Contacts of the helix formed by residues 499 - 520 (chain A) in PDB entry 6XYY
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 ARG 499 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A SER* 3.7 19.0 + - - +
498A TYR* 1.3 74.7 - - - +
500A PRO* 1.3 71.9 - - + +
501A VAL* 3.6 36.6 - - + +
502A GLU* 2.7 45.3 + - - +
503A ARG* 2.9 11.3 + - - +
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Residues in contact with PRO 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR 3.8 3.1 - - - +
499A ARG* 1.3 94.7 - - + +
501A VAL* 1.3 60.9 + - + +
503A ARG* 3.3 14.0 + - + +
504A GLU* 3.0 23.2 + - - +
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A HIS* 5.5 1.1 - - + +
499A ARG* 3.6 44.2 - - + +
500A PRO* 1.3 78.8 - - + +
502A GLU* 1.3 64.5 + - + +
504A GLU* 3.2 8.6 + - - +
505A LEU* 2.9 27.5 + - - +
544A THR* 3.0 35.9 + - + +
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Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A HIS* 2.8 32.0 + - + +
467A THR* 3.5 1.7 - - - -
468A SER* 2.7 49.7 + - - -
486A TYR* 3.2 21.9 - - - +
491A PRO* 3.6 7.6 - - - +
498A TYR* 3.8 16.0 - - + -
499A ARG* 2.7 38.7 + - + +
501A VAL* 1.3 72.8 - - + +
503A ARG* 1.3 59.2 + - - +
505A LEU* 3.2 4.0 + - - +
506A GLY 2.8 26.0 + - - -
544A THR* 4.9 0.2 - - - -
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Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PRO* 2.9 35.8 + - - +
492A LEU* 3.9 10.6 - - + +
493A ASN 3.1 21.6 + - - -
494A ASN* 3.8 31.6 + - - +
496A LEU 3.0 21.6 + - - -
497A GLN* 4.4 1.2 - - - +
498A TYR* 3.5 32.4 + - + +
499A ARG 2.9 12.9 + - - +
500A PRO* 3.6 10.9 - - + +
502A GLU* 1.3 75.6 - - - +
504A GLU* 1.3 57.0 + - - +
506A GLY* 3.3 1.2 + - - -
507A LYS* 2.9 28.9 + - - +
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A PRO 3.0 13.6 + - - +
501A VAL* 3.4 11.4 - - - +
503A ARG* 1.3 76.7 - - - +
505A LEU* 1.3 57.6 + - - +
507A LYS* 3.1 20.0 + - - +
508A ARG* 2.9 44.5 + - - +
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Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A PHE* 4.2 5.4 - - + -
465A HIS* 3.8 36.8 - - + -
486A TYR* 4.2 5.4 - - + -
501A VAL 2.9 16.7 + - - +
502A GLU* 3.8 4.9 - - - +
504A GLU* 1.3 77.0 - - - +
506A GLY* 1.3 52.5 + - - +
508A ARG* 3.1 36.6 + - - +
509A MET* 2.7 51.2 + - + +
542A PHE* 3.9 16.2 - - + -
543A SER 3.6 26.7 - - - +
544A THR* 4.3 4.5 - - - +
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Residues in contact with GLY 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A TYR* 3.6 26.6 - - - +
489A GLY* 4.9 3.4 - - - -
491A PRO* 4.0 13.5 - - - -
492A LEU* 4.8 3.1 - - - -
502A GLU 2.8 14.8 + - - -
503A ARG 3.7 2.7 - - - -
505A LEU* 1.3 75.1 - - - +
507A LYS* 1.3 62.3 + - - +
510A LEU* 3.0 28.0 + - - +
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Residues in contact with LYS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 5.0 12.9 - - + +
492A LEU* 3.9 29.2 - - + +
503A ARG 2.9 17.5 + - - +
504A GLU* 3.5 20.0 - - - +
506A GLY* 1.3 72.2 - - - +
508A ARG* 1.3 55.3 + - - +
510A LEU* 4.0 4.1 - - + +
511A SER* 2.5 50.1 + - - -
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A GLU* 2.9 28.2 + - - +
505A LEU* 3.1 34.7 + - + +
507A LYS* 1.3 76.6 - - - +
509A MET* 1.3 63.4 + - - +
511A SER* 3.4 6.0 + - - -
512A ALA* 3.1 21.0 + - - +
524A GLN* 3.8 28.0 + - - +
527A GLU* 5.8 0.4 - - - -
540A TYR* 3.3 36.2 + - - -
541A ILE 4.8 2.8 + - - -
542A PHE* 4.2 10.9 - - + -
543A SER 3.3 24.4 + - - -
544A THR* 5.3 1.0 - - - +
550A LYS* 4.4 13.5 - - - +
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Residues in contact with MET 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A PHE* 3.4 43.1 - - + -
483A GLU* 4.1 4.0 - - + -
486A TYR* 3.5 28.7 - - + +
487A PHE* 3.3 56.6 - - + -
505A LEU* 2.7 33.1 + - + +
508A ARG* 1.3 70.7 - - - +
510A LEU* 1.3 66.5 + - - +
512A ALA* 3.2 12.8 + - - +
513A VAL* 3.3 8.8 + - - +
542A PHE* 3.6 28.9 - - + -
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Residues in contact with LEU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.4 5.2 - - + -
167A MET* 3.7 38.1 - - + +
170A VAL* 3.8 34.5 - - + -
486A TYR 3.9 1.0 + - - -
487A PHE 3.4 24.2 - - - +
488A PHE 4.2 3.4 - - - +
489A GLY* 4.2 11.7 - - - -
