Contacts of the helix formed by residues 486 - 502 (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 ASN 486 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484F TYR* 3.2 26.1 + - - +
485F ALA* 1.3 76.3 - - - +
487F TYR* 1.3 64.2 + - - +
488F GLU* 3.1 18.2 - - - +
489F SER* 2.8 34.4 + - - -
490F MET 3.1 16.8 + - - -
517F ASN* 6.1 0.8 - - - +
523F VAL* 4.3 13.5 - - - -
527F TRP* 3.7 7.4 - - - -
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Residues in contact with TYR 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E VAL* 3.8 12.0 - - + +
486F ASN* 1.3 71.5 - - - +
488F GLU* 1.3 71.7 + - - +
490F MET* 3.0 32.2 + - + +
491F ALA* 2.9 23.4 + - - +
522F HIS* 2.6 46.2 + + - +
523F VAL* 3.4 30.5 + - + +
526F ARG* 3.5 11.5 - - + +
620F PHE* 3.2 25.8 - - + +
621F THR* 3.4 31.3 + - - -
622F GLU* 3.8 1.1 - - + -
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Residues in contact with GLU 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E ASP* 6.5 0.4 - - + -
156E LEU 3.6 22.9 - - - +
157E GLY* 4.0 17.2 - - - -
158E VAL* 3.8 14.9 + - - +
226E SER* 4.2 20.2 - - - +
486F ASN* 3.1 19.3 - - - +
487F TYR* 1.3 84.2 + - - +
489F SER* 1.3 57.5 + - - +
491F ALA* 3.3 4.8 + - - +
492F GLU* 2.8 31.8 + - - +
495F ARG* 5.1 0.3 + - - -
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Residues in contact with SER 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F THR* 4.3 0.3 + - - -
189F SER* 5.2 0.8 + - - -
483F CYS* 3.3 10.6 - - - +
484F TYR* 3.0 46.1 + - - -
486F ASN* 2.8 19.5 + - - -
488F GLU* 1.3 74.4 - - - +
490F MET* 1.3 65.0 + - - +
492F GLU* 3.2 22.5 + - - +
493F SER* 2.9 27.1 + - - -
527F TRP* 4.3 0.9 - - - -
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Residues in contact with MET 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486F ASN 3.1 12.6 + - - +
487F TYR* 3.0 34.4 + - + +
489F SER* 1.3 77.2 - - - +
491F ALA* 1.3 63.1 + - - +
493F SER* 3.3 4.0 + - - -
494F LEU* 3.3 19.1 + - - +
523F VAL 4.6 0.4 - - - +
526F ARG* 4.2 3.8 - - + +
527F TRP* 3.6 60.3 - - + -
530F PHE* 3.9 22.0 - - + -
618F PRO* 5.6 1.3 - - + -
619F VAL 3.6 15.0 - - - +
620F PHE* 3.2 32.3 - - + -
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Residues in contact with ALA 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E VAL* 4.0 23.3 - - + -
487F TYR 2.9 12.1 + - - +
488F GLU* 3.3 10.3 - - - +
490F MET* 1.3 76.7 - - - +
492F GLU* 1.3 63.7 + - - +
494F LEU* 3.2 13.4 + - - +
495F ARG* 3.3 27.1 + - - +
605F ASP 5.2 0.7 - - - +
606F ARG* 5.7 3.6 - - + -
620F PHE* 3.6 21.7 - - + -
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Residues in contact with GLU 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E VAL* 3.3 16.3 - - + +
226E SER* 3.1 28.3 + - - -
169F PHE* 3.8 11.4 - - + +
188F THR* 3.1 28.1 + - - +
189F SER* 3.3 17.5 + - - -
488F GLU* 2.8 21.7 + - - +
489F SER* 3.2 23.3 + - - +
491F ALA* 1.3 76.1 - - - +
493F SER* 1.3 63.1 + - - +
495F ARG* 3.2 36.9 + - - +
496F GLY 3.2 15.1 + - - -
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Residues in contact with SER 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F PHE* 4.4 10.8 - - - -
188F THR* 4.8 3.0 + - - +
480F GLY* 6.0 2.0 - - - -
483F CYS* 3.8 23.7 - - - +
489F SER 2.9 16.1 + - - -
490F MET* 3.6 7.4 + - - -
491F ALA 3.2 0.2 - - - -
492F GLU* 1.3 72.8 - - - +
494F LEU* 1.3 67.5 + - - +
496F GLY* 3.0 3.4 + - - +
497F GLY 2.8 19.9 + - - -
508F TRP* 3.2 23.4 - - - -
510F HIS* 5.0 5.4 - - - -
527F TRP* 4.2 7.2 - - - -
530F PHE* 5.0 3.4 - - - -
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Residues in contact with LEU 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490F MET 3.3 6.8 + - - +
491F ALA* 3.2 12.2 + - - +
493F SER* 1.3 76.9 - - - +
495F ARG* 1.3 58.3 + - - +
497F GLY* 3.0 2.3 + - - +
498F LEU* 2.8 41.9 + - + +
508F TRP* 4.3 1.3 - - - -
530F PHE* 3.8 27.3 - - + -
588F MET* 3.9 14.4 - - - -
605F ASP 3.3 23.6 - - - +
606F ARG* 3.7 23.1 - - - +
