Contacts of the helix formed by residues 486 - 502 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C TYR* 3.1 25.1 + - - +
485C ALA* 1.3 74.0 - - - +
487C TYR* 1.3 58.4 + - - +
488C GLU* 3.2 17.5 - - - +
489C SER* 2.8 34.8 + - - -
490C MET 3.0 21.7 + - - -
517C ASN* 5.6 2.0 + - - -
523C VAL* 4.2 13.2 - - - -
527C TRP* 3.6 7.4 - - - -
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Residues in contact with TYR 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.6 16.2 - - + +
486C ASN* 1.3 71.6 - - - +
488C GLU* 1.3 73.6 + - - +
490C MET* 3.1 16.6 + - + +
491C ALA* 3.0 19.9 + - - +
522C HIS* 2.8 41.5 + + - +
523C VAL* 3.4 31.3 + - + +
526C ARG* 3.5 28.6 - - + +
620C PHE* 3.3 35.7 - - + +
621C THR* 3.7 11.9 - - - -
622C GLU* 3.8 12.8 - - + -
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Residues in contact with GLU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU 3.8 21.3 - - - +
157B GLY* 4.3 13.9 - - - -
158B VAL* 3.9 13.0 + - - +
226B SER* 4.3 19.6 - - - +
486C ASN* 3.2 19.4 - - - +
487C TYR* 1.3 85.3 + - - +
489C SER* 1.3 56.6 + - - +
491C ALA* 3.4 3.3 + - - +
492C GLU* 3.0 30.0 + - - +
495C ARG* 5.3 0.9 + - - -
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Residues in contact with SER 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C SER* 5.5 0.2 - - - -
483C CYS* 3.4 6.2 - - - +
484C TYR* 2.9 48.9 + - - -
486C ASN* 2.8 17.3 + - - -
488C GLU* 1.3 75.3 - - - +
490C MET* 1.3 62.9 + - - +
491C ALA 3.3 0.2 - - - -
492C GLU* 3.2 24.8 + - - +
493C SER* 2.8 30.1 + - - -
527C TRP* 4.2 1.3 - - - -
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Residues in contact with MET 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C ASN 3.0 13.1 + - - +
487C TYR* 3.1 19.3 + - + +
489C SER* 1.3 76.9 - - - +
491C ALA* 1.3 63.2 + - - +
493C SER* 3.3 5.7 + - - -
494C LEU* 3.1 19.4 + - - +
523C VAL 4.7 0.9 - - - +
526C ARG* 4.2 8.5 - - + -
527C TRP* 3.6 60.3 - - + +
530C PHE* 3.7 19.3 - - + -
618C PRO* 4.3 9.9 - - + -
619C VAL 3.2 27.4 - - - +
620C PHE* 3.3 28.5 - - + -
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Residues in contact with ALA 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 4.1 21.1 - - + -
487C TYR 3.0 11.1 + - - +
488C GLU* 3.5 8.5 - - - +
490C MET* 1.3 75.2 - - - +
492C GLU* 1.3 58.1 + - - +
494C LEU* 2.7 26.5 + - - +
495C ARG* 3.0 26.0 + - + +
605C ASP 5.2 0.2 - - - +
606C ARG* 5.5 5.2 - - + -
620C PHE* 3.4 23.5 - - + -
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Residues in contact with GLU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 3.3 16.6 - - + +
226B SER* 4.5 7.8 + - - -
169C PHE* 3.4 14.6 - - - +
188C THR* 2.9 42.0 + - - +
189C SER* 3.1 16.8 + - - -
488C GLU 3.0 10.6 + - - +
489C SER* 3.2 32.9 + - - +
491C ALA* 1.3 78.7 - - - +
493C SER* 1.3 65.3 + - - +
495C ARG* 3.4 34.3 + - - +
496C GLY 3.2 16.1 + - - -
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PHE* 4.4 9.4 - - - -
188C THR* 4.5 3.3 + - - +
480C GLY* 5.4 2.4 + - - -
483C CYS* 3.5 25.6 - - - +
489C SER 2.8 22.0 + - - -
490C MET* 3.4 7.4 - - - -
491C ALA 3.0 0.8 - - - -
492C GLU* 1.3 77.6 - - - +
494C LEU* 1.3 64.6 + - - +
496C GLY* 3.2 1.7 + - - -
497C GLY 3.0 8.3 + - - -
508C TRP* 2.8 33.4 - - - -
510C HIS* 5.1 5.6 - - - -
527C TRP* 4.4 6.9 - - - -
530C PHE* 5.1 3.1 - - - -
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C MET 3.1 7.9 + - - +
491C ALA* 2.7 20.5 + - - +
493C SER* 1.3 69.6 - - - +
495C ARG* 1.3 55.8 + - - -
497C GLY* 3.1 1.7 + - - -
498C LEU* 2.8 36.5 + - + +
508C TRP* 4.3 1.1 - - - -
530C PHE* 3.5 36.5 - - + -
588C MET* 4.0 13.0 - - - -
605C ASP 3.3 24.2 - - - +
606C ARG* 3.8 22.2 - - - +
607C GLN 4.2 1.8 - - - +
608C TYR* 3.9 21.5 - - + -
618C PRO* 4.7 3.4 - - + -
620C PHE* 4.1 13.5 - - + -
