Contacts of the helix formed by residues 562 - 583 (chain A) in PDB entry 4RS6
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 PRO 562 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A PHE* 4.3 14.6 - - + -
560A ASP 3.8 7.2 - - - +
561A ALA* 1.3 87.1 - - + +
563A GLU* 1.3 66.2 + - - +
564A GLN* 3.3 13.9 - - - +
565A PHE* 2.9 44.9 + - + +
566A ILE* 3.3 8.3 + - - -
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Residues in contact with GLU 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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561A ALA 3.9 1.0 + - - -
562A PRO* 1.3 69.6 - - - +
564A GLN* 1.3 62.1 + - + +
565A PHE 3.0 5.5 + - - -
566A ILE* 3.1 33.8 + - + +
567A SER 4.4 1.7 + - - -
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Residues in contact with GLN 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PRO* 3.6 17.1 - - - +
563A GLU* 1.3 82.1 + - + +
565A PHE* 1.3 88.4 + - + +
567A SER 5.4 0.4 - - - -
568A GLN* 3.4 12.5 - - - +
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Residues in contact with PHE 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A MET* 5.4 1.3 - - - -
546A TYR* 3.3 48.9 - + - -
554A SER* 4.4 12.6 - - - -
556A PHE* 3.7 37.7 - + + -
561A ALA* 4.9 0.9 - - + -
562A PRO* 2.9 32.4 + - + +
564A GLN* 1.3 104.3 - - + +
566A ILE* 1.3 55.5 + - - +
567A SER* 3.5 2.0 - - - -
568A GLN* 2.9 24.8 + - + +
569A VAL* 2.9 34.4 + - + +
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Residues in contact with ILE 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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561A ALA* 3.9 22.2 - - + +
562A PRO 3.3 12.0 + - - +
563A GLU* 3.1 29.2 + - + +
565A PHE* 1.3 72.0 - - - +
567A SER* 1.3 72.3 + - - +
568A GLN 2.9 1.4 + - - -
569A VAL* 3.0 16.3 + - - +
570A THR* 3.0 26.2 + - + +
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Residues in contact with SER 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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563A GLU 4.4 2.2 + - - -
564A GLN 5.4 1.2 + - - -
565A PHE 3.5 0.6 - - - -
566A ILE* 1.3 82.6 - - - +
568A GLN* 1.3 70.8 + - - +
570A THR* 3.2 9.2 + - - -
571A VAL* 3.0 26.4 + - - +
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Residues in contact with GLN 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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529A PHE* 3.7 39.4 - - + -
531A ASN* 4.6 10.5 - - - +
533A ALA* 4.4 4.2 - - - +
535A MET* 3.8 9.4 - - - -
546A TYR* 3.6 30.6 + - - -
564A GLN 3.4 22.2 - - - +
565A PHE* 2.9 19.4 + - - +
566A ILE 2.9 1.0 + - - -
567A SER* 1.3 83.8 + - - +
569A VAL* 1.3 62.2 + - - +
571A VAL* 3.2 7.9 + - - +
572A LEU* 2.7 27.5 + - - +
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Residues in contact with VAL 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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535A MET* 3.7 24.7 - - + -
544A VAL* 4.6 4.0 - - + -
556A PHE* 4.1 23.3 - - + -
558A ALA* 4.2 21.5 - - + +
561A ALA* 4.2 10.8 - - + -
565A PHE 2.9 15.5 + - - +
566A ILE* 3.7 8.5 - - - +
568A GLN* 1.3 75.1 - - - +
570A THR* 1.3 69.2 + - + +
572A LEU* 2.9 5.9 + - + +
573A LYS* 2.9 44.3 + - + +
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Residues in contact with THR 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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566A ILE* 3.0 26.7 + - + +
567A SER* 3.2 11.3 + - - -
569A VAL* 1.3 80.8 - - + +
571A VAL* 1.3 60.3 + - - +
573A LYS* 3.4 13.5 + - + +
574A TYR* 2.9 26.3 + - - +
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Residues in contact with VAL 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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514A TYR* 4.2 37.9 - - + -
529A PHE* 3.8 19.7 - - + -
567A SER* 3.0 19.6 + - - +
568A GLN* 3.4 10.3 - - - +
569A VAL 3.1 0.2 - - - -
570A THR* 1.3 77.1 + - - +
572A LEU* 1.3 67.7 + - - +
574A TYR* 3.0 7.8 + - + +
575A PHE* 3.0 54.1 + - + -
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Residues in contact with LEU 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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525A VAL* 4.0 23.4 - - + +
527A VAL* 3.3 33.9 - - + -
529A PHE* 5.0 0.2 - - - -
535A MET* 2.9 43.3 - - + +
537A LEU* 3.7 33.9 - - + +
544A VAL* 4.0 15.0 - - + -
558A ALA* 6.0 0.4 - - + -
568A GLN 2.7 10.6 + - - +
569A VAL* 2.9 12.7 + - + +
571A VAL* 1.3 73.1 - - - +
573A LYS* 1.3 58.5 + - + +
575A PHE* 3.3 6.2 + - - +
576A SER* 3.0 25.3 + - - -
