Contacts of the helix formed by residues 556 - 576 (chain A) in PDB entry 1UUR
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 GLN 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A LYS* 3.1 40.4 - - - +
501A PHE* 4.1 15.7 - - - +
504A GLN 3.0 25.6 - - - +
505A LEU* 2.8 35.0 + - + +
555A HIS* 1.3 83.9 - - + +
557A GLN* 1.3 64.2 + - + +
559A PHE* 3.3 17.0 - - - +
560A ASP* 3.2 13.7 + - - +
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Residues in contact with GLN 557 (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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555A HIS* 3.2 18.2 + - + +
556A GLN* 1.3 79.0 - - + +
558A ASP* 1.3 67.0 + - - +
559A PHE 3.0 3.2 + - - -
560A ASP* 3.2 22.9 + - + +
561A LYS* 3.7 22.2 - - - +
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Residues in contact with ASP 558 (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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547A PHE* 4.4 11.2 - - - +
548A PHE* 4.1 26.4 - - + -
551A ARG* 5.5 5.3 + - - -
553A ILE 5.4 0.7 - - - +
554A ILE* 4.7 0.9 - - - -
555A HIS* 3.0 39.6 + - - +
557A GLN* 1.3 80.7 - - - +
559A PHE* 1.3 62.1 + - - +
561A LYS* 3.6 19.9 + - - +
562A PHE* 3.2 20.8 + - - +
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Residues in contact with PHE 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLY 3.8 18.2 - - - -
496A LEU* 3.7 30.5 - - + -
497A LYS* 3.5 50.7 - - + -
500A ALA* 5.4 0.7 - - + -
501A PHE* 4.1 20.2 - + + -
512A PHE* 4.1 22.7 - + - -
548A PHE* 4.7 4.6 - + + -
555A HIS 3.7 2.5 + - - +
556A GLN 3.3 14.3 + - - +
557A GLN 3.0 0.2 - - - -
558A ASP* 1.3 76.1 - - - +
560A ASP* 1.3 68.2 + - - +
561A LYS 3.0 2.0 - - - -
562A PHE* 2.9 27.4 + + - +
563A TRP* 2.9 34.8 + + + +
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Residues in contact with ASP 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LYS* 3.8 21.0 - - - +
556A GLN* 3.2 9.0 - - - +
557A GLN* 3.2 37.3 + - + +
559A PHE* 1.3 81.0 - - - +
561A LYS* 1.3 53.3 + - + +
563A TRP* 4.3 3.8 - - - +
564A VAL* 2.7 32.5 + - - +
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Residues in contact with LYS 561 (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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547A PHE* 4.3 9.5 - - + +
557A GLN* 3.7 20.9 - - - +
558A ASP* 3.8 17.0 + - - +
559A PHE 3.0 0.4 - - - -
560A ASP* 1.3 78.4 - - + +
562A PHE* 1.3 66.4 + - - +
563A TRP 3.3 0.4 - - - -
564A VAL* 3.2 24.9 + - - +
565A TRP* 3.7 2.4 + - - +
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Residues in contact with PHE 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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496A LEU* 4.8 0.2 - - + -
512A PHE* 4.0 19.7 - + - -
516A LEU* 4.0 23.1 - - + -
543A ILE* 3.6 22.2 - - + -
547A PHE* 3.5 33.8 - + + -
548A PHE* 3.8 18.2 - + + -
558A ASP 3.2 11.6 + - - +
559A PHE* 2.9 21.2 + + - +
561A LYS* 1.3 80.0 - - - +
563A TRP* 1.3 68.3 + + + +
565A TRP* 3.3 4.3 + - - +
566A PHE* 2.8 78.5 + + + +
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Residues in contact with TRP 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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488A TRP* 4.2 3.8 - + - -
489A GLU* 3.1 42.9 + - + +
