Contacts of the helix formed by residues 497 - 516 (chain D) in PDB entry 6W4E
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 SER 497 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493D GLN* 2.7 22.4 + - - +
494D GLU* 5.2 0.7 - - - -
495D LYS 3.1 1.0 - - - -
496D LEU* 1.3 77.9 - - - +
498D PRO* 1.4 69.0 - - - +
501D GLU* 2.9 35.5 + - - +
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Residues in contact with PRO 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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275A LYS* 5.2 11.7 - - + -
494D GLU* 3.1 29.4 - - - +
495D LYS* 3.4 5.4 - - - +
497D SER* 1.4 96.1 - - - +
499D LEU* 1.3 64.7 + - + +
501D GLU* 3.4 4.4 + - + +
502D GLU* 2.8 31.3 + - - +
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Residues in contact with LEU 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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272A TYR* 4.0 23.3 + - + +
275A LYS* 3.8 29.8 - - + -
279A LEU* 3.9 27.4 - - + -
495D LYS* 2.9 28.5 + - + +
496D LEU* 5.0 1.1 - - + -
498D PRO* 1.3 79.1 - - + +
500D GLY* 1.3 56.7 + - - +
502D GLU* 3.4 24.7 - - - +
503D MET* 2.7 36.9 + - - +
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Residues in contact with GLY 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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496D LEU* 3.1 28.1 + - - +
498D PRO 3.2 0.8 - - - -
499D LEU* 1.3 78.7 - - - +
501D GLU* 1.3 56.7 + - - +
503D MET* 3.8 11.7 - - - +
504D ARG* 3.0 39.8 + - - +
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Residues in contact with GLU 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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497D SER* 2.9 19.0 + - - +
498D PRO* 3.9 4.7 - - + +
500D GLY* 1.3 73.5 - - - +
502D GLU* 1.3 60.5 + - - +
504D ARG* 2.8 41.2 + - - +
505D ASP* 2.8 29.5 + - - +
508D ARG* 5.1 14.2 + - - -
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Residues in contact with GLU 502 (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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271A LEU* 3.7 22.5 - - + +
272A TYR* 4.3 0.5 - - - -
275A LYS* 2.6 32.4 + - - -
498D PRO 2.8 19.6 + - - +
499D LEU* 3.4 21.1 - - - +
501D GLU* 1.3 75.8 - - - +
503D MET* 1.3 55.1 + - - +
505D ASP* 3.1 8.5 + - + +
506D ARG* 2.6 74.2 + - + +
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 5.0 10.5 - - - +
499D LEU 2.7 22.6 + - - +
500D GLY* 3.8 11.9 - - - +
502D GLU* 1.3 73.7 - - - +
504D ARG* 1.3 65.6 + - + +
506D ARG* 3.1 20.2 + - + +
507D ALA* 2.8 34.9 + - - +
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Residues in contact with ARG 504 (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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500D GLY* 3.0 23.1 + - - +
501D GLU* 2.8 42.3 + - - +
503D MET* 1.3 84.8 - - + +
505D ASP* 1.3 58.1 + - - +
507D ALA* 3.2 9.0 + - - +
508D ARG* 2.8 41.4 + - + +
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Residues in contact with ASP 505 (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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501D GLU 2.8 17.8 + - - +
502D GLU* 3.1 8.7 + - + +
504D ARG* 1.3 73.6 - - - +
506D ARG* 1.3 60.9 + - - +
508D ARG* 3.0 40.0 + - - +
509D ALA* 2.8 30.3 + - - +
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Residues in contact with ARG 506 (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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268A GLU* 2.7 85.8 + - + +
271A LEU* 3.5 13.5 - - + +
272A TYR* 3.2 39.8 + - - -
502D GLU* 2.6 52.5 + - + +
503D MET* 3.2 22.3 - - + +
505D ASP* 1.3 76.7 - - - +
507D ALA* 1.3 50.8 + - - +
509D ALA* 3.1 8.4 + - - +
510D HIS* 2.8 43.4 + - + -
