Contacts of the helix formed by residues 569 - 584 (chain D) in PDB entry 1XSK
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 MET 569 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532D LEU 5.5 0.2 - - - +
533D LEU* 3.6 24.7 - - + -
565D LEU* 3.0 40.8 + - + +
566D LYS* 3.2 24.8 + - + +
568D ARG* 1.3 77.5 - - + +
570D MET* 1.3 52.5 + - - +
571D PRO* 3.3 3.1 - - - -
572D TYR* 3.1 16.3 + - + +
573D LEU* 2.7 51.8 + - + +
610D LEU* 5.5 4.7 - - + -
614D VAL* 6.1 4.5 - - - -
638D LEU* 4.0 24.5 - - + -
661D VAL* 6.0 1.1 - - - -
669D LEU* 6.5 0.4 - - + -
671D LEU* 4.8 15.9 - - + -
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Residues in contact with MET 570 (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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266D ALA 4.2 5.2 - - - +
269D PHE* 3.7 41.1 - - + -
566D LYS* 3.3 14.1 + - - +
567D CYS* 3.6 17.3 - - - +
568D ARG 3.2 0.4 - - - -
569D MET* 1.3 75.5 - - - +
571D PRO* 1.3 64.3 - - + +
573D LEU* 3.6 18.2 - - - -
574D TYR* 2.8 47.7 + - + +
678D PRO* 3.4 29.6 - - + +
682D TRP* 3.4 32.8 - - + +
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Residues in contact with PRO 571 (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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568D ARG 3.1 17.7 - - - +
569D MET 3.4 1.8 - - - -
570D MET* 1.3 93.3 - - + +
572D TYR* 1.3 60.4 + - - +
575D ARG* 3.6 4.9 + - - +
670D ALA* 3.6 25.1 - - + +
671D LEU 4.0 1.8 - - - +
672D GLY* 3.6 19.7 - - - +
680D TYR* 4.0 0.9 - - - +
682D TRP* 3.6 39.9 - - + +
686D THR* 5.2 0.7 - - + -
702D GLU 4.6 1.0 - - - +
703D VAL* 4.7 7.4 - - + -
704D PRO* 3.2 28.7 - - + +
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Residues in contact with TYR 572 (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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569D MET* 3.1 17.8 + - + +
571D PRO* 1.3 79.3 - - - +
573D LEU* 1.3 82.2 + - + +
575D ARG* 3.4 5.8 + - + +
576D GLU* 3.2 45.0 + - + +
610D LEU* 2.8 22.6 + - + -
611D GLY 3.3 3.8 - - - -
613D ASN* 3.0 35.9 + - - -
614D VAL* 3.1 25.5 - - + +
669D LEU* 3.4 35.7 - - + -
670D ALA* 3.6 17.8 + - - +
671D LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 573 (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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269D PHE* 5.4 4.5 - - + -
532D LEU 5.8 0.2 - - - +
534D SER 5.7 2.0 - - - +
566D LYS* 3.7 46.2 - - + +
569D MET* 2.7 31.8 + - + +
570D MET* 3.9 16.4 - - - -
572D TYR* 1.3 89.3 - - + +
574D TYR* 1.3 66.0 + - - +
576D GLU* 3.3 3.9 + - + +
577D ALA* 3.1 18.1 + - - +
587D MET* 3.5 31.5 - - + +
610D LEU* 4.2 25.8 - - + -
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Residues in contact with TYR 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D LEU* 3.4 26.4 + - + +
264D PRO 2.9 28.9 + - - -
265D PRO* 3.7 4.0 - - - +
266D ALA* 3.7 17.7 + - + -
269D PHE* 3.5 24.9 - + - -
570D MET* 2.8 32.8 + - + +
573D LEU* 1.3 72.3 - - - +
575D ARG* 1.3 64.3 + - - +
577D ALA* 3.3 3.5 + - + +
578D ALA* 3.1 19.6 + - - +
682D TRP* 3.4 31.0 - + + -
704D PRO* 4.0 7.6 - - + +
705D ALA 3.9 6.5 - - - -
706D ALA 3.1 26.9 + - - -
708D GLY* 3.9 10.8 - - - -
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Residues in contact with ARG 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D PRO 3.6 10.8 + - - +
572D TYR* 3.4 10.9 + - + +
573D LEU 3.2 0.6 - - - -
574D TYR* 1.3 78.6 - - - +
576D GLU* 1.3 65.1 + - - +
578D ALA* 3.0 24.5 + - - +
579D ARG* 3.3 40.6 + - - +
702D GLU* 3.1 63.2 + - + +
704D PRO* 3.7 17.4 - - + +
708D GLY 5.0 1.8 - - - -
710D VAL* 3.7 15.0 - - - +
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Residues in contact with GLU 576 (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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572D TYR* 3.2 35.1 + - + +
573D LEU* 3.3 7.8 + - + +
575D ARG* 1.3 80.5 - - - +
577D ALA* 1.3 57.5 + - - +
579D ARG* 2.5 54.5 + - - +
