Contacts of the helix formed by residues 571 - 586 (chain A) in PDB entry 4Y05
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 571 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 5.4 2.4 + - - -
277A GLU* 5.5 0.3 + - - -
349A GLN* 3.2 27.8 + - - -
566A SER* 3.9 21.8 - - - -
568A GLY* 2.9 12.5 + - - -
570A SER* 1.3 79.3 - - - +
572A CYS* 1.3 64.6 + - - +
573A GLU 3.3 2.5 - - - -
574A TYR* 2.9 14.8 + - - +
575A THR* 2.9 21.1 + - - -
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Residues in contact with CYS 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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280A VAL* 4.4 13.7 - - + -
291A VAL* 3.7 28.7 - - - -
292A HIS 4.8 2.2 - - - -
293A GLU* 4.3 11.9 - - - -
568A GLY 3.5 3.9 + - - -
569A ILE* 3.2 21.3 + - + +
570A SER 3.4 1.0 - - - -
571A SER* 1.3 76.0 - - - +
573A GLU* 1.3 60.6 + - + +
575A THR* 3.3 6.9 + - - -
576A LEU* 2.9 38.7 + - - +
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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
----------------------------------------------------------
293A GLU* 4.9 2.3 - - - +
570A SER 5.2 0.8 + - - -
571A SER 3.1 1.0 + - - -
572A CYS* 1.3 80.1 - - - +
574A TYR* 1.3 64.6 + - + +
576A LEU* 3.5 18.9 + - - +
577A ASN* 3.1 36.0 + - - +
580A ARG* 3.3 24.9 + - - -
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Residues in contact with TYR 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 3.6 32.3 - - + +
496A ASN* 4.7 2.1 + - - +
497A GLU* 3.7 34.3 - - + -
498A ARG* 5.2 4.5 - - + -
570A SER 4.4 9.4 - - - -
571A SER* 2.9 21.4 + - - +
573A GLU* 1.3 80.2 - - + +
575A THR* 1.3 64.6 + - - +
577A ASN* 3.3 15.9 + - - +
578A THR* 3.0 26.6 + - - -
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Residues in contact with THR 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 3.8 25.4 - - + -
291A VAL* 4.6 4.3 - - + -
349A GLN* 4.3 3.6 + - - -
565A ILE* 4.0 15.7 - - + +
566A SER 3.0 29.3 + - - -
571A SER 2.9 13.8 + - - -
572A CYS* 3.5 13.5 - - - +
574A TYR* 1.3 76.1 - - - +
576A LEU* 1.3 57.5 + - - +
578A THR* 3.1 8.6 + - - -
579A LEU* 2.9 47.0 + - + +
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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
----------------------------------------------------------
291A VAL* 4.0 23.6 - - + -
293A GLU* 3.7 19.1 - - - +
307A GLN* 3.7 21.1 - - - +
309A PHE* 3.9 19.7 - - + -
572A CYS* 2.9 31.4 + - - +
573A GLU* 3.7 27.4 - - - +
575A THR* 1.3 75.0 - - - +
577A ASN* 1.3 57.9 + - - +
579A LEU* 3.3 3.1 + - - +
580A ARG* 2.8 60.7 + - - +
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Residues in contact with ASN 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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347A TYR* 4.7 0.3 + - - -
496A ASN* 4.5 8.5 - - - +
497A GLU* 6.3 1.2 - - - +
498A ARG 6.1 0.6 - - - +
573A GLU* 3.1 17.0 + - - +
574A TYR* 3.5 20.0 - - - +
575A THR 3.3 0.2 - - - -
576A LEU* 1.3 76.1 - - - +
578A THR* 1.3 62.4 + - - +
580A ARG* 3.1 28.0 + - - +
581A TYR* 3.1 23.6 + - - +
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Residues in contact with THR 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TYR* 3.9 18.3 - - + -
348A GLY* 3.9 5.6 - - - -
349A GLN* 4.0 3.6 + - - +
496A ASN* 3.0 27.4 + - - +
563A ALA* 3.9 18.6 - - + -
564A THR 3.9 19.8 + - - +
565A ILE* 3.9 11.2 - - + -
574A TYR 3.0 13.1 + - - -
575A THR* 3.1 8.7 + - - -
577A ASN* 1.3 75.2 - - - +
579A LEU* 1.3 57.4 + - - +
581A TYR* 3.4 3.1 + - - +
582A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 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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263A VAL* 3.7 30.3 - - + -
