Contacts of the helix formed by residues 572 - 589 (chain B) in PDB entry 3P1X
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 ASN 572 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B PHE* 3.4 12.1 - - - -
570B GLY 3.1 0.9 - - - -
571B SER* 1.3 89.6 + - - +
573B LYS* 1.3 63.0 + - - +
574B LYS* 3.2 14.9 - - + +
575B VAL* 2.8 46.5 - - - +
576B ALA* 3.2 21.7 + - - +
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Residues in contact with LYS 573 (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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543B LEU* 4.0 25.4 - - + +
546B GLU* 4.8 4.4 + - - -
555B PHE* 3.6 39.9 - - + -
557B MSE 4.2 6.5 - - + +
572B ASN* 1.3 73.1 - - - +
574B LYS* 1.3 63.2 + - - +
576B ALA* 3.3 7.3 + - - +
577B LYS* 3.0 35.5 + - + +
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Residues in contact with LYS 574 (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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529B VAL* 5.6 0.5 - - - +
572B ASN* 3.2 11.1 - - - +
573B LYS* 1.3 80.5 - - - +
575B VAL* 1.3 58.3 + - - +
577B LYS* 3.4 9.2 + - - +
578B ALA* 3.0 26.5 + - + +
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Residues in contact with VAL 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ALA 4.5 0.9 - - - +
570B GLY* 3.6 22.4 - - - -
571B SER* 4.1 1.8 - - - +
572B ASN* 2.8 38.8 - - - +
574B LYS* 1.3 71.5 - - - +
576B ALA* 1.3 70.4 + - - +
578B ALA* 3.3 9.0 + - + +
579B TYR* 2.9 45.9 + - + -
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B PHE* 3.8 21.5 - - + +
557B MSE 3.6 14.4 - - + +
568B GLY* 3.3 28.6 - - - +
569B ALA 3.9 9.4 - - - -
570B GLY 4.0 2.5 - - - +
572B ASN 3.2 10.0 + - - +
573B LYS 3.6 8.1 - - - +
574B LYS 3.3 0.2 - - - -
575B VAL* 1.3 80.5 - - - +
577B LYS* 1.3 63.3 + - - +
579B TYR 3.2 1.9 + - - -
580B ALA* 3.0 19.6 + - - +
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Residues in contact with LYS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B VAL* 4.0 17.8 - - + +
541B TYR* 3.8 35.7 - - + +
557B MSE 3.0 39.0 - - + -
573B LYS* 3.0 27.1 + - + +
574B LYS* 3.6 7.2 - - - +
576B ALA* 1.3 74.5 - - - +
578B ALA* 1.3 65.9 + - - +
580B ALA* 3.1 4.9 + - - +
581B ALA* 2.9 21.7 + - - +
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Residues in contact with ALA 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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527B ASN* 6.5 0.2 - - - -
528B PRO* 3.5 23.5 - - + +
529B VAL* 3.9 13.8 - - + +
574B LYS* 3.0 14.6 + - + +
575B VAL* 3.5 16.8 - - + +
577B LYS* 1.3 76.3 - - - +
579B TYR* 1.3 58.9 + - + +
581B ALA 3.4 0.7 + - - -
582B LEU* 2.9 30.0 + - - +
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Residues in contact with TYR 579 (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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567B GLN 3.9 0.7 - - - +
568B GLY* 3.5 20.6 - - - -
569B ALA 3.5 19.1 - - - +
575B VAL* 2.9 43.4 + - + +
576B ALA 3.6 0.2 - - - +
578B ALA* 1.3 77.8 - - + +
580B ALA* 1.3 58.1 + - - +
582B LEU* 3.6 25.3 - - + +
583B ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 580 (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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541B TYR* 4.3 5.4 - - + -
557B MSE 3.9 13.2 - - + +
559B VAL* 4.0 10.8 - - + +
566B PHE* 3.7 17.8 - - - +
567B GLN* 3.6 14.6 - - - +
568B GLY* 3.4 15.0 - - - +
576B ALA 3.0 10.0 + - - +
577B LYS* 3.1 12.8 + - - +
579B TYR* 1.3 76.8 - - - +
581B ALA* 1.3 61.5 + - - +
583B ALA* 3.4 4.5 + - - +
584B ALA* 3.2 17.3 + - - +
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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
