Contacts of the helix formed by residues 614 - 636 (chain J) in PDB entry 6ALG
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 LEU 614 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487J THR 3.9 13.2 - - - +
488J ASN* 3.9 16.8 - - - +
490J ILE* 3.7 28.5 - - + -
609J TYR* 3.7 14.4 - - + +
612J LEU 3.7 0.4 + - - -
613J GLY* 1.3 73.2 - - - -
615J LYS* 1.3 62.7 + - - +
616J PRO 3.5 0.7 - - - -
617J THR* 2.8 21.1 + - - -
618J VAL* 3.0 15.4 + - + +
5K THR* 3.7 34.8 - - + -
7K GLN* 3.9 38.5 - - + +
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Residues in contact with LYS 615 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614J LEU* 1.3 77.7 - - + +
616J PRO* 1.3 64.2 - - + +
618J VAL* 3.4 7.1 + - - +
619J ILE* 3.0 31.3 + - - +
4K VAL* 5.1 10.8 - - + -
5K THR* 3.3 28.7 - - + +
7K GLN* 4.3 15.1 - - + +
8K ASP* 3.6 30.7 + - - +
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Residues in contact with PRO 616 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584J PRO* 4.3 15.4 - - + +
608J CYS* 3.8 3.0 - - - -
612J LEU* 3.3 52.7 - - + +
615J LYS* 1.3 93.7 - - + +
617J THR* 1.3 50.0 + - - +
619J ILE* 3.8 10.8 - - + +
620J PHE* 2.6 40.5 + - - +
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Residues in contact with THR 617 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490J ILE* 3.8 24.9 - - + -
605J LEU* 4.0 34.4 - - + +
608J CYS* 3.3 12.2 + - - -
609J TYR* 3.2 17.7 + - + +
613J GLY 3.1 18.0 + - - -
614J LEU 2.8 10.0 + - - -
616J PRO* 1.3 74.1 - - - +
618J VAL* 1.3 61.1 + - - +
620J PHE* 4.0 0.8 - - - +
621J ALA* 2.9 28.5 + - + +
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Residues in contact with VAL 618 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J LEU* 4.2 11.3 - - + +
364J HIS* 5.7 2.0 - - + -
487J THR* 3.9 42.0 - - + +
490J ILE* 4.8 9.0 - - + -
614J LEU* 3.0 31.2 + - + +
615J LYS* 3.8 7.9 - - - +
617J THR* 1.3 77.1 - - - +
619J ILE* 1.3 59.9 + - + +
621J ALA* 3.1 6.9 + - - +
622J ASP* 3.0 38.7 + - - +
4K VAL* 4.6 11.9 - - + -
5K THR* 4.4 4.7 - - + -
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Residues in contact with ILE 619 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362J ARG* 5.4 11.0 - - - +
584J PRO* 6.4 1.3 - - + -
615J LYS 3.0 21.0 + - - +
616J PRO* 3.8 11.7 - - + +
618J VAL* 1.3 80.4 - - + +
620J PHE* 1.3 60.3 + - + +
622J ASP* 3.5 8.7 + - + +
623J GLN* 3.0 47.8 + - + +
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Residues in contact with PHE 620 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579J LEU* 6.2 0.4 - - + -
582J ILE* 3.9 14.8 - - + -
583J VAL* 3.6 32.3 - - + -
584J PRO* 3.5 22.0 - - + -
587J LEU* 5.0 1.3 - - + -
604J MET* 3.5 42.6 - - + -
605J LEU* 3.6 23.8 - - + -
608J CYS* 3.7 22.2 - - + -
616J PRO 2.6 23.9 + - - +
617J THR 4.0 0.7 - - - +
619J ILE* 1.3 78.2 - - + +
621J ALA* 1.3 59.1 + - - +
623J GLN* 3.5 3.0 + - - -
624J ILE* 3.0 46.5 + - + +
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Residues in contact with ALA 621 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J LEU* 4.2 14.6 - - + -
452J LEU* 4.0 15.0 - - + +
500J ILE* 4.7 8.3 - - + -
605J LEU* 4.4 17.9 - - + -
617J THR* 2.9 20.5 + - + +
618J VAL* 3.1 4.7 + - - +
620J PHE* 1.3 75.2 - - - +
622J ASP* 1.3 60.5 + - - +
624J ILE* 3.3 7.8 + - - +
625J MET* 3.0 28.4 + - - +
