Contacts of the helix formed by residues 568 - 591 (chain B) in PDB entry 3N8E
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 TYR 568 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ARG* 3.5 34.5 - - - +
564B ASN* 3.1 40.9 + - - +
565B ALA 3.0 6.7 + - - +
567B LYS* 1.3 116.3 + - + +
569B ALA* 1.3 55.5 + - - +
570B GLU 3.4 2.2 - - - -
571B GLU* 3.3 37.2 + - + +
572B ASP* 2.9 31.9 + - - +
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Residues in contact with ALA 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLU* 5.5 0.7 - - - +
565B ALA 2.9 10.9 + - - +
566B GLU* 3.6 20.9 - - - +
567B LYS 3.4 3.2 + - - -
568B TYR* 1.3 75.3 - - - +
570B GLU* 1.3 59.6 + - - +
572B ASP* 3.7 7.0 - - - +
573B ARG* 3.2 26.9 + - - +
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Residues in contact with GLU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B LYS 5.0 1.2 + - - -
568B TYR 3.4 0.2 - - - -
569B ALA* 1.3 76.5 - - - +
571B GLU* 1.3 65.6 + - - +
572B ASP 3.2 0.2 - - - -
573B ARG* 2.9 43.9 + - - +
574B ARG* 3.3 55.0 + - - +
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Residues in contact with GLU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ARG* 4.2 13.9 + - - -
568B TYR* 3.3 43.6 + - + +
570B GLU* 1.3 77.2 - - - +
572B ASP* 1.3 56.2 + - - +
574B ARG* 3.4 17.0 - - - +
575B LYS* 3.1 33.8 + - + +
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Residues in contact with ASP 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLU 4.9 0.5 - - - +
491B ARG* 2.7 41.9 + - - -
492B GLU* 3.2 44.4 + - + +
493B MET* 5.1 3.5 + - - +
496B ASP* 4.1 5.4 - - - +
565B ALA* 4.9 1.7 - - - +
568B TYR 2.9 18.9 + - - +
569B ALA* 3.7 7.5 - - - +
571B GLU* 1.3 73.7 - - - +
573B ARG* 1.4 55.1 - - - +
574B ARG 3.1 1.3 - - - -
575B LYS* 3.2 9.9 + - - +
576B LYS* 2.7 38.2 + - - +
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Residues in contact with ARG 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLU* 4.2 12.7 + - - +
569B ALA 3.2 15.6 + - - +
570B GLU* 2.9 50.1 + - - +
572B ASP* 1.4 78.3 - - - +
574B ARG* 1.3 81.5 + - - +
576B LYS* 4.2 2.5 - - - +
577B GLU* 2.7 61.0 + - - +
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Residues in contact with ARG 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLU* 3.3 50.6 + - - +
571B GLU* 3.4 15.1 - - - +
572B ASP 3.1 0.4 - - - -
573B ARG* 1.3 93.2 - - - +
575B LYS* 1.4 63.4 + - - +
577B GLU* 3.4 11.9 - - + +
578B ARG* 3.2 23.7 + - - +
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Residues in contact with LYS 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 4.1 33.5 - - + +
496B ASP* 4.7 14.8 + - - +
571B GLU* 3.1 18.3 + - + +
572B ASP* 3.2 13.7 + - - +
574B ARG* 1.4 75.6 - - - +
576B LYS* 1.3 64.1 + - - +
578B ARG* 3.2 7.0 + - - +
579B VAL* 3.0 33.3 + - + +
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Residues in contact with LYS 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B VAL* 3.7 31.9 - - + +
454B PHE 3.7 12.5 + - - -
492B GLU* 3.8 54.8 + - + +
493B MET* 4.8 6.2 - - - -
572B ASP 2.7 20.6 + - - +
573B ARG* 4.2 3.8 - - - +
575B LYS* 1.3 72.4 - - - +
577B GLU* 1.3 57.1 + - - +
579B VAL* 3.8 4.9 - - - +
580B GLU* 2.9 50.3 + - + +
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Residues in contact with GLU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ILE* 4.2 24.8 - - - +
592A THR* 5.0 9.3 - - - +
573B ARG* 2.7 50.7 + - - +
574B ARG* 3.4 14.8 - - - +
576B LYS* 1.3 75.3 - - - +
578B ARG* 1.3 60.6 + - + +
580B GLU* 4.1 5.3 - - - +
581B ALA* 3.2 22.3 + - - +
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Residues in contact with ARG 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A VAL* 4.8 16.0 + - - +
585A ALA* 5.9 0.6 - - - +
586A GLU* 3.5 31.7 - - - +
589A ILE* 3.6 35.2 - - + +
574B ARG 3.2 17.4 + - - +
575B LYS* 3.2 7.9 + - - +
577B GLU* 1.3 75.4 - - + +
579B VAL* 1.3 67.2 + - + +
581B ALA* 3.2 5.7 + - - +
582B VAL* 3.2 35.1 + - + +
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Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B GLY* 3.7 31.0 - - - +
453B VAL* 3.7 22.2 - - + -
493B MET* 4.0 18.4 - - + -
575B LYS* 3.0 25.9 + - + +
576B LYS* 3.9 3.8 - - - +
578B ARG* 1.3 78.2 - - + +
580B GLU* 1.3 57.3 + - - +
582B VAL* 3.0 11.8 + - - +
583B ASN* 2.9 34.6 + - - +
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Residues in contact with GLU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B VAL* 4.0 24.1 - - + +
