Contacts of the helix formed by residues 556 - 576 (chain B) in PDB entry 2XPH
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 556 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A TRP* 3.4 37.0 - - - -
599A ASN* 5.2 2.5 - - - +
600A GLY* 4.2 9.3 - - - +
601A SER* 5.1 0.7 + - - -
498B PHE* 5.3 2.4 - - - -
528B ILE* 5.5 0.4 - - - +
530B LEU* 4.1 11.1 - - - +
548B TYR* 3.5 32.3 + - + +
555B ILE* 1.3 77.9 - - - +
557B ASN* 1.3 62.7 + - - +
558B GLU* 3.6 4.0 + - - +
559B ALA* 3.0 39.7 + - - +
560B CYS* 3.7 6.9 + - - -
588B SER* 2.9 14.1 + - - -
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Residues in contact with ASN 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 6.2 4.6 - - + +
599A ASN* 5.5 1.4 - - - +
555B ILE* 3.5 25.2 - - + +
556B ASN* 1.3 73.4 - - - +
558B GLU* 1.3 58.3 + - - +
560B CYS* 3.1 9.8 + - - +
561B ARG* 2.9 46.3 + - - +
586B LEU* 3.7 13.0 + - + +
587B PHE* 3.6 18.8 - - - +
588B SER* 3.6 27.1 + - - +
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Residues in contact with GLU 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 3.6 9.1 - - + +
464A ASN* 3.3 33.3 - - - +
465A TRP* 3.7 25.2 + - + +
601A SER* 5.1 2.2 - - - +
502B LYS* 6.1 0.2 - - + -
556B ASN* 3.2 8.9 + - - +
557B ASN* 1.3 74.2 - - - +
559B ALA* 1.3 54.5 + - - +
561B ARG* 3.0 46.0 + - + +
562B ILE* 2.8 54.1 + - + +
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Residues in contact with ALA 559 (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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465A TRP* 5.6 0.2 - - - -
498B PHE* 3.8 22.5 - - + -
528B ILE* 4.9 3.1 - - + -
537B ALA* 5.7 0.4 - - + -
548B TYR* 4.1 17.5 - - + -
556B ASN* 3.0 33.2 + - - +
558B GLU* 1.3 74.7 - - - +
560B CYS* 1.3 58.6 + - - +
562B ILE* 3.5 14.3 + - - +
563B LEU* 3.1 33.3 + - + +
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Residues in contact with CYS 560 (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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537B ALA* 5.9 1.8 - - - -
546B ILE* 3.7 21.5 - - + +
547B THR 4.6 0.7 - - - -
548B TYR* 3.8 12.8 - - - -
556B ASN 3.8 15.0 - - - -
557B ASN* 3.1 11.6 + - - +
559B ALA* 1.3 74.6 - - - +
561B ARG* 1.3 56.2 + - - +
563B LEU* 3.4 7.1 + - - +
564B LEU* 2.8 33.3 + - - +
586B LEU* 3.6 26.6 - - + +
587B PHE 3.5 28.9 - - - -
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Residues in contact with ARG 561 (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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462A HIS* 6.2 0.6 - - - +
463A LEU* 4.2 24.4 - - - +
464A ASN* 5.2 1.8 + - - -
557B ASN* 2.9 38.9 + - - +
558B GLU* 3.0 48.3 + - - +
560B CYS* 1.3 73.9 - - - +
562B ILE* 1.3 60.2 + - + +
564B LEU* 3.2 6.5 + - - +
565B GLN* 2.8 29.2 + - - +
586B LEU* 3.4 20.5 - - + +
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Residues in contact with ILE 562 (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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465A TRP* 5.3 1.3 - - + -
498B PHE* 4.0 14.4 - - + -
501B LEU* 3.9 28.0 - - + +
502B LYS* 3.7 35.7 - - + -
558B GLU* 2.8 42.5 + - + +
559B ALA* 3.7 11.2 - - - +
561B ARG* 1.3 74.1 - - + +
563B LEU* 1.3 52.2 + - - +
565B GLN* 3.0 11.9 + - + +
