Contacts of the helix formed by residues 569 - 584 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533F LEU* 4.7 9.6 - - + -
565F LEU* 2.9 47.2 + - + +
566F LYS* 3.2 5.6 + - - +
568F ARG* 1.3 77.1 - - + +
570F MET* 1.3 52.0 + - - +
571F PRO* 3.3 1.8 - - - -
572F TYR* 3.0 33.4 + - + +
573F LEU* 2.7 57.9 + - + -
610F LEU* 4.4 13.7 - - + -
614F VAL* 4.5 9.0 - - + -
638F LEU* 3.9 21.3 - - + -
661F VAL* 5.7 2.0 - - + -
669F LEU* 6.1 2.9 - - + -
670F ALA 5.0 2.0 - - - -
671F LEU* 5.1 10.5 - - + -
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Residues in contact with MET 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F ALA* 4.1 3.8 - - + +
269F PHE* 3.6 46.0 - - + -
566F LYS* 3.3 14.3 + - - +
567F CYS* 3.4 17.9 - - - +
569F MET* 1.3 79.3 - - - +
571F PRO* 1.4 67.6 - - + +
573F LEU* 4.0 14.6 - - - -
574F TYR* 3.0 50.0 + - + +
678F PRO* 3.5 34.5 - - + +
682F TRP* 3.6 20.7 - - + +
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Residues in contact with PRO 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568F ARG 3.0 16.8 - - - +
569F MET 3.4 1.6 - - - -
570F MET* 1.4 91.6 - - + +
572F TYR* 1.3 59.5 + - - +
575F ARG* 3.8 2.9 + - - +
670F ALA* 3.6 24.9 - - + +
671F LEU 3.9 1.6 - - - +
672F GLY* 3.6 22.7 - - - +
680F TYR* 3.6 9.2 - - - +
682F TRP* 3.7 37.2 - - + +
686F THR* 5.1 0.4 - - + -
702F GLU 4.5 2.1 - - - +
703F VAL* 4.8 5.3 - - + -
704F PRO* 3.1 28.4 - - + +
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Residues in contact with TYR 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569F MET* 3.0 19.0 + - + +
571F PRO* 1.3 78.7 - - - +
573F LEU* 1.3 85.3 + - + +
575F ARG* 3.1 14.9 + - + +
576F GLU* 3.2 39.1 + - + +
610F LEU 2.8 22.0 + - - -
612F ASP 3.4 2.8 + - - -
613F ASN* 2.8 40.0 + - + -
614F VAL* 3.3 24.9 - - + +
669F LEU* 3.4 30.5 - - + -
670F ALA* 3.6 17.4 + - - +
671F LEU* 5.5 0.2 - - + -
702F GLU 5.9 0.2 - - - -
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Residues in contact with LEU 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F PHE* 5.3 4.5 - - + -
534F SER 6.1 0.4 - - - +
535F SER* 6.4 0.9 - - - -
566F LYS* 3.7 29.4 - - + +
569F MET* 2.7 49.8 + - + +
570F MET* 4.0 15.7 - - - -
572F TYR* 1.3 91.0 - - + +
574F TYR* 1.3 58.1 + - - +
576F GLU* 2.9 23.8 + - + +
577F ALA 3.0 9.5 + - - -
587F MET* 3.5 27.9 - - + +
610F LEU* 4.1 26.2 - - + -
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Residues in contact with TYR 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F LEU* 3.5 20.1 - - + +
264F PRO 3.0 28.1 + - - -
265F PRO* 4.2 1.7 - - - +
266F ALA* 3.8 19.2 + - + +
269F PHE* 3.7 25.1 - + - -
570F MET* 3.0 34.9 + - + +
573F LEU* 1.3 73.7 - - - +
575F ARG* 1.3 60.4 + - - +
576F GLU 3.3 0.2 - - - -
577F ALA* 3.4 6.0 + - + +
578F ALA* 3.2 18.5 + - - +
682F TRP* 3.3 31.2 - + + -
704F PRO* 4.2 6.0 - - + +
705F ALA 4.3 0.2 - - - -
706F ALA 3.3 26.6 + - - -
708F GLY* 3.9 18.2 - - - -
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Residues in contact with ARG 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571F PRO 3.8 11.2 - - - +
572F TYR* 3.1 12.6 + - + +
573F LEU 3.1 1.0 - - - -
574F TYR* 1.3 77.0 - - - +
576F GLU* 1.3 73.5 + - - +
578F ALA* 3.3 15.7 + - - +
579F ARG* 2.7 46.0 + - - +
702F GLU* 3.5 47.8 + - + +
704F PRO* 3.9 21.2 - - + +
708F GLY 4.7 4.5 - - - -
710F VAL* 3.8 21.3 - - - +
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Residues in contact with GLU 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572F TYR* 3.4 34.7 - - + +
573F LEU* 2.9 10.4 + - + +