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Residues in contact with ASP 622 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J LEU 4.5 0.8 - - - +
362J ARG* 4.0 19.7 + - + +
363J LEU* 3.4 41.5 + - - +
364J HIS* 5.6 0.7 - - - -
450J HIS* 3.6 10.6 + - - -
618J VAL* 3.0 29.1 + - - +
619J ILE* 3.9 9.8 - - + +
620J PHE 3.4 0.2 - - - -
621J ALA* 1.3 76.0 - - - +
623J GLN* 1.3 59.9 + - + +
625J MET* 3.3 6.3 + - - +
626J TYR* 3.0 46.6 + - + -
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Residues in contact with GLN 623 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582J ILE* 3.6 40.7 - - + +
619J ILE* 3.0 32.3 + - + +
620J PHE* 4.0 2.5 - - - +
621J ALA 3.3 0.2 - - - -
622J ASP* 1.3 74.8 - - - +
624J ILE* 1.3 60.8 + - - +
626J TYR* 3.9 26.4 - - - +
627J THR* 3.0 31.6 + - - +
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Residues in contact with ILE 624 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452J LEU* 6.1 0.4 - - + -
502J PRO* 4.1 14.6 - - + -
506J VAL* 3.9 7.2 - - + +
510J LEU* 4.1 10.6 - - + +
579J LEU* 5.1 5.6 - - + -
582J ILE* 4.6 4.9 - - + -
601J ILE* 3.8 31.0 - - + -
604J MET* 4.1 13.0 - - - -
605J LEU* 4.5 9.4 - - + -
620J PHE* 3.0 58.1 + - + +
621J ALA* 3.3 6.7 + - - +
623J GLN* 1.3 77.1 - - - +
625J MET* 1.3 58.4 + - - +
627J THR* 3.5 6.9 - - - +
628J GLY* 2.9 27.9 + - - -
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Residues in contact with MET 625 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359J PRO* 3.4 28.0 - - + +
361J LEU 3.8 2.9 - - - +
450J HIS* 3.3 41.5 - - + +
451J PRO* 3.6 22.0 - - + -
452J LEU* 3.8 20.2 - - + -
506J VAL* 4.3 8.7 - - + -
621J ALA 3.0 16.6 + - - +
622J ASP* 3.7 4.7 - - - +
624J ILE* 1.3 78.7 - - - +
626J TYR* 1.3 78.3 + - + +
628J GLY* 3.9 0.2 - - - -
629J PHE* 3.0 43.7 + - + -
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Residues in contact with TYR 626 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H ASN* 6.4 1.3 - - - -
359J PRO* 3.2 26.5 - - + -
360J TYR* 3.4 16.5 + - - -
361J LEU 3.3 19.5 + - - -
362J ARG* 3.8 11.7 + - + +
622J ASP* 3.0 27.9 + - + +
623J GLN* 3.4 30.0 + - - +
624J ILE 3.3 0.2 - - - -
625J MET* 1.3 92.6 - - + +
627J THR* 1.3 58.2 + - - +
629J PHE* 3.5 3.8 + + - +
630J ALA* 3.0 29.2 + - - +
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Residues in contact with THR 627 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509J GLY 5.6 0.2 - - - -
510J LEU* 4.5 4.7 - - + -
513J MET* 3.9 9.4 - - + +
578J ILE* 5.4 2.1 + - - +
579J LEU* 4.2 17.3 - - + -
582J ILE* 3.7 25.2 - - + +
623J GLN 3.0 21.5 + - - +
624J ILE* 3.5 11.7 - - - +
626J TYR* 1.3 77.2 - - - +
628J GLY* 1.3 60.2 + - - +
630J ALA* 3.8 5.4 - - - -
631J TYR* 3.0 50.8 + - - +
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Residues in contact with GLY 628 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506J VAL* 4.1 11.3 - - - -
509J GLY* 3.8 4.3 - - - -
510J LEU* 3.6 21.8 - - - -
624J ILE 2.9 18.8 + - - -
625J MET 3.9 0.7 - - - -
627J THR* 1.3 74.9 - - - +
629J PHE* 1.3 65.6 + - - +
632J ALA* 2.9 31.7 + - - +
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Residues in contact with PHE 629 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808I ASN* 3.6 21.7 + - - +
809I GLY* 3.5 16.8 - - - +
812I PHE* 3.5 28.5 - + - -
359J PRO* 3.6 35.4 - - + -
451J PRO* 4.2 6.1 - - + -
452J LEU* 6.0 0.2 - - + -
505J ASP* 3.6 30.7 - - + -
506J VAL* 3.7 16.2 - - + -
625J MET* 3.0 39.8 + - + +