566B TYR* 2.7 33.8 + - - +
569B GLN* 5.0 0.2 + - - -
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Residues in contact with LEU 563 (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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493B PHE* 5.9 0.7 - - + -
497B PHE* 4.5 11.4 - - + -
498B PHE* 4.8 9.9 - - + -
501B LEU* 4.8 5.6 - - + -
526B VAL* 3.8 36.3 - - + -
528B ILE* 4.9 0.2 - - + -
537B ALA* 3.4 32.1 - - + -
539B VAL* 4.7 8.1 - - + -
546B ILE* 3.7 22.9 - - + -
559B ALA 3.1 20.6 + - - +
560B CYS 3.7 5.2 - - - +
562B ILE* 1.3 76.0 - - - +
564B LEU* 1.3 63.4 + - - +
566B TYR* 3.4 18.9 + - + +
567B LEU* 3.2 26.3 + - + +
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Residues in contact with LEU 564 (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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546B ILE* 4.6 12.1 - - + +
560B CYS 2.8 15.8 + - - +
561B ARG* 3.4 11.0 - - - +
563B LEU* 1.3 75.5 - - - +
565B GLN* 1.3 62.6 + - - +
567B LEU* 3.1 31.3 + - + +
568B LYS* 3.7 20.6 + - - +
579B PHE* 4.7 7.0 - - + -
581B THR* 4.7 20.6 - - + +
584B TRP* 4.6 24.7 - - + +
586B LEU* 4.4 17.7 - - + -
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Residues in contact with GLN 565 (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 ARG 2.8 13.6 + - - +
562B ILE* 3.1 17.9 - - + +
564B LEU* 1.3 75.2 - - - +
566B TYR* 1.3 55.3 + - - +
567B LEU 3.4 0.2 + - - -
568B LYS* 3.5 30.9 + - - +
569B GLN* 2.7 46.7 + - - +
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Residues in contact with TYR 566 (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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493B PHE* 3.9 30.2 - + - -
497B PHE* 3.9 25.3 - + - -
501B LEU* 3.9 25.1 - - + -
506B TYR* 3.5 32.5 - + - -
509B VAL* 4.1 6.5 + - + -
513B THR* 4.0 5.9 + - - +
518B VAL* 4.6 4.8 - - + +
524B LEU* 5.4 1.3 - - + -
562B ILE 2.7 15.8 + - - +
563B LEU* 3.5 19.3 - - + +
564B LEU 3.3 0.2 - - - -
565B GLN* 1.3 73.4 - - - +
567B LEU* 1.3 73.0 + - + +
569B GLN* 3.4 10.2 + - - +
570B GLU* 3.0 61.4 + - + +
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Residues in contact with LEU 567 (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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518B VAL* 4.6 4.5 - - + -
519B PHE* 3.4 27.5 - - + -
524B LEU* 4.2 16.4 - - + -
539B VAL* 4.0 13.7 - - + -
541B PHE* 3.9 28.9 - - + -
546B ILE* 3.9 27.6 - - + -
563B LEU 3.2 12.0 + - - +
564B LEU* 3.1 16.1 + - + +
566B TYR* 1.3 89.1 - - + +
568B LYS* 1.3 61.3 + - - +
570B GLU* 4.1 1.1 - - - -
571B SER 3.6 1.6 + - - -
579B PHE* 3.6 34.4 - - + +
584B TRP* 4.6 3.6 - - + -
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Residues in contact with LYS 568 (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 LEU* 4.0 22.8 - - - +
565B GLN* 3.5 34.6 + - - +
566B TYR 3.2 0.4 - - - -
567B LEU* 1.3 74.5 - - - +
569B GLN* 1.3 68.6 + - - +
570B GLU 3.1 0.9 - - - -
571B SER* 2.9 14.0 + - - -
572B ILE* 2.9 26.1 + - + +
578B GLU* 5.8 5.2 - - + -
579B PHE* 3.8 30.5 - - + +
581B THR* 3.7 28.9 - - + -
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Residues in contact with GLN 569 (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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501B LEU* 5.3 3.0 - - - +
