Contacts of the helix formed by residues 569 - 589 (chain D) in PDB entry 1S77
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 ASP 569 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D LYS* 3.7 26.8 + - + -
539D SER* 6.4 0.2 - - - -
567D VAL 3.6 5.4 + - - +
568D GLN* 1.3 75.4 - - - +
570D ILE* 1.3 64.6 + - - +
571D TYR* 3.8 7.6 - - - -
572D GLY* 2.8 34.7 + - - -
573D ILE* 2.9 17.6 + - - +
627D ARG* 2.8 48.3 + - - -
901D POP 4.4 2.8 + - - -
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Residues in contact with ILE 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D CYS* 4.2 13.5 - - + -
543D ILE* 4.2 11.9 - - + -
555D GLY* 6.2 0.4 - - - -
558D ALA* 3.6 33.3 + - + +
559D VAL* 4.2 13.0 - - + -
569D ASP* 1.3 72.3 + - - +
571D TYR* 1.3 95.6 + - + +
573D ILE* 3.5 10.6 + - + +
574D VAL* 3.1 23.6 + - + +
634D VAL* 3.8 17.9 - - + -
688D THR* 4.3 14.8 - - + -
689D VAL* 4.1 19.7 - - + -
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Residues in contact with TYR 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D CYS* 3.2 31.4 - - + +
569D ASP* 3.0 8.4 + - - +
570D ILE* 1.3 90.3 - - + +
572D GLY* 1.3 61.4 + - - +
574D VAL* 3.4 1.6 + - - +
575D ALA* 2.9 24.4 + - - +
627D ARG* 3.3 43.7 - - + +
630D THR* 3.1 15.1 + - - +
631D LYS* 2.8 49.9 + - + -
634D VAL* 3.5 26.7 - - + -
635D MET* 3.9 16.3 - - + +
901D POP 3.3 20.8 + - - -
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Residues in contact with GLY 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569D ASP* 2.8 23.7 + - - -
571D TYR* 1.3 73.5 - - - +
573D ILE* 1.3 66.0 + - - +
575D ALA* 3.0 9.9 + - - +
576D LYS* 2.9 31.9 + - - +
627D ARG* 3.8 8.3 - - - +
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Residues in contact with ILE 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558D ALA* 4.2 21.8 - - + -
568D GLN* 4.6 12.3 - - - +
569D ASP 2.9 25.4 + - - +
570D ILE* 3.5 17.9 - - + +
572D GLY* 1.3 74.7 - - - +
574D VAL* 1.3 65.5 + - - +
576D LYS* 2.8 21.3 + - - +
577D LYS* 3.0 39.3 + - - +
688D THR* 4.7 10.5 - - + +
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Residues in contact with VAL 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D ILE* 3.1 18.9 + - + +
571D TYR 3.7 2.5 - - - +
573D ILE* 1.3 80.8 - - + +
575D ALA* 1.3 56.7 + - - +
577D LYS* 3.5 9.5 + - - +
578D VAL* 3.0 30.3 + - + +
630D THR* 3.9 15.0 - - + -
634D VAL* 3.4 38.4 - - + -
681D ILE* 4.5 7.4 - - + +
684D SER* 4.2 14.4 - - - +
685D VAL* 4.1 20.2 - - + +
688D THR* 4.6 11.0 - - - +
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Residues in contact with ALA 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D TYR 2.9 15.2 + - - +
572D GLY* 3.2 14.1 - - - +
573D ILE 3.0 0.2 - - - -
574D VAL* 1.3 74.7 - - - +
576D LYS* 1.3 59.8 + - + +
578D VAL* 3.3 5.5 + - - +
579D ASN* 3.0 33.4 + - - +
625D VAL* 4.6 5.4 - - + +
626D THR* 3.9 11.7 - - - +
627D ARG* 3.9 22.4 - - - +
630D THR* 4.1 11.2 + - + +
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Residues in contact with LYS 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D GLY* 2.9 19.8 + - - +
573D ILE* 2.8 15.6 + - - +
575D ALA* 1.3 69.9 - - + +
577D LYS* 1.3 58.2 + - + +
579D ASN* 2.8 32.5 + - + +
580D GLU* 2.8 20.3 + - + +
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Residues in contact with LYS 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D ILE* 3.0 39.6 + - + +
574D VAL* 3.7 7.2 - - - +
576D LYS* 1.3 79.9 - - + +
578D VAL* 1.3 64.0 + - - +
580D GLU* 3.2 23.9 + - - +
581D ILE* 3.1 25.9 + - + +
684D SER* 3.7 22.4 - - - +
687D VAL* 3.6 30.5 - - + -
688D THR* 3.3 19.6 + - - +
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Residues in contact with VAL 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D VAL* 3.0 23.2 + - + +
575D ALA* 3.5 10.1 - - - +
577D LYS* 1.3 74.6 - - - +
579D ASN* 1.3 57.0 + - - +
581D ILE* 3.2 8.5 - - - +
582D LEU* 2.9 34.3 + - + +
625D VAL* 3.9 23.1 - - + -
630D THR* 4.3 3.4 - - + -
677D MET* 4.0 17.0 - - - -
680D LEU* 4.1 20.0 - - + +
681D ILE* 4.1 15.0 - - + +
684D SER* 3.7 19.3 - - - +
