Contacts of the helix formed by residues 561 - 577 (chain A) in PDB entry 2A8B
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 ALA 561 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ASP 4.4 0.2 + - - -
560A SER* 1.3 73.1 + - - +
562A GLN* 1.3 65.3 + - - +
563A PRO 3.3 1.3 - - - -
564A LEU* 3.1 4.9 + - - +
565A LEU* 2.9 22.5 + - - +
639A PHE* 3.8 22.1 - - + -
642A HIS* 4.1 8.2 - - + +
643A ALA* 3.7 37.7 - - + +
646A LEU* 3.7 11.7 - - + +
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Residues in contact with GLN 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASN* 3.6 8.5 + - - +
560A SER* 3.3 11.7 + - - +
561A ALA* 1.3 76.2 - - - +
563A PRO* 1.3 88.5 - - + +
565A LEU* 3.2 3.5 + - - +
566A GLN* 2.5 53.9 + - - +
646A LEU* 3.3 20.2 - - + +
650A ARG* 4.3 17.1 + - - +
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Residues in contact with PRO 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASN* 3.5 35.0 - - - +
528A TYR* 3.9 5.5 - - - -
549A TYR* 3.6 25.6 - - + +
551A SER* 5.1 2.7 - - - +
558A PRO* 6.1 0.4 - - + -
560A SER* 3.5 21.8 - - - +
561A ALA 3.5 3.1 - - - -
562A GLN* 1.3 105.8 - - + +
564A LEU* 1.3 55.3 + - - +
566A GLN* 3.3 4.4 + - + +
567A LEU* 3.1 25.8 + - - +
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 4.7 7.6 - - + -
549A TYR* 3.9 15.1 + - + +
552A TRP* 3.9 26.5 - - + -
560A SER 5.1 0.2 + - - -
561A ALA* 3.1 8.5 + - - +
563A PRO* 1.3 76.7 - - - +
565A LEU* 1.3 61.8 + - - +
567A LEU* 3.3 15.3 + - + +
568A MET* 2.8 28.3 + - + +
597A CYS 4.8 0.9 - - - +
598A PHE* 4.2 34.7 - - + +
601A THR* 4.4 23.1 - - + +
639A PHE* 3.8 32.1 - - + -
643A ALA* 5.1 3.4 - - + -
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A ALA 2.9 13.7 + - - +
562A GLN* 3.4 9.0 - - - +
564A LEU* 1.3 74.5 - - - +
566A GLN* 1.3 59.4 + - - +
568A MET* 3.1 19.9 + - + +
569A LEU* 2.8 41.4 + - + +
601A THR* 4.6 7.6 - - + -
605A CYS* 4.2 4.3 - - - -
643A ALA* 4.1 13.1 - - + +
646A LEU* 3.8 20.6 - - + -
647A TYR* 3.7 55.4 - - + +
650A ARG* 4.0 20.4 - - - +
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Residues in contact with GLN 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A CYS* 5.9 2.5 - - - -
526A ASP* 4.8 14.4 - - - +
527A ASN* 3.4 18.2 + - - -
528A TYR* 3.1 24.6 + - + +
562A GLN* 2.5 43.1 + - - +
563A PRO 3.4 10.3 - - - +
564A LEU 3.3 0.2 - - - -
565A LEU* 1.3 71.3 - - - +
567A LEU* 1.3 58.5 + - - +
569A LEU* 3.3 11.9 + - + +
570A ASP* 2.9 30.7 + - - +
650A ARG* 5.9 0.9 - - - +
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Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A VAL* 3.7 23.3 - - + -
491A ILE* 4.7 1.8 - - + -
528A TYR* 3.2 25.7 + - + -
547A TYR* 3.3 45.3 - - + -
549A TYR* 4.1 26.7 - - + -
563A PRO 3.1 6.4 + - - +
564A LEU* 3.4 14.8 - - + +
566A GLN* 1.3 79.9 - - - +
568A MET* 1.3 62.8 + - - +
570A ASP* 3.8 0.7 - - - +
571A VAL* 2.9 33.9 + - + +
598A PHE* 3.8 17.0 - - + -
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Residues in contact with MET 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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564A LEU* 2.8 18.1 + - + +
565A LEU* 3.4 16.2 - - + +
567A LEU* 1.3 74.3 - - - +
569A LEU* 1.3 78.1 + - + +
571A VAL* 3.6 1.9 + - - +
572A GLU* 2.8 61.2 + - + +
598A PHE* 3.8 15.7 - - + +
601A THR* 4.2 6.5 - - + +
602A SER* 3.3 36.7 + - - +
605A CYS* 3.7 31.9 - - - -
647A TYR* 4.3 7.0 - - + -
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Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU* 2.8 35.3 + - + +
566A GLN* 3.6 8.1 - - + +
568A MET* 1.3 95.5 - - + +
570A ASP* 1.3 65.4 + - - +
572A GLU* 3.4 17.5 + - - +