506B TYR* 2.9 62.4 + - + +
565B GLN* 2.7 51.2 + - - +
566B TYR* 3.4 11.2 - - - +
568B LYS* 1.3 77.9 - - + +
570B GLU* 1.3 55.8 + - - +
572B ILE* 3.9 11.2 + - + +
573B ASP* 3.3 16.8 + - - +
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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
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506B TYR* 3.1 18.4 + - - +
509B VAL 5.4 0.2 - - - +
510B LYS* 4.2 1.4 - - - +
513B THR* 2.5 33.8 + - - +
516B VAL 4.3 4.7 - - - +
518B VAL* 4.7 10.6 + - + +
519B PHE* 4.1 17.4 - - + -
566B TYR* 3.0 47.2 + - + +
567B LEU 4.9 0.2 - - - -
569B GLN* 1.3 74.4 - - - +
571B SER* 1.3 67.9 + - - +
572B ILE 3.3 0.2 - - - -
574B LYS* 2.7 59.5 + - + +
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Residues in contact with SER 571 (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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519B PHE* 3.7 20.6 - - - -
567B LEU 3.6 16.3 + - - -
568B LYS 2.9 8.6 + - - -
570B GLU* 1.3 77.6 - - - +
572B ILE* 1.3 64.0 + - - +
575B LYS* 2.9 28.0 + - - +
576B ARG 3.3 2.3 + - - -
577B LYS* 2.9 28.0 + - - +
578B GLU 3.9 6.2 + - - -
579B PHE* 3.7 15.9 - - - +
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Residues in contact with ILE 572 (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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568B LYS* 2.9 24.9 + - + +
569B GLN* 3.9 9.0 - - + +
571B SER* 1.3 77.7 - - - +
573B ASP* 1.3 66.3 + - - +
574B LYS 3.0 1.7 + - - -
576B ARG* 3.1 24.7 + - - +
577B LYS 3.6 11.9 - - - +
578B GLU* 4.7 20.2 - - + +
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Residues in contact with ASP 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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506B TYR* 3.2 26.4 + - + +
510B LYS* 2.6 42.8 + - - +
569B GLN 3.3 6.9 + - - +
570B GLU 3.5 1.3 + - - +
572B ILE* 1.3 81.9 - - + +
574B LYS* 1.3 86.4 + - - +
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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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506B TYR* 3.9 2.2 + - - -
510B LYS 2.9 24.3 + - - -
511B ARG* 5.7 0.2 - - - +
513B THR* 3.0 26.6 + - - +
514B LYS* 5.0 4.5 - - - +
516B VAL 5.1 4.7 - - - +
517B ASP* 5.8 2.7 - - - +
519B PHE* 5.8 1.6 - - + -
570B GLU* 2.7 55.7 + - + +
572B ILE 3.0 1.0 + - - -
573B ASP* 1.3 104.4 + - - +
575B LYS* 1.3 68.7 + - + +
576B ARG* 3.2 8.0 + - - +
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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
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517B ASP* 3.7 35.2 - - - +
519B PHE* 4.6 15.4 - - + +
571B SER* 2.9 19.9 + - - +
574B LYS* 1.3 83.2 - - + +
576B ARG* 1.3 67.7 + - - +
577B LYS* 2.7 23.3 + - + +
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Residues in contact with ARG 576 (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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571B SER 3.3 0.2 + - - -
572B ILE* 3.1 25.1 + - - +
574B LYS 3.2 4.1 + - - +
575B LYS* 1.3 80.0 + - - +
577B LYS* 1.3 78.2 + - + +
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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