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Residues in contact with ASN 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D ALA* 3.0 18.1 + - - +
576D LYS* 2.8 19.8 + - + +
578D VAL* 1.3 74.7 - - - +
580D GLU* 1.3 56.1 - - - +
582D LEU* 3.7 13.0 - - - +
583D GLN* 2.6 46.9 + - + +
621D LEU* 4.6 9.9 - - - +
625D VAL* 3.6 37.4 + - - +
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Residues in contact with GLU 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576D LYS* 2.8 25.0 + - + +
577D LYS* 3.4 28.4 - - - +
579D ASN* 1.3 70.5 - - - +
581D ILE* 1.3 54.8 + - + +
583D GLN* 3.4 7.3 - - - +
584D ALA* 2.8 36.7 + - - +
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Residues in contact with ILE 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D LYS 3.1 10.5 + - - +
578D VAL* 3.2 7.2 - - - +
579D ASN 3.1 0.2 - - - -
580D GLU* 1.3 77.3 - - + +
582D LEU* 1.3 56.1 + - - +
584D ALA* 2.8 10.3 + - - +
585D ASP* 2.7 46.9 + - - +
680D LEU* 3.3 46.9 - - + +
683D GLU* 4.6 12.1 - - + +
684D SER* 3.5 23.3 - - - +
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Residues in contact with LEU 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D VAL* 2.9 25.8 + - + +
579D ASN* 3.7 17.5 - - - +
581D ILE* 1.3 73.4 - - - +
583D GLN* 1.3 53.3 + - - +
585D ASP 3.3 0.3 + - - -
586D ALA* 2.8 35.5 + - - +
617D ALA* 3.5 20.2 - - + +
620D TRP* 3.8 13.0 - - + -
621D LEU* 3.9 20.0 - - + -
625D VAL* 3.6 30.7 - - + -
676D TYR* 3.4 23.8 - - + +
677D MET* 4.2 1.1 - - + -
680D LEU* 3.4 23.3 - - + -
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Residues in contact with GLN 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D ASN* 2.6 34.1 + - + +
580D GLU* 3.4 7.9 - - - +
582D LEU* 1.3 72.8 - - - +
584D ALA* 1.3 63.9 + - - +
586D ALA* 3.1 19.8 - - - +
587D ILE* 3.7 9.5 + - - +
621D LEU* 3.9 23.5 - - + +
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Residues in contact with ALA 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580D GLU 2.8 17.9 + - - +
581D ILE* 2.8 13.1 + - - +
583D GLN* 1.3 73.3 - - - +
585D ASP* 1.3 61.7 + - - +
586D ALA 3.2 0.7 + - - -
587D ILE* 3.7 4.3 + - - +
588D ASN* 2.7 35.5 + - - +
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Residues in contact with ASP 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581D ILE* 2.7 30.6 + - - +
582D LEU 3.9 2.7 - - - +
584D ALA* 1.3 72.6 - - - +
586D ALA* 1.3 62.2 + - - +
588D ASN 4.0 2.9 - - - +
589D GLY* 3.3 19.3 + - - -
613D THR* 2.9 27.5 + - + +
614D LYS* 2.9 27.3 - - - +
617D ALA* 3.9 1.6 - - + -
676D TYR* 2.9 27.9 + - - +
680D LEU* 4.6 1.0 - - - +
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Residues in contact with ALA 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LEU 2.8 14.6 + - - +
583D GLN* 3.1 16.2 - - - +
584D ALA 3.1 0.2 - - - -
585D ASP* 1.3 76.0 - - - +
587D ILE* 1.3 64.0 + - + +
614D LYS* 2.8 38.3 - - - +
617D ALA* 4.5 0.9 - - - -
618D GLY* 5.4 1.3 - - - +
621D LEU* 3.7 19.7 - - + -
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Residues in contact with ILE 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D GLN 3.7 9.2 + - - +
584D ALA* 3.7 5.5 + - - +
586D ALA* 1.3 81.5 - - + +
588D ASN* 1.3 85.7 + - + +
589D GLY 4.1 0.2 - - - -
614D LYS* 4.1 9.8 + - - +
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Residues in contact with ASN 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584D ALA* 2.7 31.2 + - - +
585D ASP* 3.9 5.0 - - - +
587D ILE* 1.3 98.3 - - + +
589D GLY* 1.3 55.9 + - - +
590D THR 4.2 0.4 - - - -
614D LYS* 4.6 2.5 - - - +
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Residues in contact with GLY 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D ASP* 3.3 26.4 + - - -
588D ASN* 1.3 75.3 - - - +
590D THR* 1.3 84.5 + - - +
613D THR* 2.9 21.9 - - - -
614D LYS* 3.9 6.6 - - - +
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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
------------------------------------------------------------
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