607F GLN 4.1 2.7 - - - +
608F TYR* 3.8 25.8 - - + -
618F PRO* 4.5 6.3 - - + -
620F PHE* 4.2 13.5 - - + -
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Residues in contact with ARG 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E VAL* 3.9 15.2 + - - +
226E SER* 5.9 0.4 - - - +
168F ARG 3.8 3.4 - - - +
169F PHE 2.8 26.4 + - - +
170F THR 3.3 21.8 + - - +
171F ALA* 4.3 4.0 - - - +
172F LEU* 4.0 17.8 - - + +
488F GLU 5.1 0.2 + - - -
491F ALA* 3.5 18.2 + - - +
492F GLU* 3.2 41.0 + - - +
493F SER 3.2 0.6 - - - -
494F LEU* 1.3 76.2 - - - +
496F GLY* 1.3 58.1 + - - +
498F LEU* 3.3 9.3 + - - +
499F SER* 2.8 34.4 + - - +
605F ASP* 3.6 35.5 + - + +
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Residues in contact with GLY 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU* 3.9 11.8 - - - +
168F ARG 3.1 22.6 + - - -
169F PHE* 4.1 13.9 - - - -
492F GLU 3.2 4.9 + - - -
493F SER 3.0 7.5 + - - -
495F ARG* 1.3 80.4 - - - +
497F GLY* 1.3 56.2 + - - +
499F SER* 3.2 2.4 + - - -
500F ILE* 2.8 30.3 + - - +
508F TRP* 4.7 0.9 - - - -
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Residues in contact with GLY 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493F SER 2.8 14.6 + - - -
494F LEU 3.5 2.7 - - - -
496F GLY* 1.3 72.5 - - - +
498F LEU* 1.3 63.1 + - - +
500F ILE* 3.0 19.4 - - - +
501F GLY* 3.1 5.4 + - - -
508F TRP* 3.4 41.4 - - - +
588F MET* 4.5 10.3 - - - +
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Residues in contact with LEU 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F LEU* 4.2 14.6 - - + -
494F LEU* 2.8 29.6 + - + +
495F ARG* 3.7 5.4 - - - +
497F GLY* 1.3 70.8 - - - -
499F SER* 1.3 64.5 + - - +
501F GLY* 3.1 4.0 + - - -
502F LEU* 3.0 27.0 + - - +
588F MET* 3.7 31.0 - - + +
589F ARG 4.0 16.4 - - - -
590F ALA* 4.0 10.1 + - + +
593F MET* 5.5 0.9 - - - +
604F LEU 4.5 4.9 - - - +
605F ASP* 4.0 29.8 - - - +
607F GLN 4.0 14.6 - - - +
608F TYR* 3.7 15.3 - - + -
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Residues in contact with SER 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F GLY* 4.3 2.8 - - - -
166F GLY 3.5 17.9 - - - -
168F ARG 3.7 8.2 + - - -
172F LEU* 3.5 13.4 - - - +
174F ARG* 3.3 26.2 + - - -
495F ARG 2.8 26.3 + - - -
496F GLY 3.2 4.2 + - - -
498F LEU* 1.3 75.1 - - - +
500F ILE* 1.3 61.9 + - - +
502F LEU* 3.1 20.6 + - - +
503F SER* 3.0 18.0 + - - -
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Residues in contact with ILE 500 (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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166F GLY 4.2 0.6 + - - -
167F GLU* 3.9 22.9 - - + +
195F LYS* 3.6 32.3 - - + -
478F HIS* 4.1 13.5 - - + -
496F GLY 2.8 12.6 + - - +
497F GLY 3.0 17.7 - - - +
498F LEU 3.2 0.2 - - - -
499F SER* 1.3 76.7 - - - +
501F GLY* 1.3 63.4 + - - +
503F SER* 2.9 21.5 + - - -
505F PHE* 3.3 52.2 + - + +
507F PHE 5.5 0.4 - - - +
508F TRP* 3.9 24.5 - - + -
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Residues in contact with GLY 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F LEU* 3.8 13.0 - - - +
497F GLY 3.1 3.7 + - - -
498F LEU 3.1 7.7 + - - -
500F ILE* 1.3 84.0 - - - +
502F LEU* 1.3 57.5 + - - +
503F SER 3.0 4.9 + - - -
504F GLY* 3.3 9.9 + - - -
505F PHE 3.3 19.6 + - - -
586F PRO* 3.7 25.1 - - - +
588F MET 4.8 3.4 - - - -
593F MET* 4.8 0.4 - - - -
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Residues in contact with LEU 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F TYR* 3.9 28.7 - - + -
164F GLY* 4.3 12.8 - - - +
172F LEU* 4.2 10.1 - - + -
199F PHE* 3.5 18.7 - - - -
201F MET* 3.4 36.8 - - + +
251F LEU* 3.9 11.1 - - - +
498F LEU 3.0 23.9 + - - +
499F SER* 3.1 10.7 + - - +
501F GLY* 1.3 74.1 - - - +
503F SER* 1.3 57.5 + - - +
504F GLY 3.6 0.7 - - - -
590F ALA* 4.0 17.9 - - + -
592F MET* 4.0 17.0 - - - -
593F MET* 4.2 17.5 - - + -
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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