576B LYS* 2.9 38.3 + - + +
577B GLU* 4.2 6.1 - - - +
579B VAL* 1.3 74.8 - - - +
581B ALA* 1.3 56.2 + - - +
583B ASN* 3.4 23.9 + - - +
584B MET* 3.1 27.7 + - - +
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Residues in contact with ALA 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ALA* 3.6 16.7 - - + +
588A ILE* 4.0 21.8 - - + +
589A ILE* 4.0 18.6 - - + -
577B GLU 3.2 15.5 + - - +
578B ARG 3.4 10.5 - - - +
579B VAL 3.2 0.6 - - - -
580B GLU* 1.3 73.7 - - - +
582B VAL* 1.4 57.4 + - - +
584B MET* 3.5 6.4 + - - +
585B ALA* 3.1 27.4 + - - +
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Residues in contact with VAL 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ARG* 3.6 33.7 - - - +
581A ALA* 4.6 9.6 - - + -
582A VAL* 4.5 17.9 - - + +
585A ALA* 3.7 18.2 - - + -
578B ARG* 3.3 28.5 - - + +
579B VAL* 3.0 10.7 + - - +
581B ALA* 1.4 74.2 - - - +
583B ASN* 1.3 61.2 + - - +
585B ALA* 3.4 2.3 + - - +
586B GLU* 2.9 36.4 + - - +
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Residues in contact with ASN 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B LEU* 3.1 54.6 + - + +
451B GLY* 4.3 2.6 - - - -
453B VAL* 4.5 0.6 - - - +
513B ARG* 4.3 5.2 + - - -
579B VAL* 2.9 24.7 + - - +
580B GLU* 3.6 32.1 + - - +
581B ALA 3.4 0.2 - - - -
582B VAL* 1.3 80.9 - - - +
584B MET* 1.3 61.1 + - - +
586B GLU* 3.5 10.3 + - - +
587B GLY* 3.4 15.8 + - - -
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Residues in contact with MET 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A ILE* 4.9 12.8 - - + -
580B GLU 3.1 16.9 + - - +
581B ALA* 3.8 6.5 - - - +
582B VAL 3.3 0.2 - - - -
583B ASN* 1.3 74.1 - - - +
585B ALA* 1.3 55.0 + - - +
587B GLY* 3.1 4.4 + - - -
588B ILE* 2.9 52.2 + - + +
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Residues in contact with ALA 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A ALA* 3.3 32.8 - - - +
584A MET* 3.7 28.9 - - + -
585A ALA 4.1 2.2 - - - +
588A ILE* 4.5 2.4 - - + +
581B ALA 3.1 17.9 + - - +
582B VAL 3.4 3.8 + - - +
584B MET* 1.3 74.7 - - - +
586B GLU* 1.4 53.3 + - - +
588B ILE* 3.2 3.0 + - - +
589B ILE* 2.8 39.7 + - - +
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Residues in contact with GLU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A ARG* 3.3 32.4 + - - -
581A ALA* 3.8 18.2 - - + -
450B LEU* 3.5 24.6 - - - +
475B ALA 4.8 2.9 - - - +
513B ARG* 3.5 25.8 + - - +
582B VAL* 2.9 23.4 + - - +
583B ASN* 3.6 8.7 - - - +
584B MET 3.2 0.2 - - - -
585B ALA* 1.4 74.9 - - - +
587B GLY* 1.3 56.7 + - - +
589B ILE* 3.9 4.8 - - - +
590B HIS* 3.1 28.4 + - - +
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Residues in contact with GLY 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ARG* 3.8 19.5 - - - +
583B ASN 3.4 6.8 + - - -
584B MET* 3.1 7.2 + - - -
586B GLU* 1.3 76.1 - - - +
588B ILE* 1.3 64.7 + - - +
590B HIS* 3.0 6.2 + - - +
591B ASP* 3.0 24.3 + - - +
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A MET* 3.7 30.3 - - + -
588A ILE* 4.8 6.7 - - + -
584B MET* 2.9 46.0 + - + +
585B ALA* 3.7 6.7 - - - +
587B GLY* 1.3 72.7 - - - +
589B ILE* 1.3 63.4 + - - +
591B ASP* 3.1 17.7 + - - +
592B THR* 3.5 12.6 + - + +
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Residues in contact with ILE 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A GLU* 4.3 28.5 - - + +
580A GLU* 3.6 24.9 - - + +
581A ALA* 3.5 39.3 - - + +
584A MET* 4.2 19.5 - - + -
585B ALA 2.8 18.6 + - - +
586B GLU* 3.9 5.8 - - - +
588B ILE* 1.3 74.1 - - - +
590B HIS* 1.3 60.6 + - - +
591B ASP 3.2 0.3 + - - -
592B THR* 3.2 31.9 + - + +
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Residues in contact with HIS 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ARG* 6.2 0.2 - - - -
577A GLU* 5.7 6.1 - - - -
477B ASP* 2.7 38.7 + - - -
512B PRO* 4.5 7.0 - - + -
513B ARG* 3.5 49.8 + - + +
586B GLU 3.1 17.3 + - - +
587B GLY* 3.0 8.7 + - - +
589B ILE* 1.3 76.1 - - - +
591B ASP* 1.3 56.6 + - - +
592B THR* 3.5 1.9 + - - -
593B GLU* 5.1 4.0 + - - +
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Residues in contact with ASP 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B GLY 3.0 14.0 + - - +
588B ILE* 3.1 11.8 + - - +
590B HIS* 1.3 75.7 - - - +
592B THR* 1.3 62.3 + - - +
593B GLU* 3.4 3.5 - - - +
595B LYS* 3.1 33.7 + - - +
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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