490A GLY* 4.4 2.8 - - - +
492A ALA* 3.8 14.1 - - + -
493A GLY* 3.4 34.4 - - - -
496A LEU* 4.0 24.0 - - + -
559A PHE* 2.9 28.5 + + + +
560A ASP* 4.3 4.9 - - - +
562A PHE* 1.3 80.8 - + - +
564A VAL* 1.3 66.5 + - - +
565A TRP 3.1 2.0 - - - -
566A PHE* 4.4 1.8 - + - -
567A GLY* 3.1 35.6 + - - +
570A MET* 3.0 39.9 - - + -
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Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU* 4.2 5.0 - - - +
560A ASP 2.7 28.5 + - - +
561A LYS* 3.2 17.7 - - - +
562A PHE 3.2 0.4 - - - -
563A TRP* 1.3 79.0 - - - +
565A TRP* 1.3 58.1 + - + +
568A LYS* 3.3 25.3 - - - +
618A PRO* 4.1 8.1 - - + +
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Residues in contact with TRP 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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542A TYR* 3.6 31.2 - + - -
547A PHE* 3.2 41.1 - + + -
561A LYS 3.7 1.3 + - - +
562A PHE 3.3 1.4 + - - -
564A VAL* 1.3 78.9 - - + +
566A PHE* 1.3 86.5 + + - +
567A GLY 3.3 0.9 - - - -
568A LYS* 2.9 21.7 + - - +
569A SER* 3.2 7.1 + - - -
591A TYR* 3.8 31.2 - + - -
613A PHE* 3.6 28.5 - + + -
614A SER 2.8 32.4 + - - -
615A GLU* 3.4 21.1 + - - -
618A PRO* 3.4 30.2 - - + +
619A GLY 4.7 1.5 + - - -
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Residues in contact with PHE 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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516A LEU* 3.7 16.4 - - + -
520A PHE* 4.1 3.8 - + - -
535A LEU* 4.1 14.8 - - + -
543A ILE* 3.6 25.8 - - + -
562A PHE* 2.8 55.9 + + + +
563A TRP* 4.4 1.3 - + - -
565A TRP* 1.3 85.8 - + + +
567A GLY* 1.3 63.1 + - - +
569A SER* 2.5 28.5 + - - -
570A MET* 3.1 38.1 + - + +
591A TYR* 3.4 40.4 - + - -
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Residues in contact with GLY 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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488A TRP* 4.1 5.4 - - - -
489A GLU* 4.4 8.1 - - - +
563A TRP* 3.1 53.5 + - - -
566A PHE* 1.3 77.7 - - - +
568A LYS* 1.3 56.4 + - - +
570A MET* 3.4 4.4 + - - +
571A GLN* 3.0 25.3 + - - +
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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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489A GLU* 2.9 33.4 + - - +
563A TRP 4.2 0.2 + - - -
564A VAL 3.3 21.3 - - - +
565A TRP 2.9 8.3 + - - +
567A GLY* 1.3 72.7 - - - +
569A SER* 1.3 66.2 + - - +
570A MET 3.0 1.6 - - - -
571A GLN* 3.0 27.8 + - - +
572A THR* 3.0 16.1 + - - -
618A PRO* 3.8 15.0 - - + +
619A GLY* 3.7 19.9 - - - +
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Residues in contact with SER 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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565A TRP* 3.2 11.4 + - - -
566A PHE* 2.5 26.8 + - - -
568A LYS* 1.3 78.1 - - - +
570A MET* 1.3 56.8 + - - +
572A THR* 3.5 1.4 - - - -
573A LEU* 3.1 28.2 + - - +
591A TYR* 2.9 36.0 + - - -
613A PHE* 3.4 33.9 - - - -
619A GLY* 4.1 5.5 - - - +
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Residues in contact with MET 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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488A TRP* 3.9 13.1 - - + -
496A LEU* 5.2 0.9 - - + -
516A LEU* 4.5 7.2 - - + -