----------------------------------------------------------
528B PRO* 3.6 30.3 - - - +
529B VAL* 3.7 4.9 - - - +
532B LEU* 3.8 13.9 - - + +
541B TYR* 3.3 24.1 - - - +
559B VAL* 4.8 0.2 - - - -
577B LYS 2.9 12.5 + - - +
578B ALA 3.8 1.6 - - - +
580B ALA* 1.3 74.7 - - - +
582B LEU* 1.3 61.2 + - - +
584B ALA* 3.1 4.2 + - - +
585B LEU* 2.9 31.6 + - - +
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Residues in contact with LEU 582 (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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528B PRO* 3.7 22.1 - - + +
578B ALA 2.9 18.2 + - - +
579B TYR* 3.6 28.7 - - + +
581B ALA* 1.3 77.0 - - - +
583B ALA* 1.3 56.1 + - - +
585B LEU* 3.7 9.6 - - + +
586B GLU* 2.9 56.9 + - + +
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Residues in contact with ALA 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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566B PHE* 3.9 14.8 - - + -
567B GLN 4.0 14.4 - - - +
579B TYR 2.9 17.0 + - - +
580B ALA 3.6 5.8 - - - +
582B LEU* 1.3 77.0 - - - +
584B ALA* 1.3 63.9 + - - +
586B GLU* 3.5 5.3 + - - +
587B LYS* 3.1 25.8 + - - +
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Residues in contact with ALA 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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532B LEU* 4.1 12.3 - - + -
559B VAL* 4.7 0.7 - - + -
561B VAL* 4.1 17.7 - - + -
566B PHE* 3.6 35.8 - - + -
580B ALA 3.2 7.6 + - - +
581B ALA 3.1 8.4 + - - +
583B ALA* 1.3 80.2 - - - +
585B LEU* 1.3 56.9 + - - +
588B LEU* 2.8 36.7 + - + +
589B PHE* 4.1 2.0 - - - -
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Residues in contact with LEU 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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528B PRO* 3.5 37.0 - - + +
531B GLU* 4.2 13.5 - - + +
532B LEU* 3.7 34.3 - - + +
535B LYS* 4.9 4.3 - - + +
581B ALA 2.9 19.0 + - - +
582B LEU* 3.7 10.8 - - + +
583B ALA 3.3 0.2 - - - -
584B ALA* 1.3 77.7 - - - +
586B GLU* 1.3 59.1 - - + +
589B PHE* 2.7 57.4 + - + +
590B PRO 5.3 0.2 - - - -
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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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582B LEU* 2.9 49.8 + - + +
583B ALA* 3.9 6.1 - - - +
585B LEU* 1.3 78.1 - - - +
587B LYS* 1.3 61.6 + - - +
589B PHE 4.6 0.7 + - - -
590B PRO 4.8 18.2 - - - +
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Residues in contact with LYS 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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564B GLN* 4.6 11.3 - - - +
566B PHE* 3.7 25.1 - - + -
583B ALA 3.1 17.6 + - - +
586B GLU* 1.3 80.3 - - - +
588B LEU* 1.3 70.8 + - + +
590B PRO 5.6 0.2 - - - -
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Residues in contact with LEU 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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561B VAL* 3.9 30.1 - - + +
562B ASP* 4.0 13.0 - - + +
564B GLN* 3.4 29.6 - - - +
566B PHE* 3.6 30.3 - - + -
584B ALA 2.8 20.9 + - - +
587B LYS* 1.3 84.3 - - + +
589B PHE* 1.3 79.7 + - + +
590B PRO 4.0 2.0 - - - -
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Residues in contact with PHE 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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532B LEU* 3.8 30.1 - - + -
535B LYS* 3.9 34.3 - - + -
536B ARG* 3.7 42.2 - - + -
561B VAL* 4.3 8.5 - - + -
562B ASP* 4.1 9.0 - - - -
584B ALA 4.1 4.9 - - - -
585B LEU* 2.7 39.7 + - + +
588B LEU* 1.3 93.5 - - + +
590B PRO* 1.3 69.6 - - - +
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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