580D ALA* 3.3 4.5 + - - +
585D THR 4.7 1.6 - - - +
587D MET* 4.2 17.8 - - + +
589D ARG* 3.2 10.5 + - - +
611D GLY* 3.7 17.7 - - - -
612D ASP* 2.7 42.3 + - - +
613D ASN* 5.5 0.9 + - - -
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Residues in contact with ALA 577 (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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263D LEU* 3.6 23.1 - - + +
269D PHE* 3.8 11.9 - - + -
507D PHE* 3.7 20.5 - - + -
573D LEU 3.1 13.0 + - - +
574D TYR* 3.5 12.6 - - + +
575D ARG 3.1 0.4 - - - -
576D GLU* 1.3 71.8 - - - +
578D ALA* 1.3 67.0 + - - +
579D ARG 3.0 1.8 - - - -
580D ALA* 3.2 13.2 + - - +
581D ASN 3.2 8.1 + - - -
587D MET* 3.8 15.0 - - - -
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Residues in contact with ALA 578 (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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263D LEU* 4.0 9.4 - - + +
574D TYR 3.1 11.1 + - - +
575D ARG* 3.0 22.5 + - - +
577D ALA* 1.3 76.5 - - - +
579D ARG* 1.3 56.2 + - - +
581D ASN* 3.2 7.0 + - - +
582D ALA* 2.9 30.2 + - - +
708D GLY* 3.4 32.1 - - - +
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Residues in contact with ARG 579 (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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575D ARG* 3.3 39.4 + - - +
576D GLU* 2.5 46.0 + - - +
577D ALA 3.0 0.2 - - - -
578D ALA* 1.3 76.7 - - - +
580D ALA* 1.3 59.2 + - - +
582D ALA* 4.4 4.7 - - - +
583D ARG* 2.8 34.5 + - + +
584D GLY 3.5 2.6 + - - -
585D THR* 3.7 11.8 + - - -
589D ARG* 3.9 12.1 - - - +
612D ASP* 2.9 30.0 + - - -
702D GLU* 4.1 15.4 + - - -
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Residues in contact with ALA 580 (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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261D PRO* 3.5 11.2 - - - +
506D GLY* 4.1 17.3 - - - +
507D PHE* 3.7 24.0 - - + -
576D GLU 3.3 4.6 + - - +
577D ALA* 3.2 12.0 + - - +
579D ARG* 1.3 78.0 - - - +
581D ASN* 1.3 58.1 + - - +
584D GLY* 2.9 25.6 + - - -
585D THR 2.9 25.2 + - - +
586D PRO* 4.7 0.4 - - + -
587D MET 4.9 2.0 - - - +
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Residues in contact with ASN 581 (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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260D ARG* 3.7 24.0 - - - +
261D PRO 2.7 30.4 + - - +
262D ALA* 3.9 6.7 - - - +
263D LEU* 4.0 28.8 - - + +
507D PHE* 4.9 0.2 - - - -
577D ALA 3.2 8.3 + - - +
578D ALA* 3.2 10.7 + - - +
579D ARG 3.1 0.2 - - - -
580D ALA* 1.3 82.8 - - - +
582D ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 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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260D ARG* 3.1 25.7 + - - +
578D ALA 2.9 17.0 + - - +
579D ARG* 4.3 3.4 - - - +
581D ASN* 1.3 79.1 - - - +
583D ARG* 1.3 67.3 + - + +
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Residues in contact with ARG 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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248D LYS* 3.5 32.6 + - - +
249D ALA* 3.8 7.3 - - - +
252D ASP* 2.9 46.1 + - - +
260D ARG* 3.5 10.5 - - - +
579D ARG* 2.8 18.8 + - + +
582D ALA* 1.3 82.0 - - + +
584D GLY* 1.3 61.9 + - - +
585D THR* 3.2 16.5 + - - +
3004D SO4 2.7 41.6 + - - -
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Residues in contact with GLY 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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251D LEU* 3.8 17.9 - - - +
255D THR* 3.6 26.8 - - - +
260D ARG* 3.9 2.0 - - - +
261D PRO* 4.0 8.6 - - - +
501D GLY 5.1 1.0 - - - +
504D GLY 5.1 4.7 - - - +
506D GLY* 5.6 1.4 - - - -
580D ALA* 2.9 18.7 + - - -
581D ASN 4.7 0.2 + - - -
582D ALA 3.7 1.0 - - - -
583D ARG* 1.3 78.0 - - - +
585D THR* 1.3 62.5 + - - +
586D PRO* 3.5 8.7 - - - +
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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