Contacts of the helix formed by residues 556 - 576 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A PHE* 5.0 2.6 - - - -
502A LYS* 3.8 20.0 - - - +
528A ILE* 5.5 0.4 - - - +
530A LEU* 4.5 12.5 - - - +
548A TYR* 3.4 32.6 + - + -
555A ILE* 1.3 81.7 + - - +
557A ASN* 1.3 52.7 - - - +
558A GLU* 2.6 19.7 + - - +
559A ALA* 2.3 42.2 + - - +
560A CYS* 3.5 6.5 + - - -
588A SER* 3.2 10.3 + - - -
1645A GOL 4.7 3.6 - - - -
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Residues in contact with ASN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ILE* 3.6 13.9 - - + +
556A ASN* 1.3 74.1 - - - +
558A GLU* 1.3 74.6 + - - +
560A CYS* 3.9 10.3 + - - +
561A ARG* 2.9 48.9 + - - +
586A LEU* 4.9 1.4 - - - +
587A PHE* 6.3 0.9 - - - +
588A SER* 4.4 3.8 + - - +
1645A GOL 4.0 14.3 + - - -
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Residues in contact with GLU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LYS* 3.6 23.1 - - - +
556A ASN* 2.6 13.6 + - - +
557A ASN* 1.3 80.5 + - - +
559A ALA* 1.3 59.7 + - - +
560A CYS 3.0 1.8 - - - -
561A ARG* 2.6 56.3 + - - +
562A ILE* 2.7 45.7 + - + +
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Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A PHE* 3.6 26.4 - - + -
528A ILE* 5.1 2.7 - - + -
537A ALA* 5.6 0.7 - - + -
548A TYR* 4.3 14.1 - - + -
556A ASN* 2.3 48.8 + - + +
558A GLU* 1.3 66.7 - - - +
560A CYS* 1.3 61.1 + - - +
562A ILE* 3.2 10.7 + - - +
563A LEU* 3.0 32.3 + - + +
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Residues in contact with CYS 560 (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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537A ALA* 5.6 2.0 - - - -
546A ILE* 4.0 27.6 - - + +
547A THR 4.4 1.1 - - - -
548A TYR* 4.0 21.3 - - - -
556A ASN 3.5 8.0 + - - -
557A ASN* 4.1 7.9 - - - +
558A GLU 2.9 1.2 + - - -
559A ALA* 1.3 74.1 - - - +
561A ARG* 1.3 65.6 + - - +
563A LEU* 3.0 4.8 + - - +
564A LEU* 3.0 19.8 + - - +
586A LEU* 3.7 27.8 - - + +
587A PHE* 3.9 26.7 - - - -
588A SER* 5.4 0.2 - - - -
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Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASN* 2.9 57.9 + - - +
558A GLU* 2.6 42.5 + - - +
560A CYS* 1.3 73.0 - - - +
562A ILE* 1.3 63.8 + - + +
563A LEU 3.1 0.2 + - - -
564A LEU* 3.2 3.8 + - - +
565A GLN* 2.8 26.5 + - - +
586A LEU* 3.5 20.2 - - + +
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Residues in contact with ILE 562 (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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498A PHE* 4.4 8.1 - - + -
501A LEU* 3.6 28.7 - - + +
502A LYS* 3.9 27.8 - - + +
558A GLU* 2.7 63.8 + - + +
559A ALA* 3.4 11.4 - - - +
561A ARG* 1.3 73.3 - - - +
563A LEU* 1.3 58.1 + - - +
565A GLN* 3.5 15.6 - - - +
566A TYR* 2.9 26.9 + - - +
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Residues in contact with LEU 563 (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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497A PHE* 4.5 14.4 - - + -
498A PHE* 4.3 15.0 - - + -
501A LEU* 4.5 7.4 - - + -
526A VAL* 4.1 31.9 - - + -
537A ALA* 3.7 30.3 - - + -
539A VAL* 4.8 9.2 - - + -
546A ILE* 4.3 20.0 - - + -
559A ALA 3.0 18.4 + - - +
560A CYS* 3.0 6.7 + - - +
562A ILE* 1.3 75.8 - - - +
564A LEU* 1.3 61.6 + - - +
566A TYR* 2.9 10.7 + - + +
567A LEU* 2.8 34.4 + - + +
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Residues in contact with LEU 564 (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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546A ILE* 3.7 13.2 - - + +
560A CYS 3.0 9.9 + - - +
561A ARG* 3.8 5.6 - - - +
563A LEU* 1.3 74.4 - - - +
565A GLN* 1.3 56.5 + - - +
567A LEU* 3.1 13.1 + - + +
568A LYS* 2.9 30.5 + - + +
579A PHE* 3.8 22.4 - - + -
581A THR* 3.7 37.7 - - + -
584A TRP* 4.8 12.3 - - + +
586A LEU* 3.8 26.9 - - + -
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Residues in contact with GLN 565 (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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561A ARG 2.8 17.5 + - - +
562A ILE* 3.5 15.9 - - - +
564A LEU* 1.3 75.3 - - - +
566A TYR* 1.3 53.5 + - - +
568A LYS* 3.3 15.6 - - + +
569A GLN* 2.8 62.6 + - + +
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Residues in contact with TYR 566 (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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493A PHE* 3.7 16.5 - + - -
497A PHE* 3.4 37.4 - + - -
501A LEU* 4.2 19.3 - - + -
506A TYR* 3.6 21.1 - + - -
509A VAL* 4.3 3.8 - - + -
510A LYS 5.5 0.2 - - - -
513A THR* 3.4 22.4 + - - +
518A VAL* 4.8 4.5 - - + +
524A LEU* 5.6 0.7 - - + -
562A ILE 2.9 16.4 + - - +