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Residues in contact with ALA 507 (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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503D MET* 2.8 19.7 + - - +
504D ARG* 3.4 13.7 - - - +
506D ARG* 1.3 76.2 - - - +
508D ARG* 1.3 53.6 + - - +
510D HIS* 3.1 7.9 + - - +
511D VAL* 2.7 46.9 + - + +
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Residues in contact with ARG 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D GLU* 5.1 13.3 + - - -
504D ARG* 2.8 25.2 + - + +
505D ASP* 3.0 42.7 + - - +
507D ALA* 1.3 75.6 - - - +
509D ALA* 1.3 53.4 + - - +
511D VAL* 4.1 3.3 - - - +
512D ASP* 2.7 41.4 + - - +
515D ARG* 4.5 4.3 + - - +
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Residues in contact with ALA 509 (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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264A LYS* 3.0 49.8 + - + +
505D ASP* 2.8 17.7 + - - +
506D ARG* 3.1 11.2 + - - +
508D ARG* 1.3 72.2 - - - +
510D HIS* 1.3 57.5 + - + +
512D ASP* 4.1 5.3 - - - +
513D ALA* 3.1 16.0 + - - +
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Residues in contact with HIS 510 (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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261A PHE* 3.6 35.2 - + + -
264A LYS* 5.7 9.3 - - + +
265A TRP* 4.6 11.2 - + - -
268A GLU* 2.8 28.9 + - - -
506D ARG* 2.8 31.5 + - + -
507D ALA* 3.1 11.4 + - - +
509D ALA* 1.3 77.0 - - + +
511D VAL* 1.3 62.6 + - + +
513D ALA* 3.1 7.0 + - - +
514D LEU* 2.9 37.4 + - + +
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507D ALA* 2.7 29.3 + - + +
508D ARG* 4.1 2.9 - - - +
510D HIS* 1.3 70.2 - - + +
512D ASP* 1.3 60.4 + - - +
514D LEU* 3.0 19.4 + - + +
515D ARG* 2.9 54.3 + - + +
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Residues in contact with ASP 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LYS* 5.8 1.3 + - - +
508D ARG 2.7 26.2 + - - +
509D ALA* 4.1 6.0 - - - +
511D VAL* 1.3 72.6 - - - +
513D ALA* 1.3 63.4 + - - +
515D ARG* 3.0 47.3 + - - +
516D THR* 3.3 12.1 + - - -
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Residues in contact with ALA 513 (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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260A ASP* 3.7 11.0 - - - +
261A PHE* 3.9 16.6 - - + -
264A LYS* 3.6 16.4 - - - +
509D ALA 3.1 18.1 + - - +
510D HIS 3.1 5.7 + - - +
512D ASP* 1.3 78.5 + - - +
514D LEU* 1.3 51.3 + - - +
516D THR* 2.8 10.1 + - - -
517D HIS* 2.8 45.9 + - + +
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Residues in contact with LEU 514 (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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261A PHE* 4.0 22.4 - - + -
510D HIS* 2.9 25.2 + - + +
511D VAL* 3.0 23.8 + - + +
513D ALA* 1.3 76.1 - - - +
515D ARG* 1.3 57.7 + - - +
517D HIS* 3.0 10.8 + - + +
518D LEU* 2.7 58.7 + - + +
519D ALA 3.3 6.2 + - - -
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Residues in contact with ARG 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508D ARG* 4.5 4.2 + - - +
511D VAL* 2.9 39.5 + - + +
512D ASP* 3.0 46.3 + - - +
514D LEU* 1.3 77.1 - - + +
516D THR* 1.3 57.9 + - - +
519D ALA* 3.3 14.0 - - - +
520D PRO* 3.3 15.3 - - - +
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Residues in contact with THR 516 (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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253A LYS* 5.4 0.2 + - - -
257A TYR* 3.8 8.5 + - - -
512D ASP* 3.3 13.5 + - - -
513D ALA* 2.8 9.2 + - - -
515D ARG* 1.3 78.7 - - - +
517D HIS* 1.3 68.8 + - - +
520D PRO* 3.5 19.1 - - + +
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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