Contacts of the helix formed by residues 447 - 468 (chain P) in PDB entry 6LTJ
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 ASP 447 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690O SER* 5.3 9.9 - - - +
693O ALA* 5.6 0.9 - - - -
443P SER 3.8 4.7 + - - +
444P PHE 3.1 3.1 + - - -
446P ARG* 1.3 85.5 - - - +
448P PRO* 1.3 68.9 - - - +
449P GLN* 3.1 3.3 + - + +
450P GLY* 4.2 18.0 + - - +
451P PHE* 3.0 19.1 + - - +
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Residues in contact with PRO 448 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866N LEU* 3.5 41.5 - - + +
870N ALA* 4.0 14.4 - - + -
689O ALA* 5.9 3.4 - - + +
693O ALA* 4.6 12.3 - - + -
444P PHE* 3.3 45.3 - - + +
445P ALA 4.4 0.4 - - - +
446P ARG 4.2 3.4 - - - +
447P ASP* 1.3 83.2 - - - +
449P GLN* 1.3 57.0 + - - +
451P PHE* 4.0 2.4 - - + +
452P ILE* 2.9 37.7 + - - +
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Residues in contact with GLN 449 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866N LEU* 4.1 12.0 - - + +
681O ALA* 2.8 36.5 + - + +
682O SER* 4.6 4.0 + - - +
684O VAL* 2.4 34.0 + - - -
685O ASP 4.3 1.6 - - - -
686O PRO* 3.5 33.1 - - - +
689O ALA* 3.5 13.8 - - + +
447P ASP* 3.1 2.8 + - + -
448P PRO* 1.3 78.1 - - - +
450P GLY* 1.3 67.8 + - - +
452P ILE* 3.1 5.0 + - - +
453P ASN* 2.8 33.7 + - - +
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Residues in contact with GLY 450 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447P ASP* 3.5 19.9 + - - +
449P GLN* 1.3 80.1 - - - +
451P PHE* 1.3 56.7 + - - +
453P ASN* 3.3 10.6 + - - +
454P ASP* 2.9 36.8 + - - +
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Residues in contact with PHE 451 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966L PRO* 5.6 0.4 - - + -
1967L LEU* 3.6 27.6 - - + -
440P PHE* 3.4 44.0 - + - -
443P SER* 3.2 44.9 - - - +
444P PHE* 3.3 38.4 - + + -
447P ASP* 3.0 21.0 + - - +
448P PRO 4.0 1.3 - - - +
450P GLY* 1.3 75.3 - - - +
452P ILE* 1.3 62.6 + - - +
454P ASP* 4.2 6.1 - - + -
455P TRP* 2.8 34.6 + + + +
203Q ILE* 4.3 5.8 - - + -
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Residues in contact with ILE 452 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866N LEU* 4.0 7.2 - - + -
674O MET* 4.1 17.3 - - + -
677O VAL* 4.0 30.5 - - + +
678O ALA* 4.1 24.9 - - + +
681O ALA* 3.7 24.2 - - + -
444P PHE* 4.2 19.1 - - + -
448P PRO 2.9 26.4 + - - +
449P GLN 3.1 4.5 + - - +
451P PHE* 1.3 77.3 - - + +
453P ASN* 1.3 61.7 + - - +
455P TRP* 3.5 5.9 - - - +
456P LEU* 2.9 34.4 + - + +
203Q ILE* 5.4 1.6 - - + -
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Residues in contact with ASN 453 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657O GLY* 5.4 7.9 - - - -
658O PRO* 5.6 1.0 - - - +
661O TYR* 4.0 14.9 + - - +
681O ALA* 5.6 1.7 - - - +
682O SER* 5.4 12.2 - - - +
449P GLN* 2.8 32.2 + - - +
450P GLY* 3.6 9.8 - - - +
452P ILE* 1.3 80.7 - - - +
454P ASP* 1.3 65.7 + - - +
456P LEU* 3.2 15.3 + - - +
457P GLN* 3.0 31.0 + - + +
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Residues in contact with ASP 454 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967L LEU* 3.6 19.5 - - + +