289A LEU* 3.7 19.5 - - + -
291A VAL* 3.5 32.1 - - + -
309A PHE* 3.9 23.3 - - + -
311A PHE* 3.7 14.9 - - + -
565A ILE* 4.3 9.9 - - + -
575A THR* 2.9 33.1 + - + +
576A LEU* 3.8 4.7 - - - +
578A THR* 1.3 73.1 - - + +
580A ARG* 1.3 60.0 + - - +
582A ALA* 3.8 3.8 - - - +
583A ASP* 2.9 31.7 + - - +
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Residues in contact with ARG 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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307A GLN* 5.1 8.6 + - - +
309A PHE* 4.7 12.6 - - + -
573A GLU* 3.3 21.6 + - - -
576A LEU* 2.8 48.7 + - - +
577A ASN* 3.1 30.2 + - - +
579A LEU* 1.3 76.3 - - - +
581A TYR* 1.3 61.1 + - - +
583A ASP* 3.3 18.4 - - - +
584A ARG* 3.3 19.7 + - - +
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Residues in contact with TYR 581 (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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347A TYR* 3.1 56.1 - + - +
520A LEU* 2.8 38.3 + - + -
521A LEU* 4.6 8.1 - - + -
523A LEU* 4.0 13.0 - - - +
524A LYS* 3.6 40.0 + - + +
561A MET* 3.9 10.6 - - - +
577A ASN 3.1 15.0 + - - +
578A THR 3.5 2.5 - - - +
579A LEU 3.3 0.2 - - - -
580A ARG* 1.3 75.9 - - - +
582A ALA* 1.3 65.3 + - - +
584A ARG* 3.0 19.0 + - - +
585A VAL* 3.3 26.9 + - + +
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Residues in contact with ALA 582 (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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261A VAL* 3.6 23.0 - - + +
311A PHE* 3.8 21.7 - - + -
561A MET* 5.3 3.4 - - - -
563A ALA* 3.9 21.3 - - + -
578A THR 2.9 18.0 + - - +
579A LEU* 4.0 1.6 - - - +
581A TYR* 1.3 82.5 - - + +
583A ASP* 1.3 61.4 + - - +
585A VAL* 3.3 20.1 + - - +
586A LYS* 4.1 2.6 + - - +
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Residues in contact with ASP 583 (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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309A PHE* 3.6 26.3 - - - -
310A CYS 4.8 10.1 + - - +
311A PHE* 4.0 8.6 - - + -
579A LEU 2.9 18.9 + - - +
580A ARG* 3.3 10.1 - - - +
582A ALA* 1.3 77.2 - - - +
584A ARG* 1.3 59.4 + - + +
586A LYS 3.6 15.6 - - - +
587A GLU* 4.6 4.5 - - - +
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Residues in contact with ARG 584 (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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524A LYS* 3.6 33.8 - - + +
525A GLU* 5.2 4.6 + - - -
528A ARG* 2.7 44.0 + - - +
580A ARG* 3.4 17.7 - - - +
581A TYR* 3.0 9.4 + - - +
583A ASP* 1.3 76.8 - - + +
585A VAL* 1.3 61.7 + - - +
586A LYS 3.5 1.3 + - - -
587A GLU* 3.7 19.0 + - - +
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Residues in contact with VAL 585 (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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259A ILE* 4.4 1.9 - - + +
261A VAL* 3.6 20.2 - - + -
524A LYS* 3.9 16.6 - - + -
527A ILE* 3.5 37.9 - - + +
528A ARG* 3.6 23.4 - - - +
561A MET* 4.2 14.8 - - + -
581A TYR* 3.3 41.0 + - + +
582A ALA* 3.3 11.5 + - - +
584A ARG* 1.3 77.0 - - - +
586A LYS* 1.3 58.3 + - - +
587A GLU 3.7 1.2 + - - +
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Residues in contact with LYS 586 (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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257A HIS* 3.2 17.8 + - - +
259A ILE* 3.0 44.0 + - + +
261A VAL* 3.6 18.2 - - + -
312A ASP* 2.9 36.3 + - - +
582A ALA 4.1 3.6 + - - +
583A ASP 3.6 12.0 - - - +
585A VAL* 1.3 75.7 - - - +
587A GLU* 1.3 58.2 + - - +
588A LEU* 4.3 0.4 - - - -
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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