626J TYR* 4.2 3.8 - + - +
628J GLY* 1.3 79.1 - - - +
630J ALA* 1.3 59.4 + - - +
632J ALA* 3.8 3.5 - - + +
633J ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 630 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808I ASN* 4.0 14.6 - - - +
538J ARG* 5.7 5.4 - - - +
626J TYR 3.0 19.5 + - - +
627J THR* 4.0 6.5 - - - +
628J GLY 3.3 0.2 - - - -
629J PHE* 1.3 78.3 - - - +
631J TYR* 1.3 67.9 + - + +
633J ALA* 3.1 6.6 + - - +
634J ARG* 3.0 28.5 + - + +
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Residues in contact with TYR 631 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509J GLY* 4.4 11.1 - - - +
512J TYR* 4.5 5.9 - - + -
513J MET* 3.5 26.5 - - + -
534J GLU* 4.7 6.9 + - - +
537J TYR* 3.4 35.0 - + - -
538J ARG* 3.8 26.6 + - - -
544J LEU* 4.1 15.6 - - + +
578J ILE* 3.4 26.9 - - + +
627J THR* 3.0 45.4 + - - +
630J ALA* 1.3 81.5 - - + +
632J ALA* 1.3 61.3 + - - +
634J ARG* 3.7 15.1 - - + +
635J SER* 3.0 25.1 + - - -
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Residues in contact with ALA 632 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806I PRO* 3.3 26.5 - - + +
505J ASP* 3.9 14.4 - - + +
508J LEU* 5.0 1.6 - - + -
509J GLY* 3.6 17.8 - - - +
628J GLY 2.9 23.0 + - - +
629J PHE* 3.8 7.0 - - + +
631J TYR* 1.3 78.2 - - - +
633J ALA* 1.3 60.0 + - - +
635J SER* 2.3 28.6 + - - +
636J GLY 3.5 2.6 + - - -
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Residues in contact with ALA 633 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805I MET* 3.7 3.2 - - - +
806I PRO 3.3 10.7 + - - +
807I TRP* 4.4 7.0 - - + +
808I ASN* 3.5 36.1 - - - +
1214I ASP* 5.5 3.8 - - - +
1221I PHE* 3.2 25.5 - - + -
629J PHE 3.0 15.3 + - - +
630J ALA 3.1 10.0 + - - +
632J ALA* 1.3 79.0 - - - +
634J ARG* 1.3 61.8 + - + +
635J SER 3.3 0.7 + - - -
636J GLY 3.5 3.6 + - - -
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Residues in contact with ARG 634 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214I ASP* 4.8 12.1 - - - -
1217I THR* 5.1 6.5 - - - -
1219I GLU* 3.1 35.4 + - - +
1220I GLN 5.4 5.3 + - - -
1221I PHE* 4.2 10.2 - - - +
1222I GLU* 4.2 18.6 + - - +
512J TYR* 5.0 2.2 - - - -
537J TYR* 2.8 60.6 + - - +
538J ARG* 3.6 30.0 - - - +
544J LEU* 5.4 0.9 - - + -
630J ALA* 3.0 19.0 + - + +
631J TYR* 3.7 21.1 - - + +
632J ALA 3.3 0.2 - - - -
633J ALA* 1.3 75.0 - - + +
635J SER* 1.3 64.5 + - - +
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Residues in contact with SER 635 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806I PRO* 4.8 1.4 - - - +
1221I PHE* 5.0 0.2 - - - -
1222I GLU* 2.8 26.4 - - - +
1223I ARG* 4.2 5.2 - - - +
508J LEU* 5.6 1.8 - - - +
509J GLY* 5.6 0.2 - - - -
512J TYR* 3.5 37.7 + - - -
631J TYR 3.0 15.1 + - - -
632J ALA* 2.3 30.4 + - - +
634J ARG* 1.3 78.0 - - - +
636J GLY* 1.3 65.1 + - - +
637J ALA* 3.3 19.7 + - - +
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Residues in contact with GLY 636 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805I MET* 4.2 21.8 - - - -
806I PRO* 4.8 0.2 - - - -
1221I PHE* 4.6 3.8 - - - -
1222I GLU 4.2 2.9 - - - -
1223I ARG* 3.2 19.6 - - - +
1225I VAL* 3.4 21.2 - - - +
632J ALA 3.5 4.4 + - - -
633J ALA 3.5 2.6 + - - -
634J ARG 3.5 1.8 - - - -
635J SER* 1.3 82.7 + - - +
637J ALA* 1.3 57.2 + - - -
638J SER* 2.8 10.4 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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