492A LEU* 4.1 17.0 - - + -
506A GLY 3.0 17.9 + - - +
507A LYS* 4.0 3.4 - - + +
509A MET* 1.3 77.2 - - - +
511A SER* 1.3 61.7 + - - +
513A VAL* 3.0 5.6 + - - +
514A ILE* 3.0 35.6 + - + +
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Residues in contact with SER 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A LYS* 2.5 43.1 + - - -
508A ARG* 3.8 7.0 - - - -
509A MET 3.3 0.2 - - - -
510A LEU* 1.3 74.4 - - - +
512A ALA* 1.3 60.7 + - - +
514A ILE* 4.4 7.9 - - - +
515A GLU* 2.9 39.2 + - - +
522A PRO 4.8 1.1 - - - -
524A GLN* 5.3 14.8 - - - -
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Residues in contact with ALA 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LEU* 4.9 5.2 - - + -
487A PHE* 4.8 4.3 - - + -
508A ARG 3.1 13.3 + - - +
509A MET 3.3 10.5 - - - +
511A SER* 1.3 75.7 - - - +
513A VAL* 1.3 62.0 + - - +
516A PHE* 3.0 25.8 + - - +
522A PRO* 3.6 30.5 - - + +
524A GLN* 6.2 0.4 - - - +
529A TRP* 4.4 4.3 - - + -
542A PHE* 4.1 22.9 - - + -
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Residues in contact with VAL 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.6 27.4 - - + -
167A MET* 3.7 18.6 - - + -
233A THR* 6.5 0.2 - - + -
235A PHE* 4.8 7.4 - - + -
261A MET* 3.8 22.9 - - + -
360A LEU* 5.1 2.5 - - + -
487A PHE* 3.7 38.4 - - + +
509A MET 3.3 2.2 + - - +
510A LEU 3.0 8.6 + - - +
512A ALA* 1.3 77.6 - - + +
514A ILE* 1.3 59.7 + - + +
516A PHE* 3.2 10.2 + - + +
517A ALA* 2.8 28.4 + - - +
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 5.0 2.2 - - + -
167A MET* 4.0 20.0 - - + -
170A VAL* 6.2 0.4 - - + -
171A GLY* 3.8 29.2 - - - +
173A VAL* 4.0 21.3 - - + -
510A LEU* 3.0 26.6 + - + +
511A SER* 4.1 6.1 - - - +
513A VAL* 1.3 78.0 - - + +
515A GLU* 1.3 60.3 + - + +
517A ALA* 3.2 6.5 + - - +
518A LYS* 2.8 64.4 + - + +
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Residues in contact with GLU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A SER* 2.9 24.0 + - - +
514A ILE* 1.3 79.7 - - + +
516A PHE* 1.3 58.0 + - - +
518A LYS* 4.2 15.1 - - - +
519A THR* 2.8 53.4 + - - +
521A ASN 3.4 11.9 - - - +
522A PRO 3.8 11.2 - - - +
523A ALA 4.3 13.3 - - - +
524A GLN* 5.1 8.7 - - + +
525A ASP* 5.6 2.6 - - - +
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Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A THR* 3.8 20.4 - - + -
259A ARG* 3.5 9.0 - - + -
260A GLY 3.3 38.4 - - - -
261A MET* 4.0 6.7 - - + -
358A ASP* 3.3 27.6 - - + -
359A ILE 3.8 2.2 - - - -
360A LEU* 3.6 36.1 - - + -
459A HIS* 6.2 0.2 - - - -
512A ALA 3.0 20.7 + - - +
513A VAL* 3.4 7.6 - - + +
515A GLU* 1.3 74.3 - - - +
517A ALA* 1.3 63.9 + - + +
520A GLY* 2.5 51.4 + - - -
521A ASN 3.6 8.7 + - - +
522A PRO* 4.1 11.0 - - + -
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Residues in contact with ALA 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.6 6.2 - - + +
144A LEU* 3.4 38.4 - - + -
173A VAL* 5.7 0.7 - - + -
231A TRP* 3.2 13.0 + - - +
233A THR* 3.5 23.4 + - + +
259A ARG* 3.0 18.2 + - - +
513A VAL 2.8 19.8 + - - +
514A ILE* 3.7 5.2 - - - +
516A PHE* 1.3 75.2 - - - +
518A LYS* 1.3 57.5 - - + +
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Residues in contact with LYS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.1 20.4 - - + -
171A GLY 2.7 29.7 + - - -
172A ASN* 4.4 6.6 + - - +
173A VAL* 4.1 8.5 - - + +
231A TRP* 3.2 34.5 + - + +
259A ARG* 3.7 2.6 + - - -
514A ILE* 2.8 36.0 + - + +
515A GLU* 3.8 15.0 - - - +
517A ALA* 1.3 78.8 - - - +
519A THR* 1.3 67.7 + - + +
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Residues in contact with THR 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG* 3.7 10.8 + - - +
358A ASP* 5.2 0.3 - - - +
515A GLU* 2.8 32.5 + - - +
518A LYS* 1.3 88.2 - - + +
520A GLY* 1.3 60.1 + - - +
521A ASN* 3.1 24.2 + - - +
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Residues in contact with GLY 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG* 3.4 21.8 - - - -
358A ASP* 3.8 21.8 - - - +
359A ILE 5.7 0.2 - - - +
457A SER* 4.8 5.2 + - - +
459A HIS* 4.5 6.4 + - - -
516A PHE* 2.5 40.3 + - - -
519A THR* 1.3 71.0 - - - +
521A ASN* 1.3 56.5 + - - +
522A PRO* 4.3 1.7 - - - +
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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