573A GLU* 3.0 29.5 + - - +
647A TYR* 3.9 16.6 - - + -
650A ARG* 3.9 30.3 - - - +
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Residues in contact with ASP 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A CYS* 5.0 4.5 - - - -
528A TYR* 2.4 32.0 + - - +
547A TYR* 3.6 23.1 + - + +
566A GLN* 2.9 15.4 + - - +
567A LEU 3.8 3.6 - - - +
569A LEU* 1.3 76.7 - - - +
571A VAL* 1.3 63.0 + - - +
573A GLU* 3.2 21.9 + - - +
574A ASP* 3.1 22.5 + - - +
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Residues in contact with VAL 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A PHE* 5.5 1.3 - - + -
487A VAL* 4.2 4.3 - - + -
489A VAL* 3.6 24.2 - - + -
547A TYR* 3.8 19.3 - - + -
567A LEU* 2.9 25.4 + - + +
568A MET 3.8 3.8 - - - +
570A ASP* 1.3 73.7 - - - +
572A GLU* 1.3 60.2 + - - +
574A ASP* 3.0 10.4 + - - +
575A ARG* 3.0 32.6 + - - +
584A VAL* 4.1 32.5 - - + -
598A PHE* 4.0 17.7 - - + -
602A SER* 5.8 0.2 - - - +
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Residues in contact with GLU 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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568A MET* 2.8 41.2 + - + +
569A LEU* 3.5 21.4 - - - +
570A ASP 3.3 0.4 - - - -
571A VAL* 1.3 76.3 - - - +
573A GLU* 1.3 61.3 + - + +
575A ARG* 3.3 18.0 + - - +
576A LEU* 3.2 22.4 + - + +
602A SER 5.2 3.8 - - - +
605A CYS* 5.2 1.6 - - - +
606A GLN* 5.6 5.9 + - - +
647A TYR* 4.5 12.4 + - - -
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Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A LEU* 3.0 16.5 + - - +
570A ASP* 3.2 27.1 + - - +
572A GLU* 1.3 76.3 - - + +
574A ASP* 1.3 60.0 + - - +
576A LEU* 3.6 7.3 + - - +
577A ALA* 3.1 26.5 + - - +
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Residues in contact with ASP 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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487A VAL* 3.5 18.4 - - + -
545A LYS* 2.7 36.8 + - + +
547A TYR* 2.4 39.4 + - - -
570A ASP 3.1 9.0 + - - +
571A VAL* 3.0 9.8 + - - +
573A GLU* 1.3 74.6 - - - +
575A ARG* 1.3 61.3 + - - +
577A ALA* 3.3 7.2 + - - +
578A SER* 2.8 35.9 + - - +
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Residues in contact with ARG 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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454A GLY* 5.4 1.8 - - - -
455A TYR 5.9 0.2 - - - +
458A LYS* 5.6 5.1 - - - +
461A ALA* 3.6 32.9 + - - +
462A PHE* 4.0 23.0 - - - -
486A PRO* 5.6 2.7 - - + -
487A VAL* 5.6 0.4 - - + -
571A VAL* 3.0 25.3 + - - +
572A GLU* 3.3 16.4 + - - +
574A ASP* 1.3 76.4 - - + +
576A LEU* 1.3 58.5 + - - +
578A SER* 3.0 28.8 + - - +
579A GLN* 3.7 2.4 + - - -
584A VAL* 3.6 32.1 - - + +
602A SER* 5.1 5.9 + - - -
603A ILE* 6.3 0.4 - - - +
606A GLN* 3.6 25.0 + - - +
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Residues in contact with LEU 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 GLU* 3.2 15.6 + - + +
573A GLU* 3.9 8.7 - - - +
574A ASP 3.4 0.2 - - - -
575A ARG* 1.3 75.6 - - - +
577A ALA* 1.3 58.4 + - - +
578A SER 3.2 0.9 + - - -
579A GLN* 4.2 12.3 + - - +
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Residues in contact with ALA 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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573A GLU 3.1 18.7 + - - +
574A ASP* 3.6 9.4 - - - +
575A ARG 3.2 0.2 - - - -
576A LEU* 1.3 74.8 - - - +
578A SER* 1.3 59.4 + - - +
579A GLN 3.7 2.3 + - - -
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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
------------------------------------------------------------
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