Contacts of the helix formed by residues 619 - 635 (chain A) in PDB entry 1WBB
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 GLY 619 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A MET 3.4 1.0 - - - -
618A GLY* 1.3 79.7 - - - +
620A LYS* 1.3 64.5 + - - +
622A THR* 3.5 1.9 + - - -
623A TYR* 3.2 19.6 + - - +
747A LEU* 3.5 17.3 - - - +
1801A ADP 3.2 41.3 + - - -
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Residues in contact with LYS 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 4.2 11.4 - - + +
613A THR* 3.8 21.1 - - - +
614A GLY* 3.1 20.9 + - - +
615A PRO 3.0 25.5 + - - -
616A ASN* 3.6 4.9 - - - +
619A GLY* 1.3 78.0 - - - +
621A SER* 1.3 63.4 + - - +
623A TYR* 3.5 5.2 + - - +
624A MET* 3.4 27.1 + - - +
693A ASP* 5.3 0.4 - - - +
694A GLU* 3.4 25.5 + - - -
726A ALA* 4.1 17.7 - - + +
727A THR 4.5 8.1 - - - +
728A HIS* 5.8 0.7 - - - +
747A LEU* 3.9 22.9 - - + -
1801A ADP 2.6 34.4 + - - +
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Residues in contact with SER 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LYS* 1.3 76.0 - - - +
622A THR* 1.3 60.5 + - - +
624A MET* 3.2 7.0 + - - +
625A ARG* 2.9 54.7 + - - +
693A ASP* 2.5 27.5 + - - -
1801A ADP 3.0 13.6 + - - -
1802A MG 1.9 33.3 - - - -
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Residues in contact with THR 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A HIS* 3.7 29.2 - - + -
588A VAL* 4.5 7.4 - - + +
596A PHE* 4.1 5.6 - - + -
619A GLY 3.8 1.8 - - - -
620A LYS 3.3 0.2 - - - -
621A SER* 1.3 72.0 - - - +
623A TYR* 1.3 66.0 + - - +
625A ARG* 3.4 9.1 + - - +
626A GLN* 2.9 37.2 + - - +
1801A ADP 2.7 71.9 + - + +
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Residues in contact with TYR 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ASN* 4.0 17.0 - - + +
600A PRO 2.7 27.7 + - - -
601A LEU* 3.4 32.2 - - + +
610A LEU* 4.6 4.9 - - + +
612A ILE* 4.1 33.7 - - + -
619A GLY 3.2 11.2 + - - +
620A LYS* 3.5 11.0 - - - +
621A SER 3.2 0.2 - - - -
622A THR* 1.3 79.8 - - - +
624A MET* 1.3 59.6 + - - +
626A GLN* 3.5 18.5 + - - +
627A THR* 2.8 30.6 + - - -
724A LEU* 5.0 3.1 - - + -
745A VAL* 4.7 4.0 - - + +
747A LEU* 4.9 2.5 - - + -
762A VAL* 3.3 44.1 - - + +
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Residues in contact with MET 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 3.9 14.8 - - + -
620A LYS 3.4 13.7 - - - +
621A SER 3.2 5.3 + - - +
622A THR 3.2 0.8 - - - -
623A TYR* 1.3 73.6 - - - +
625A ARG* 1.3 67.0 + - + +
627A THR* 3.0 15.2 + - - -
628A ALA 3.2 9.4 + - - -
691A LEU* 3.8 27.8 - - + +
692A MET 3.7 6.1 - - - +
693A ASP* 3.2 46.4 - - + +
724A LEU* 3.8 40.4 - - + +
726A ALA* 3.4 22.4 - - + -
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Residues in contact with ARG 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ASN* 3.1 58.9 + - - +
277A LEU* 3.5 16.6 - - + +
278A GLU* 5.7 2.4 + - - -
283A LEU* 5.1 10.7 - - - +
585A HIS* 3.9 20.2 - - - +
621A SER* 2.9 42.1 + - - +
622A THR* 3.8 8.9 + - - +
624A MET* 1.3 76.5 - - + +
626A GLN* 1.3 57.4 + - - +
628A ALA* 3.3 1.1 + - - -
629A LEU* 2.9 32.5 + - + +
657A VAL* 5.4 4.6 - - - +
691A LEU* 4.6 2.9 - - + +
693A ASP* 5.0 3.0 + - - -
1801A ADP 5.2 3.6 + - - -
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Residues in contact with GLN 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ILE* 6.0 0.8 - - + +
583A GLY* 3.3 30.1 + - - -
584A ARG* 3.9 3.0 - - - +
585A HIS* 3.7 29.6 - - + +
596A PHE* 3.5 23.4 - - - -
599A ASN* 4.4 19.4 + - - +
622A THR* 2.9 21.9 + - - +
623A TYR* 3.5 21.0 - - + +
625A ARG* 1.3 75.9 - - - +
627A THR* 1.3 65.2 + - - +
629A LEU* 3.8 7.5 - - - +
630A ILE* 2.9 41.4 + - + +
1801A ADP 5.0 1.0 + - - -
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Residues in contact with THR 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ILE* 4.2 18.3 - - + +
580A ILE* 4.6 12.2 - - + +
601A LEU* 3.3 33.1 - - + +
623A TYR* 2.8 21.5 + - - -
624A MET 3.0 9.6 + - - -