575F ARG* 1.3 86.6 - - - +
577F ALA* 1.3 61.2 + - - +
579F ARG* 3.1 27.7 + - - +
580F ALA* 3.3 5.4 + - - +
585F THR 4.5 1.9 - - - +
587F MET* 4.0 19.2 - - + +
589F ARG* 3.3 9.9 + - - +
611F GLY* 3.8 17.9 - - - -
612F ASP* 2.6 48.2 + - - +
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Residues in contact with ALA 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F LEU* 3.8 15.9 - - + +
269F PHE* 4.0 12.8 - - + -
507F PHE* 3.6 30.8 - - + -
573F LEU 3.0 10.1 + - - +
574F TYR* 3.4 17.0 - - + +
576F GLU* 1.3 74.6 - - - +
578F ALA* 1.3 63.7 + - - +
579F ARG 3.0 1.8 - - - -
580F ALA* 3.0 16.2 + - - +
581F ASN* 3.2 10.0 + - - +
587F MET* 4.0 5.6 - - - +
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Residues in contact with ALA 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F LEU* 4.1 9.8 - - + +
574F TYR 3.2 8.3 + - - +
575F ARG* 3.3 17.4 + - - +
577F ALA* 1.3 79.0 - - - +
579F ARG* 1.3 57.6 + - - +
580F ALA 3.3 0.2 - - - -
581F ASN* 3.3 11.9 + - - +
582F ALA* 3.0 29.1 + - - +
708F GLY* 3.5 32.8 - - - +
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Residues in contact with ARG 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575F ARG* 2.7 49.1 + - - +
576F GLU* 3.1 35.2 + - - +
577F ALA 3.0 0.4 - - - -
578F ALA* 1.3 77.3 - - - +
580F ALA* 1.3 58.9 + - - +
582F ALA* 4.8 3.1 - - - -
583F ARG* 2.8 40.7 + - + +
584F GLY 3.5 2.4 + - - -
585F THR* 3.8 10.2 + - - +
589F ARG* 3.9 12.3 - - - +
612F ASP* 2.8 30.0 + - - -
702F GLU* 4.4 9.4 + - - -
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Residues in contact with ALA 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PRO* 3.6 11.4 - - + +
506F GLY* 4.0 19.3 - - - +
507F PHE* 3.8 19.3 - - + -
576F GLU 3.3 5.3 + - - +
577F ALA* 3.0 10.6 + - - +
579F ARG* 1.3 78.2 - - - +
581F ASN* 1.3 58.3 + - - +
584F GLY* 2.8 26.9 + - - -
585F THR 3.0 28.0 + - - +
586F PRO* 4.5 0.2 - - + -
587F MET 4.8 1.1 - - - +
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Residues in contact with ASN 581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F ARG* 3.6 23.6 + - - +
261F PRO* 2.9 27.7 + - - +
262F ALA* 3.6 4.9 - - - +
263F LEU* 3.6 34.6 - - + +
507F PHE* 5.1 0.4 - - - -
577F ALA 3.2 7.9 + - - +
578F ALA* 3.5 11.6 - - - +
579F ARG 3.2 0.2 - - - -
580F ALA* 1.3 81.2 - - - +
582F ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F ARG* 3.2 23.5 + - - +
578F ALA 3.0 16.8 + - - +
579F ARG* 4.2 2.9 - - - +
581F ASN* 1.3 83.1 - - - +
583F ARG* 1.3 68.7 + - + +
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Residues in contact with ARG 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F LYS* 3.7 35.1 + - - +
249F ALA* 4.0 5.1 - - - +
251F LEU 3.7 0.2 - - - -
252F ASP* 2.7 49.6 + - - +
260F ARG* 3.5 11.7 - - - +
579F ARG* 2.8 21.5 + - + +
582F ALA* 1.3 82.2 - - + +
584F GLY* 1.3 63.7 + - - +
585F THR* 3.4 14.3 + - - +
3003F SO4 2.8 42.4 + - - -
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Residues in contact with GLY 584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F LEU* 4.1 14.0 - - - +
255F THR* 3.5 28.6 + - - +
260F ARG* 4.0 0.6 - - - +
261F PRO* 4.3 4.6 - - - +
504F GLY* 5.0 7.3 - - - -
506F GLY* 5.4 1.3 - - - -
580F ALA* 2.8 19.9 + - - -
581F ASN 4.7 0.2 - - - -
582F ALA 3.8 0.4 - - - -
583F ARG* 1.3 78.9 - - - +
585F THR* 1.3 62.9 + - - +
586F PRO* 3.2 10.7 - - - +
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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
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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