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Residues in contact with ARG 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 3.8 20.0 + - - +
226B SER* 5.8 1.0 - - - +
168C ARG 3.9 4.0 - - - +
169C PHE 2.8 20.0 + - - +
170C THR 3.2 27.6 + - - +
171C ALA* 4.4 4.5 - - - +
172C LEU* 4.1 15.2 - - + +
488C GLU 5.3 1.0 + - - -
491C ALA* 3.0 18.9 + - + +
492C GLU* 3.4 32.2 - - - +
493C SER 3.3 0.2 - - - -
494C LEU* 1.3 76.6 - - - +
496C GLY* 1.3 58.9 + - - +
498C LEU* 3.4 9.2 + - - +
499C SER* 2.8 34.5 + - - +
605C ASP* 3.3 37.4 + - + +
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Residues in contact with GLY 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 4.0 11.0 - - - +
168C ARG 3.2 18.5 + - - -
169C PHE* 3.9 17.5 - - - -
492C GLU 3.2 10.5 + - - -
493C SER 3.2 4.0 + - - -
494C LEU 3.1 0.6 - - - -
495C ARG* 1.3 78.6 - - - +
497C GLY* 1.3 56.5 + - - +
499C SER* 3.3 2.8 + - - -
500C ILE* 2.9 30.0 + - - +
508C TRP* 4.5 1.1 - - - -
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Residues in contact with GLY 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C SER 3.0 11.1 + - - -
494C LEU 3.1 2.6 + - - -
496C GLY* 1.3 72.4 - - - +
498C LEU* 1.3 66.6 + - - +
500C ILE* 3.2 18.2 - - - +
501C GLY* 3.3 4.2 + - - -
508C TRP* 3.4 42.6 - - - +
588C MET* 4.6 9.5 - - - +
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Residues in contact with LEU 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 4.0 14.4 - - + -
494C LEU* 2.8 26.8 + - + +
495C ARG* 3.7 3.4 - - - +
497C GLY* 1.3 73.9 - - - +
499C SER* 1.3 64.4 + - - +
501C GLY* 3.2 12.0 + - - -
502C LEU* 3.2 18.3 + - - +
588C MET* 4.1 16.2 - - + +
589C ARG* 3.9 2.2 - - - -
590C ALA* 3.7 27.5 + - + +
593C MET* 5.3 1.4 - - - +
604C LEU 4.4 4.3 - - - +
605C ASP* 3.6 39.7 - - + +
607C GLN 3.9 9.2 - - - +
608C TYR* 3.7 26.7 - - + -
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Residues in contact with SER 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLY* 4.3 3.5 + - - -
166C GLY 3.4 18.4 - - - -
168C ARG 3.8 9.2 + - - -
172C LEU* 3.5 13.2 - - - +
174C ARG* 3.3 24.7 + - - -
495C ARG 2.8 23.0 + - - -
496C GLY 3.5 4.0 - - - -
498C LEU* 1.3 77.2 - - - +
500C ILE* 1.3 63.3 + - - +
502C LEU* 3.0 24.1 + - - +
503C SER* 3.1 14.2 + - - -
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Residues in contact with ILE 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLY 4.1 4.2 + - - -
167C GLU* 3.9 21.5 - - + +
195C LYS* 3.6 31.9 - - + -
478C HIS* 4.2 13.2 - - + -
496C GLY 2.9 13.3 + - - +
497C GLY 3.2 15.0 - - - +
499C SER* 1.3 77.6 - - - +
501C GLY* 1.3 62.9 + - - +
503C SER* 2.9 20.9 + - - -
505C PHE* 3.3 53.7 + - + +
507C PHE 5.5 0.2 - - - +
508C TRP* 4.1 22.2 - - + -
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Residues in contact with GLY 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LEU* 3.7 10.0 - - - +
497C GLY 3.3 3.4 + - - -
498C LEU 3.2 8.2 + - - -
500C ILE* 1.3 79.4 - - - +
502C LEU* 1.3 57.5 + - - +
503C SER 3.0 9.4 + - - -
504C GLY* 3.5 9.2 + - - -
505C PHE 3.3 18.5 + - - +
584C GLY 5.0 0.3 - - - +
586C PRO* 3.7 31.2 - - - +
588C MET 4.8 2.7 - - - -
593C MET* 4.6 1.1 - - - -
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Residues in contact with LEU 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TYR* 3.7 31.9 - - + -
164C GLY* 4.1 14.3 - - - +
172C LEU* 4.4 7.4 - - + -
199C PHE* 3.7 18.2 - - - -
201C MET* 4.1 32.3 - - + +
251C LEU* 4.2 7.6 - - - +
498C LEU 3.2 20.2 + - - +
499C SER* 3.0 14.2 + - - +
501C GLY* 1.3 74.3 - - - +
503C SER* 1.3 61.0 + - - +
504C GLY 3.7 0.7 - - - -
590C ALA* 4.2 15.7 - - + -
592C MET* 4.2 14.6 - - - -
593C MET* 3.6 24.2 - - + -
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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