1969L THR* 5.3 12.7 - - + +
450P GLY* 2.9 19.5 + - - +
451P PHE* 3.6 9.5 - - + +
453P ASN* 1.3 78.4 - - - +
455P TRP* 1.3 57.3 + - - +
457P GLN* 3.3 19.0 + - - +
458P SER* 2.9 29.8 + - - -
461P ARG* 5.3 0.2 + - - -
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Residues in contact with TRP 455 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967L LEU* 4.0 16.3 - - + +
665O PRO* 4.8 1.8 - - + -
666O PHE* 4.6 5.6 - - + -
671O ASN* 4.2 0.2 - - - -
674O MET* 3.6 44.2 - - + -
440P PHE* 3.7 27.5 - + - -
451P PHE* 2.8 25.8 + + + +
452P ILE* 3.5 7.6 - - - +
454P ASP* 1.3 74.1 - - - +
456P LEU* 1.3 80.2 + - + +
458P SER* 3.3 1.0 + - - -
459P GLN* 2.9 52.9 + - + +
199Q ASN* 3.4 26.3 + - + +
200Q HIS* 3.5 33.9 - + - -
203Q ILE* 3.5 23.5 - - + +
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Residues in contact with LEU 456 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658O PRO* 3.6 39.3 - - + +
661O TYR* 3.6 21.3 - - + -
665O PRO* 3.6 13.9 - - + +
666O PHE* 3.7 31.4 - - + -
678O ALA* 4.3 12.3 - - + -
452P ILE* 2.9 26.9 + - + +
453P ASN* 3.6 11.0 - - - +
455P TRP* 1.3 94.2 - - + +
457P GLN* 1.3 62.6 + - - +
460P CYS* 2.9 26.5 + - - +
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Residues in contact with GLN 457 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969L THR* 5.7 5.5 - - - +
1971L LEU* 5.3 5.1 - - - +
661O TYR* 3.4 38.1 + - + +
453P ASN* 3.0 22.8 + - - +
454P ASP* 3.5 20.6 + - - +
456P LEU* 1.3 77.6 - - - +
458P SER* 1.3 57.5 + - - +
460P CYS* 3.2 1.9 + - - +
461P ARG* 2.9 60.5 + - - +
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Residues in contact with SER 458 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967L LEU* 3.5 18.3 - - - -
1968L CYS* 2.8 34.5 + - - +
1969L THR 4.7 2.0 - - - -
454P ASP 2.9 18.2 + - - -
455P TRP 3.3 3.3 + - - -
457P GLN* 1.3 75.6 - - - +
459P GLN* 1.3 59.7 + - - +
461P ARG* 3.2 13.8 - - - +
462P ASP* 3.0 40.2 + - - -
195Q ARG* 4.4 0.3 - - - -
199Q ASN* 4.2 5.2 + - - -
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Residues in contact with GLN 459 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665O PRO* 3.4 23.3 - - + -
455P TRP* 2.9 46.0 + - + +
458P SER* 1.3 76.3 - - - +
460P CYS* 1.3 57.1 + - - +
462P ASP* 3.3 3.7 + - - +
463P LEU* 2.9 28.1 + - - +
196Q PHE* 3.1 43.3 + - + -
199Q ASN* 3.2 32.0 + - - +
200Q HIS* 3.2 29.9 + - - +
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Residues in contact with CYS 460 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661O TYR* 3.6 25.6 - - + -
663O PRO* 3.1 50.3 - - - +
665O PRO* 3.8 5.7 - - + +
456P LEU 2.9 19.9 + - - +
457P GLN* 3.7 3.6 - - - +
459P GLN* 1.3 73.8 - - - +
461P ARG* 1.3 67.5 + - - +
463P LEU* 3.2 2.0 + - - +
464P LYS* 3.0 38.0 + - - +
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Residues in contact with ARG 461 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968L CYS* 4.3 13.5 - - - -
1969L THR* 3.7 23.4 - - - +
1970L LEU 3.4 31.6 + - - +
1971L LEU* 3.3 34.6 - - - +
1972L ASP* 5.0 5.1 - - + +
457P GLN* 2.9 55.8 + - - +
458P SER* 3.2 15.4 - - - +
460P CYS* 1.3 75.9 - - - +
462P ASP* 1.3 58.3 + - - +
