
673A PRO* 3.9 37.5 - - + -
677A LYS* 4.3 21.0 + - - +
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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