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Residues in contact with LYS 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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537A LEU* 4.7 15.5 - - + -
541A LYS 5.5 4.0 - - - -
558A ALA* 4.1 21.8 - - - +
559A THR* 4.0 27.1 - - - +
569A VAL* 2.9 25.0 + - + +
570A THR* 3.5 17.0 - - + +
572A LEU* 1.3 74.6 - - + +
574A TYR* 1.3 68.9 + - - +
576A SER* 3.2 7.3 + - - -
577A HIS* 3.0 41.0 + - + +
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Residues in contact with TYR 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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510A TYR* 4.2 30.1 + + - -
514A TYR* 5.2 8.1 - + - -
570A THR 2.9 14.7 + - - +
571A VAL* 3.0 12.8 + - + +
573A LYS* 1.3 79.0 - - - +
575A PHE* 1.3 77.7 + + - +
577A HIS* 3.0 4.1 + - + +
578A TYR* 2.9 49.5 + + + +
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Residues in contact with PHE 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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508A VAL* 3.3 35.4 - - + -
510A TYR* 3.8 30.1 - + + -
514A TYR* 4.4 10.5 - + + -
515A GLY 3.9 14.4 - - - -
516A PHE 4.7 0.7 - - - -
517A GLY* 3.7 25.1 - - - -
525A VAL* 4.9 4.0 - - + -
527A VAL* 4.5 13.2 - - + -
571A VAL* 3.0 47.8 + - + -
572A LEU* 3.4 11.0 - - - +
574A TYR* 1.3 85.2 - + - +
576A SER* 1.3 62.7 + - - +
578A TYR* 4.0 6.8 - - + +
579A MET* 3.1 38.3 + - + +
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Residues in contact with SER 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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519A GLN* 5.5 2.4 + - - +
525A VAL* 3.7 25.0 - - - +
537A LEU* 4.8 7.2 - - - -
541A LYS* 2.9 31.2 + - - -
572A LEU 3.0 14.1 + - - -
573A LYS* 3.5 12.6 - - - -
574A TYR 3.1 0.4 + - - -
575A PHE* 1.3 75.1 - - - +
577A HIS* 1.3 66.1 + - - +
579A MET* 3.8 3.1 - - - +
580A GLU* 2.9 29.2 + - - +
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Residues in contact with HIS 577 (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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541A LYS* 6.1 3.2 - - - -
573A LYS* 3.0 36.0 + - + +
574A TYR* 3.0 6.2 + - + +
576A SER* 1.3 81.3 + - - +
578A TYR* 1.3 63.4 + - - +
579A MET 3.3 0.2 - - - -
580A GLU* 3.9 20.6 + - - +
581A GLU* 2.9 45.5 + - - +
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Residues in contact with TYR 578 (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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508A VAL* 4.3 24.9 - - + -
574A TYR* 2.9 43.6 + + + +
575A PHE* 4.0 8.1 - - - +
577A HIS* 1.3 75.7 - - - +
579A MET* 1.3 56.1 + - + +
582A ASN* 2.8 68.8 + - + +
583A LEU* 4.0 26.5 - - + +
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Residues in contact with MET 579 (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 LYS* 3.0 41.7 + - + +
508A VAL* 3.8 23.1 - - + -
518A TYR* 3.5 45.5 - - - +
519A GLN* 3.8 13.0 - - + +
525A VAL* 3.9 14.8 - - + -
575A PHE* 3.1 29.4 + - + +
576A SER* 3.8 4.9 - - - +
578A TYR* 1.3 80.4 - - - +
580A GLU* 1.3 65.0 + - - +
583A LEU* 3.3 31.6 + - + +
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Residues in contact with GLU 580 (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 LYS* 3.9 12.3 + - - +
519A GLN* 5.9 4.4 + - - +
541A LYS* 5.9 3.1 + - - -
576A SER* 2.9 20.3 + - - +
577A HIS* 3.9 23.3 - - - +
578A TYR 3.3 0.4 - - - -
579A MET* 1.3 78.5 - - - +
581A GLU* 1.3 63.1 + - + +
583A LEU 4.2 3.5 - - - +
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Residues in contact with GLU 581 (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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577A HIS* 2.9 41.4 + - - +
578A TYR* 4.9 0.2 - - - -
580A GLU* 1.3 85.4 - - + +
582A ASN* 1.3 72.2 + - - +
583A LEU 3.9 0.4 - - - -
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Residues in contact with ASN 582 (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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578A TYR* 2.8 71.8 + - + +
581A GLU* 1.3 86.6 - - - +
583A LEU* 1.3 66.2 + - + +
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Residues in contact with LEU 583 (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 LYS* 2.8 31.2 + - + -
507A TRP 3.5 27.8 - - - +
508A VAL* 4.6 1.3 - - + -
578A TYR* 4.0 27.8 - - + +
579A MET* 3.3 28.1 + - + +
580A GLU 4.2 4.3 - - - +
581A GLU 3.9 0.2 - - - -
582A ASN* 1.3 88.3 - - + +
584A MET* 1.3 61.7 + - - +
512B ASN* 6.2 1.6 - - - +
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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
------------------------------------------------------------
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