464P LYS* 3.5 14.0 + - - +
465P THR* 2.5 38.6 + - - +
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Residues in contact with ASP 462 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968L CYS* 4.2 0.9 - - - -
458P SER* 3.0 23.6 + - - +
459P GLN* 3.8 15.7 - - - +
460P CYS 3.1 0.2 - - - -
461P ARG* 1.3 80.1 - - - +
463P LEU* 1.3 60.7 + - - +
465P THR* 3.6 7.3 + - - -
466P MET* 2.9 36.0 + - - +
192Q ALA* 3.7 24.4 - - + +
195Q ARG* 2.4 40.6 + - - -
196Q PHE* 3.8 14.2 + - + -
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Residues in contact with LEU 463 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1646L VAL* 3.5 21.8 - - + -
1649L THR* 4.3 14.1 - - + +
663O PRO* 3.8 17.9 - - + +
664O ILE 3.2 29.2 - - - +
665O PRO* 3.6 14.1 - - + +
459P GLN 2.9 11.3 + - - +
460P CYS* 3.2 6.0 + - - +
462P ASP* 1.3 77.0 - - - +
464P LYS* 1.3 60.3 + - - +
466P MET* 3.2 6.6 + - + +
467P THR* 2.9 48.4 + - + +
196Q PHE* 3.8 19.5 - - + -
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Residues in contact with LYS 464 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972L ASP* 4.6 16.2 + - - +
663O PRO* 3.6 24.5 - - + -
460P CYS* 3.0 33.1 + - - +
461P ARG* 3.8 12.6 - - - +
463P LEU* 1.3 75.7 - - - +
465P THR* 1.3 63.1 + - - +
467P THR* 4.0 5.6 - - - -
468P ASP* 3.0 22.7 + - - -
469P VAL* 3.3 33.5 + - + +
470P VAL* 4.9 0.2 - - - +
471P GLY 4.4 29.6 - - - +
472P ASN* 4.4 10.3 - - - +
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Residues in contact with THR 465 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461P ARG* 2.5 25.7 + - - +
462P ASP* 3.6 6.6 + - - -
463P LEU 3.2 0.2 - - - -
464P LYS* 1.3 78.4 - - - +
466P MET* 1.3 59.1 + - - +
468P ASP* 4.2 2.4 + - - +
188Q MET* 3.5 39.5 - - + +
189Q LYS* 3.6 19.1 - - - +
192Q ALA* 3.5 24.5 - - + -
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Residues in contact with MET 466 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1649L THR* 3.8 28.0 - - - +
1650L GLN 4.4 1.3 - - - -
1651L PRO* 3.2 13.8 - - + +
1652L VAL* 2.8 29.5 + - - +
462P ASP 2.9 22.6 + - - +
463P LEU* 3.5 11.4 - - - +
465P THR* 1.3 75.7 - - - +
467P THR* 1.3 68.1 + - + +
468P ASP 3.7 0.9 - - - -
189Q LYS* 3.9 14.6 + - - +
192Q ALA* 3.8 2.2 - - + +
193Q THR* 3.6 37.0 - - + +
196Q PHE* 3.5 42.8 - - + -
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Residues in contact with THR 467 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649L THR* 3.9 22.0 - - + -
1650L GLN 4.6 2.9 - - - +
1652L VAL* 4.0 16.3 - - + +
663O PRO* 5.9 1.2 - - - +
463P LEU* 2.9 30.4 + - + +
466P MET* 1.3 91.1 - - + +
468P ASP* 1.3 64.6 + - - +
469P VAL* 2.9 31.7 + - - +
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Residues in contact with ASP 468 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1652L VAL* 3.9 14.9 - - - +
1654L LYS* 5.6 1.9 - - - +
464P LYS 3.0 7.7 + - - -
465P THR 4.2 2.0 + - - +
466P MET 3.7 0.4 - - - -
467P THR* 1.3 77.4 - - - +
469P VAL* 1.3 63.2 + - - +
470P VAL* 3.6 12.6 + - - +
189Q LYS* 3.0 35.5 + - - -
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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