Contacts of the helix formed by residues 486 - 502 (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 ASN 486 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D TYR* 3.2 25.3 + - - +
485D ALA* 1.3 76.5 - - - +
487D TYR* 1.3 58.3 + - - +
488D GLU* 3.1 18.1 - - - +
489D SER* 2.8 32.9 + - - -
490D MET 3.0 20.3 + - - -
517D ASN* 5.1 5.7 - - - +
523D VAL* 4.1 14.3 - - - +
527D TRP* 3.6 8.5 - - - -
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Residues in contact with TYR 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.9 10.3 - - + -
486D ASN* 1.3 71.9 - - - +
488D GLU* 1.3 74.2 + - - +
489D SER 3.1 1.6 - - - -
490D MET* 2.8 38.2 + - + +
491D ALA* 2.9 13.9 + - - +
522D HIS* 2.8 39.4 + + - +
523D VAL* 3.4 32.8 + - + -
526D ARG* 3.5 20.9 - - + +
620D PHE* 3.2 29.8 - - + +
621D THR* 3.7 12.4 + - - -
622D GLU* 3.7 17.4 - - + -
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Residues in contact with GLU 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU 3.6 21.9 - - - +
157A GLY* 4.1 16.2 - - - -
158A VAL* 4.0 13.8 + - - +
226A SER* 4.1 19.7 - - - +
486D ASN* 3.1 19.5 - - - +
487D TYR* 1.3 82.4 + - - +
489D SER* 1.3 57.3 + - - +
491D ALA* 3.3 5.3 + - - +
492D GLU* 3.0 32.4 + - - +
495D ARG* 5.1 0.3 + - - -
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Residues in contact with SER 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D THR* 4.8 1.9 + - - -
189D SER* 5.0 0.6 + - - -
483D CYS* 3.7 7.3 - - - +
484D TYR* 3.0 43.3 + - - +
486D ASN* 2.8 24.4 + - - -
488D GLU* 1.3 76.7 - - - +
490D MET* 1.3 63.0 + - - +
492D GLU* 3.6 21.2 + - - +
493D SER* 3.2 22.2 + - - -
527D TRP* 4.0 2.2 - - - -
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Residues in contact with MET 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D ASN 3.0 7.5 + - - +
487D TYR* 2.8 31.7 + - + +
489D SER* 1.3 77.5 - - - +
491D ALA* 1.3 61.8 + - - +
493D SER* 3.3 5.4 - - - -
494D LEU* 3.2 17.2 + - - +
523D VAL 4.9 0.2 - - - +
526D ARG* 4.3 4.3 - - + +
527D TRP* 3.5 66.2 - - + -
530D PHE* 3.8 25.7 - - + -
618D PRO* 5.3 1.6 - - + -
619D VAL 3.6 14.8 - - - +
620D PHE* 3.3 30.3 - - + -
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Residues in contact with ALA 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.2 17.7 - - + -
487D TYR 2.9 9.1 + - - +
488D GLU* 3.5 8.7 - - - +
490D MET* 1.3 74.7 - - - +
492D GLU* 1.3 66.0 + - - +
493D SER 3.0 1.3 - - - -
494D LEU* 3.0 5.4 + - - +
495D ARG* 3.0 38.5 + - + +
605D ASP 5.3 0.3 - - - +
606D ARG* 5.8 3.8 - - + -
620D PHE* 3.5 26.4 - - + -
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Residues in contact with GLU 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 3.0 27.7 - - + +
226A SER* 2.9 31.0 + - - -
169D PHE* 3.4 14.0 - - + +
188D THR* 3.2 23.5 + - - +
189D SER* 3.4 15.6 + - - -
488D GLU* 3.0 26.2 + - - +
489D SER* 3.6 19.9 + - - +
490D MET 3.4 0.2 - - - -
491D ALA* 1.3 76.5 - - - +
493D SER* 1.3 61.8 + - - +
495D ARG* 3.4 25.3 - - - +
496D GLY 3.2 16.6 + - - -
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Residues in contact with SER 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D PHE* 4.5 9.6 - - - -
188D THR* 5.5 3.5 + - - -
480D GLY* 5.7 1.9 + - - -
483D CYS* 4.8 10.8 - - - +
489D SER 3.2 12.2 + - - -
490D MET* 3.3 12.6 - - - -
491D ALA 3.0 0.4 - - - -
492D GLU* 1.3 78.5 - - - +
494D LEU* 1.3 64.3 + - - +
496D GLY* 3.3 2.0 + - - +
497D GLY 3.1 17.0 + - - -
508D TRP* 3.1 26.7 - - - -
510D HIS* 4.3 12.5 + - - +
527D TRP* 4.6 10.2 - - - -
530D PHE* 4.7 1.3 - - - -
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Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D MET 3.2 9.4 + - - +
491D ALA* 3.0 9.2 + - - +
493D SER* 1.3 73.2 - - - +
495D ARG* 1.3 60.9 + - - +
497D GLY* 3.0 2.8 + - - -
498D LEU* 2.8 36.7 + - + +
508D TRP* 4.5 1.3 - - - -
530D PHE* 3.8 23.1 - - + -
588D MET* 3.8 19.3 - - - -
605D ASP 3.5 23.6 - - - +
606D ARG* 3.8 22.0 - - - +
607D GLN 4.2 0.4 - - - +
608D TYR* 3.7 32.1 - - + -
