Contacts of the helix formed by residues 567 - 588 (chain A) in PDB entry 5AM8
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 567 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 4.0 18.4 - - + +
217A GLN* 4.3 26.3 + - + +
218A LEU* 4.2 25.4 - - + -
506A VAL* 4.4 8.3 - - + -
566A ASP* 1.3 74.3 + - - +
568A GLN* 1.3 65.8 + - - +
569A PRO 3.3 1.3 - - - -
570A LEU* 3.1 19.2 + - - +
571A LEU* 3.1 15.5 + - + +
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Residues in contact with GLN 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 4.2 10.6 + - - +
566A ASP* 3.3 17.5 + - - +
567A ALA* 1.3 77.9 - - - +
569A PRO* 1.3 65.6 - - + +
571A LEU* 3.0 28.6 + - - +
572A LYS* 2.8 34.2 + - + +
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Residues in contact with PRO 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PHE* 3.5 30.0 - - - +
510A GLN* 3.9 17.9 - - + +
513A GLU* 3.4 30.3 - - + +
525A LEU* 3.8 4.6 - - + +
566A ASP* 3.4 23.3 - - + +
567A ALA 3.5 0.7 - - - -
568A GLN* 1.3 95.6 - - + +
570A LEU* 1.3 60.8 + - - +
572A LYS* 3.4 7.6 + - + +
573A TYR* 3.0 24.1 + - - +
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Residues in contact with LEU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.8 28.5 - - + -
221A LEU* 4.1 9.6 - - + -
432A LYS* 5.8 1.8 - - + -
433A ILE* 3.9 15.3 - - + -
436A LEU* 4.5 14.4 - - + -
505A PHE* 3.7 14.8 - - + +
506A VAL* 4.5 9.2 + - + +
509A PHE* 3.6 44.6 - - + +
566A ASP 5.1 0.6 + - - -
567A ALA* 3.1 14.1 + - - +
569A PRO* 1.3 78.0 - - - +
571A LEU* 1.3 65.8 + - - +
573A TYR* 3.3 1.7 + - - +
574A PHE* 3.1 43.3 + - + -
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Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 4.1 26.9 - - + +
218A LEU* 4.6 4.3 - - + -
221A LEU* 3.5 41.1 - - + -
567A ALA* 3.1 19.4 + - + +
568A GLN* 3.0 36.4 + - - +
570A LEU* 1.3 81.9 - - + +
572A LYS* 1.3 58.4 - - - +
574A PHE* 3.2 3.1 + - - +
575A GLN* 2.9 32.8 + - - +
578A THR* 5.0 0.9 + - - -
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Residues in contact with LYS 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 2.7 37.3 + - - +
525A LEU* 4.0 22.7 - - + +
526A HIS* 5.6 1.0 + - - -
568A GLN* 2.8 20.9 + - + +
569A PRO* 3.5 4.7 - - + +
571A LEU* 1.3 77.7 - - - +
573A TYR* 1.3 62.2 + - - +
575A GLN* 2.9 44.9 + - - +
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Residues in contact with TYR 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 4.1 9.9 + - + +
401A THR* 5.7 0.2 - - - +
424A TYR* 3.4 24.6 + - - -
425A LEU* 3.6 28.6 - - + +
428A MET* 3.7 18.2 - - + +
509A PHE* 3.5 35.2 - + + -
512A HIS* 4.2 23.3 - + - -
525A LEU* 4.1 14.8 - - + +
526A HIS* 3.5 43.1 + - + +
569A PRO 3.0 16.2 + - - +
570A LEU 3.5 4.7 - - - +
572A LYS* 1.3 79.7 - - - +
574A PHE* 1.3 85.3 + + - +
575A GLN 3.7 0.3 + - - -
576A LEU 5.2 0.2 + - - -
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Residues in contact with PHE 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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221A LEU* 4.5 6.5 - - + -
425A LEU* 3.6 18.8 - - + -
428A MET* 3.8 8.3 - - + -
429A ALA* 3.6 28.0 - - + -
432A LYS* 4.0 20.2 - - + -
433A ILE* 3.9 17.7 - - + -
509A PHE* 3.6 24.2 - + - -
570A LEU* 3.1 38.3 + - + +
571A LEU 3.2 2.7 + - - +
573A TYR* 1.3 100.4 - + - +
575A GLN* 1.3 64.3 + - - +
576A LEU 2.9 4.9 + - - -
577A VAL* 3.0 24.6 + - + +
578A THR* 3.0 19.9 + - - +
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Residues in contact with GLN 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU 2.9 15.8 + - - +
572A LYS* 2.9 40.9 + - - +
573A TYR 3.5 0.8 + - - -
574A PHE* 1.3 76.2 - - - +
576A LEU* 1.3 68.4 + - + +
578A THR* 3.4 7.9 + - - -
579A GLN* 3.0 24.4 + - - +
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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
----------------------------------------------------------
421A ASP* 3.9 17.0 - - + +
422A ILE* 3.9 14.4 - - + +
425A LEU* 4.1 11.2 - - + +
526A HIS* 3.8 29.8 - - + +
573A TYR 5.2 0.2 + - - -
574A PHE 2.9 3.4 + - - -
575A GLN* 1.3 82.6 - - + +
577A VAL* 1.3 58.6 + - - +
579A GLN* 3.4 6.6 + - - +
580A TRP* 3.0 26.5 + - - +
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Residues in contact with VAL 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ILE* 4.0 20.8 - - + +
425A LEU* 3.8 34.3 - - + +
426A LEU* 3.9 24.9 - - + +
429A ALA* 4.6 4.3 - - + -
574A PHE* 3.0 24.1 + - + +
576A LEU* 1.3 75.2 - - - +
578A THR* 1.3 66.0 + - - +
580A TRP* 4.1 6.5 - - + -
581A LEU* 2.8 57.5 + - + +