519A HIS* 5.2 3.8 - - + +
520A PHE* 3.7 37.7 - - + +
523A ALA* 4.2 20.0 - - + +
524A THR* 6.1 0.7 - - + -
563A TRP* 3.0 47.3 - - + -
566A PHE* 3.1 28.6 + - + +
567A GLY* 3.6 6.7 - - - +
568A LYS 3.0 0.4 - - - -
569A SER* 1.3 82.2 + - - +
571A GLN* 1.3 60.2 + - - +
572A THR 3.0 1.8 - - - -
573A LEU* 3.6 7.5 - - + +
574A ARG* 2.8 32.4 + - - +
591A TYR* 4.4 0.2 - - - +
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Residues in contact with GLN 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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485A GLU 3.3 23.6 + - - -
486A CYS* 3.9 14.0 + - - +
488A TRP* 4.2 13.8 - - + +
489A GLU* 4.1 29.2 - - + +
567A GLY 3.0 12.3 + - - +
568A LYS* 3.0 21.2 + - - +
570A MET* 1.3 76.7 - - - +
572A THR* 1.3 58.6 + - - +
575A TYR* 2.9 47.0 + - + +
576A GLN 3.9 0.2 + - - -
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Residues in contact with THR 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 11.2 + - - -
569A SER* 3.5 12.1 - - - +
571A GLN* 1.3 77.6 - - - +
573A LEU* 1.3 62.4 + - - +
576A GLN* 3.0 55.3 + - - +
579A ILE* 3.6 20.2 - - + +
613A PHE* 4.4 2.7 - - + -
619A GLY* 3.1 24.1 + - - +
621A PHE* 4.1 13.9 - - + -
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Residues in contact with LEU 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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520A PHE* 3.7 37.5 - - + -
524A THR* 4.3 14.6 - - + -
569A SER 3.1 14.0 + - - +
570A MET* 3.1 10.8 + - - +
572A THR* 1.3 82.1 - - - +
574A ARG* 1.3 60.0 + - - +
575A TYR 3.7 0.2 + - - -
576A GLN 4.5 1.9 - - - +
579A ILE* 3.9 18.6 - - + +
580A SER* 2.9 33.6 + - - -
583A TRP* 3.7 38.6 - - + -
591A TYR* 3.8 15.5 - - + +
613A PHE* 4.4 10.1 - - + -
621A PHE* 5.6 0.4 - - + -
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Residues in contact with ARG 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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373A VAL* 5.8 2.8 - - - +
374A VAL 4.6 12.1 + - - -
376A SER* 5.4 4.9 + - - -
482A ILE* 5.9 0.4 - - - +
488A TRP* 3.2 37.7 - - + +
522A ILE* 3.7 15.5 + - - +
523A ALA* 2.9 36.6 + - + +
524A THR* 5.4 2.0 - - - +
525A LYS* 3.2 36.4 + - - +
570A MET 2.8 16.3 + - - +
573A LEU* 1.3 78.7 - - - +
575A TYR* 1.3 97.9 + - + +
580A SER* 5.1 1.8 - - - -
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Residues in contact with TYR 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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376A SER* 5.3 2.3 + - - -
482A ILE* 4.2 9.2 - - - +
485A GLU* 3.7 48.5 - - + +
488A TRP* 3.1 48.6 - + + +
571A GLN* 2.9 41.2 + - + +
574A ARG* 1.3 116.3 + - + +
576A GLN* 1.3 62.6 - - - +
577A ARG* 3.2 4.0 + - - +
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Residues in contact with GLN 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 GLN 3.9 0.8 + - - -
572A THR* 3.0 40.6 + - + +
573A LEU 4.5 1.7 - - - +
575A TYR* 1.3 75.3 - - - +
577A ARG* 1.3 69.2 + - + +
578A HIS 3.4 0.7 + - - -
579A ILE* 3.1 39.6 + - + +
580A SER 4.2 2.4 + - - -
619A GLY 4.8 4.8 + - - -
621A PHE* 5.0 6.4 - - - -
644A THR* 4.0 26.7 + - + +
651A PHE* 4.3 8.4 - - + +
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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