563A LEU* 2.9 18.1 + - + +
565A GLN* 1.3 74.2 - - - +
567A LEU* 1.3 73.8 + - + +
569A GLN* 3.8 5.1 - - - +
570A GLU* 2.9 71.1 + - + +
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Residues in contact with LEU 567 (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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518A VAL* 4.5 5.8 - - + -
519A PHE* 4.0 12.8 - - + -
524A LEU* 4.1 16.8 - - + -
539A VAL* 4.5 13.7 - - + -
541A PHE* 4.0 24.5 - - + -
546A ILE* 3.9 24.9 - - + -
563A LEU 2.8 21.7 + - - +
564A LEU* 3.1 10.1 + - + +
566A TYR* 1.3 77.7 - - + +
568A LYS* 1.3 57.0 + - - +
570A GLU* 3.0 4.2 + - - +
571A SER* 2.7 37.1 + - - -
579A PHE* 3.9 32.8 - - + -
584A TRP* 4.6 2.7 - - + -
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Residues in contact with LYS 568 (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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564A LEU* 2.9 13.7 + - + +
565A GLN* 3.3 20.7 - - + +
567A LEU* 1.3 77.5 - - - +
569A GLN* 1.3 70.6 + - - +
571A SER* 3.2 2.6 + - - -
572A ILE* 3.0 46.8 + - - +
578A GLU* 6.4 2.0 - - - -
579A PHE* 4.0 20.9 + - + +
581A THR* 4.6 21.1 - - + -
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Residues in contact with GLN 569 (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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506A TYR* 3.7 50.6 - - + +
565A GLN* 2.8 54.6 + - + +
566A TYR* 3.8 4.9 - - - +
568A LYS* 1.3 87.0 - - + +
570A GLU* 1.3 57.4 + - - +
572A ILE* 3.3 16.1 - - + +
573A ASP 3.1 21.3 + - - -
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Residues in contact with GLU 570 (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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506A TYR* 2.9 29.4 + - - +
510A LYS 5.1 0.5 - - - +
513A THR* 3.1 29.4 + - - +
516A VAL 4.8 4.5 - - - +
518A VAL* 4.4 11.8 + - + +
519A PHE* 4.3 15.8 - - + -
566A TYR* 2.9 52.9 + - + +
567A LEU* 3.5 6.5 - - - +
569A GLN* 1.3 73.7 - - - +
571A SER* 1.3 62.6 + - - +
572A ILE 3.2 1.3 - - - -
573A ASP 2.4 33.1 - - - +
574A LYS* 3.9 11.7 - - + +
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Residues in contact with SER 571 (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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519A PHE* 3.9 20.0 - - - -
567A LEU 2.7 18.4 + - - -
568A LYS 3.8 3.6 - - - -
570A GLU* 1.3 72.3 - - - +
572A ILE* 1.3 62.6 + - - +
575A LYS* 3.2 22.8 + - - +
576A ARG 2.9 19.1 + - - -
577A LYS* 3.2 21.3 + - - +
578A GLU 4.0 5.5 + - - -
579A PHE* 3.8 21.3 - - - +
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Residues in contact with ILE 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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568A LYS* 3.0 41.2 + - - +
569A GLN* 3.3 14.8 - - + +
570A GLU 3.2 0.2 - - - -
571A SER* 1.3 74.5 - - - +
573A ASP* 1.3 60.1 + - + +
574A LYS 3.5 0.5 + - - -
576A ARG* 2.8 33.0 + - - +
577A LYS 3.1 17.5 + - - +
578A GLU* 4.6 8.3 - - + -
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Residues in contact with ASP 573 (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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506A TYR* 3.5 31.1 + - - +
507A GLN* 4.4 4.7 + - - -
510A LYS* 3.7 31.4 + - + -
569A GLN 3.1 8.4 + - - +
570A GLU* 2.4 20.6 - - - +
572A ILE* 1.3 75.6 - - - +
574A LYS* 1.3 71.8 + - - +
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Residues in contact with LYS 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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513A THR 3.9 4.8 + - - +
514A LYS* 5.5 0.2 - - - +
515A LYS* 4.7 4.2 - - - +
516A VAL 2.4 47.3 + - - +
517A ASP* 4.1 13.5 - - - +
518A VAL 5.6 0.2 - - - +
519A PHE* 5.9 3.6 - - + -
570A GLU* 3.9 14.1 + - + +
572A ILE 3.5 2.2 + - - -
573A ASP* 1.3 85.1 + - - +
575A LYS* 1.3 103.5 + - + +
576A ARG* 3.5 3.8 - - - +
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Residues in contact with LYS 575 (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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517A ASP* 3.8 26.4 + - - +
519A PHE* 4.9 11.7 - - + -
571A SER* 3.2 28.1 + - - +
574A LYS* 1.3 122.3 + - + +
576A ARG* 1.3 62.4 + - - +
577A LYS* 2.6 40.2 + - + +
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Residues in contact with ARG 576 (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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571A SER 2.9 0.8 + - - -
572A ILE* 2.8 25.3 + - - +
574A LYS 3.5 3.5 - - - +
575A LYS* 1.3 77.9 - - - +
577A LYS* 1.3 61.0 + - - +
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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