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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
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221A LEU* 3.7 45.6 - - + +
224A ASN* 5.4 5.7 - - + +
571A LEU 5.0 1.0 + - - -
574A PHE* 3.0 17.1 + - - +
575A GLN* 3.4 12.9 + - - -
577A VAL* 1.3 79.3 - - - +
579A GLN* 1.3 62.9 + - - +
581A LEU* 4.0 6.1 - - - +
582A GLN* 3.2 30.7 + - - +
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Residues in contact with GLN 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLN 3.0 13.5 + - - +
576A LEU* 3.5 11.7 - - - +
578A THR* 1.3 75.7 - - - +
580A TRP* 1.3 63.9 + - - +
582A GLN* 3.2 19.0 + - - +
583A GLU* 3.0 49.0 + - - +
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Residues in contact with TRP 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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228A PHE* 3.8 26.9 - + - -
270A PRO* 3.6 37.9 - - + -
271A PHE* 4.5 14.0 - + - -
422A ILE* 3.8 35.5 - - + +
426A LEU* 5.2 2.7 - - + -
576A LEU 3.0 14.6 + - - +
577A VAL* 3.8 6.3 - - + +
578A THR 3.3 0.2 - - - -
579A GLN* 1.3 80.5 - - - +
581A LEU* 1.3 74.4 + - + +
583A GLU* 3.1 18.3 + - - +
584A GLN* 2.9 71.6 + - + +
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Residues in contact with LEU 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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221A LEU 5.4 1.6 - - - +
224A ASN* 4.3 14.4 - - + +
225A LEU* 4.3 27.1 - - + +
228A PHE* 3.5 44.6 - - + -
426A LEU* 4.3 7.9 - - + -
429A ALA* 5.2 2.9 - - + -
577A VAL* 2.8 42.3 + - + +
578A THR* 4.0 6.1 - - - +
580A TRP* 1.3 83.9 - - + +
582A GLN* 1.3 66.0 + - - +
584A GLN* 3.3 3.1 + - - +
585A ASN* 3.0 32.1 + - - +
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Residues in contact with GLN 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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224A ASN* 3.5 27.1 + - - +
578A THR* 3.2 19.3 + - - +
579A GLN* 3.2 21.0 + - - +
581A LEU* 1.3 80.0 - - - +
583A GLU* 1.3 59.0 + - + +
585A ASN* 3.4 1.6 + - - +
586A GLN* 3.0 53.4 + - + +
592A LEU* 6.3 1.1 - - + -
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Residues in contact with GLU 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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579A GLN* 3.0 44.8 + - - +
580A TRP* 3.1 21.4 + - - +
582A GLN* 1.3 76.5 - - + +
584A GLN* 1.3 71.8 + - - +
586A GLN* 3.5 8.9 + - - +
587A GLN* 3.0 37.8 + - - +
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Residues in contact with GLN 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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228A PHE* 4.2 18.9 - - + -
580A TRP* 2.9 71.2 + - + +
581A LEU 3.6 6.3 - - - +
583A GLU* 1.3 81.4 + - - +
585A ASN* 1.3 57.9 + - - +
587A GLN* 3.5 25.1 + - - +
588A ASN* 3.0 40.0 + - - +
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Residues in contact with ASN 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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224A ASN* 2.9 51.4 + - - +
227A ALA* 4.0 7.8 - - - +
228A PHE* 3.4 27.3 + - - +
581A LEU 3.0 18.8 + - - +
582A GLN 3.8 3.4 - - - +
584A GLN* 1.3 75.2 - - - +
586A GLN* 1.3 64.3 + - + +
588A ASN* 3.2 1.6 + - - -
589A GLY 3.0 4.0 + - - -
590A GLU* 2.9 49.9 + - + +
592A LEU* 4.0 8.0 - - + +
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Residues in contact with GLN 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLN* 3.0 50.3 + - + +
583A GLU* 3.8 8.6 - - - +
585A ASN* 1.3 76.6 - - + +
587A GLN* 1.3 59.1 + - + +
589A GLY* 2.9 20.9 + - - +
590A GLU 5.1 0.4 - - - +
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Residues in contact with GLN 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLU* 3.0 28.7 + - - +
584A GLN* 3.6 28.0 + - - +
586A GLN* 1.3 77.2 - - + +
588A ASN* 1.3 65.9 + - - +
589A GLY 3.3 0.7 + - - -
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Residues in contact with ASN 588 (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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228A PHE* 6.0 3.4 - - - -
231A ARG* 3.8 22.5 + - - +
235A ARG* 3.9 24.5 + - - +
584A GLN* 3.0 26.3 + - - +
585A ASN* 4.0 2.2 + - - +
586A GLN 3.2 0.4 - - - -
587A GLN* 1.3 82.8 - - - +
589A GLY* 1.3 63.2 + - - +
590A GLU* 3.3 23.7 + - - +
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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
------------------------------------------------------------
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