618D PRO* 4.7 3.1 - - + -
620D PHE* 4.1 14.1 - - + -
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Residues in contact with ARG 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 3.9 15.0 + - - +
226A SER* 5.8 0.4 - - - +
168D ARG 3.8 3.4 - - - +
169D PHE 2.7 22.1 + - - +
170D THR 3.1 28.7 + - - +
171D ALA* 4.4 4.0 - - - +
172D LEU* 3.9 16.9 - - + +
488D GLU 5.1 0.2 + - - -
491D ALA* 3.0 21.4 + - + +
492D GLU* 3.4 38.9 - - - +
494D LEU* 1.3 77.3 - - - +
496D GLY* 1.3 57.0 + - - +
498D LEU* 3.8 9.0 - - - +
499D SER* 2.9 32.6 + - - +
605D ASP* 3.6 35.9 + - + +
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Residues in contact with GLY 496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D GLU* 3.8 11.7 - - - +
168D ARG 3.0 19.9 + - - -
169D PHE* 4.0 15.5 - - - -
492D GLU 3.2 7.7 + - - -
493D SER 3.3 3.7 + - - -
494D LEU 3.1 0.8 - - - -
495D ARG* 1.3 79.1 - - - +
497D GLY* 1.3 62.8 + - - +
499D SER* 3.3 3.0 + - - -
500D ILE* 3.0 24.8 + - - +
508D TRP* 4.7 0.4 - - - -
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Residues in contact with GLY 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D SER 3.1 7.3 + - - -
494D LEU 3.0 6.7 + - - -
496D GLY* 1.3 73.5 - - - +
498D LEU* 1.3 65.8 + - - +
500D ILE* 3.2 19.0 - - - +
501D GLY* 3.4 3.6 + - - -
508D TRP* 3.4 41.6 - - - +
588D MET* 4.7 10.4 - - - +
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Residues in contact with LEU 498 (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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172D LEU* 4.0 16.6 - - + -
494D LEU* 2.8 26.2 + - + +
495D ARG* 3.8 5.6 - - - +
497D GLY* 1.3 75.8 - - - +
499D SER* 1.3 64.6 + - - +
501D GLY* 3.1 13.0 + - - -
502D LEU* 3.1 17.3 + - - +
588D MET* 3.7 21.9 - - + +
590D ALA* 3.9 26.6 + - + +
593D MET* 5.7 0.2 - - - +
604D LEU 4.5 1.3 - - - +
605D ASP* 3.7 32.3 - - - +
607D GLN 4.0 13.2 - - - +
608D TYR* 3.7 24.5 - - + -
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Residues in contact with SER 499 (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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164D GLY* 4.2 3.4 + - - -
166D GLY 3.3 17.4 - - - +
168D ARG 3.9 11.4 + - - -
172D LEU* 3.5 12.1 - - - +
174D ARG* 3.3 23.2 + - - -
495D ARG 2.9 19.8 + - - -
496D GLY 3.4 4.9 - - - -
498D LEU* 1.3 77.9 - - - +
500D ILE* 1.3 61.1 + - - +
502D LEU* 3.2 19.6 + - - +
503D SER* 2.9 20.4 + - - -
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Residues in contact with ILE 500 (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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166D GLY* 4.0 3.8 + - - -
167D GLU* 4.0 18.8 - - + +
195D LYS* 3.5 31.9 - - + -
197D ILE* 6.3 0.2 - - + -
478D HIS* 4.0 14.8 - - + -
496D GLY 3.0 10.3 + - - +
497D GLY 3.2 18.2 - - - +
499D SER* 1.3 74.0 - - - +
501D GLY* 1.3 70.5 + - - +
503D SER* 3.0 15.0 + - - -
505D PHE* 3.0 56.8 + - + +
507D PHE 5.4 0.9 - - - +
508D TRP* 4.0 23.8 - - + -
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Residues in contact with GLY 501 (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* 3.6 15.6 - - - +
497D GLY 3.4 3.4 + - - -
498D LEU 3.1 8.0 + - - -
500D ILE* 1.3 79.6 - - - +
502D LEU* 1.3 57.7 + - - +
503D SER 2.9 9.5 + - - -
504D GLY* 3.3 10.0 + - - -
505D PHE 3.2 20.6 + - - +
586D PRO* 3.8 23.0 - - - +
588D MET 4.9 2.0 - - - -
593D MET* 4.6 0.4 - - - -
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Residues in contact with LEU 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D TYR* 3.8 30.7 - - + -
164D GLY* 4.0 15.1 - - - +
172D LEU* 4.3 8.5 - - + -
199D PHE* 3.7 17.7 - - - -
201D MET* 4.0 27.9 - - + +
251D LEU* 4.2 5.2 - - - -
498D LEU 3.1 23.0 + - - +
499D SER* 3.2 15.2 + - - +
501D GLY* 1.3 75.1 - - - +
503D SER* 1.3 58.5 + - - +
504D GLY 3.6 0.7 - - - -
590D ALA* 4.2 17.0 - - + -
592D MET* 4.1 15.0 - - - -
593D MET* 3.4 27.8 - - + -
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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