626A GLN* 1.3 83.0 - - - +
628A ALA* 1.3 56.8 + - - +
630A ILE* 3.5 2.6 + - - +
631A ALA* 3.1 25.6 + - - +
689A LEU* 4.4 8.7 - - + -
691A LEU* 5.3 0.2 - - - -
724A LEU* 3.6 22.4 - - + +
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Residues in contact with ALA 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.8 26.0 - - + +
624A MET 3.2 2.2 + - - -
625A ARG 3.7 6.5 - - - +
627A THR* 1.3 77.6 - - - +
629A LEU* 1.3 61.3 + - - +
631A ALA* 3.3 3.7 + - - +
632A LEU* 2.8 29.3 + - - +
653A ILE* 4.7 11.8 - - + +
689A LEU* 4.1 15.7 - - + +
691A LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 4.1 35.7 - - + +
279A ILE* 5.5 0.4 - - + -
291A LEU* 3.9 37.9 - - + -
585A HIS* 3.3 41.5 - - + +
586A PRO* 3.9 18.4 - - + -
587A VAL* 5.1 1.3 - - + -
625A ARG 2.9 19.2 + - - +
626A GLN* 3.8 4.5 - - - +
628A ALA* 1.3 76.2 - - - +
630A ILE* 1.3 58.6 + - - +
632A LEU* 3.3 9.5 + - + +
633A MET* 2.8 35.5 + - - +
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Residues in contact with ILE 630 (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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578A ILE* 5.7 0.4 - - + -
580A ILE* 4.2 24.2 - - + -
583A GLY* 4.5 9.0 - - - -
584A ARG 4.1 23.8 - - - +
586A PRO* 5.4 0.2 - - + -
626A GLN* 2.9 29.8 + - + +
627A THR 3.8 4.0 - - - +
629A LEU* 1.3 74.3 - - + +
631A ALA* 1.3 59.9 + - - +
633A MET* 3.3 4.7 + - - -
634A ALA* 2.9 30.0 + - - +
640A VAL* 3.5 23.5 - - + +
641A PRO* 3.9 24.9 - - + +
645A VAL* 3.9 20.9 - - + -
647A ILE* 5.2 2.7 - - + -
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Residues in contact with ALA 631 (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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267A ILE* 5.5 1.6 - - + -
578A ILE* 5.2 1.6 - - + -
627A THR 3.1 14.1 + - - +
628A ALA* 3.4 12.1 - - - +
630A ILE* 1.3 75.8 - - - +
632A LEU* 1.3 64.0 + - - +
634A ALA* 3.4 0.7 + - - +
635A TYR* 3.1 30.1 + - + -
647A ILE* 3.5 26.4 - - + +
650A ILE* 3.9 18.6 - - + -
653A ILE* 4.7 7.0 - - + -
689A LEU* 4.6 7.0 - - + -
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Residues in contact with LEU 632 (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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267A ILE* 5.7 0.9 - - - -
269A MET* 4.1 10.1 - - + -
277A LEU* 4.2 14.8 - - + -
279A ILE* 4.0 27.6 - - + -
291A LEU* 4.6 17.0 - - + -
311A LEU* 3.3 35.2 - - + +
314A PRO* 4.1 16.9 - - + +
628A ALA 2.8 16.3 + - - +
629A LEU* 3.5 7.9 - - + +
631A ALA* 1.3 76.4 - - - +
633A MET* 1.3 66.0 + - - +
635A TYR* 3.0 14.6 + - - +
636A ILE* 3.2 22.9 + - + +
653A ILE* 5.2 4.7 - - + +
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Residues in contact with MET 633 (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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291A LEU* 3.9 25.6 - - + -
295A LEU* 3.8 28.5 - - + -
567A TYR* 3.4 35.4 - - + +
586A PRO* 4.0 10.5 - - - -
629A LEU 2.8 24.5 + - - +
630A ILE 3.9 3.1 - - - +
632A LEU* 1.3 74.4 - - + +
634A ALA* 1.3 63.5 + - - +
636A ILE* 3.2 25.3 - - + +
638A SER* 3.2 17.6 + - - +
639A TYR 3.5 13.7 - - - +
640A VAL* 4.0 10.5 - - + -
641A PRO* 3.8 20.4 - - + -
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Residues in contact with ALA 634 (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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321A LEU* 4.0 0.7 - - - +
325A GLN* 4.7 0.2 + - - -
570A PRO* 3.9 30.2 - - + +
572A PHE* 3.6 20.5 - - + -
630A ILE 2.9 17.9 + - - +
631A ALA* 3.5 7.0 - - - +
633A MET* 1.3 76.4 - - - +
635A TYR* 1.3 59.0 + - + +
637A GLY* 3.4 15.4 + - - -
638A SER 4.1 1.4 + - - +
640A VAL* 3.7 3.2 - - + +
645A VAL* 5.3 1.3 - - + -
647A ILE* 4.2 24.7 - - + -
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Residues in contact with TYR 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 3.6 18.8 - - + -
314A PRO* 3.3 18.8 - - + +
315A VAL 2.8 50.1 + - - +
316A ARG* 4.7 10.8 - - + -
318A THR* 6.6 0.2 - - + -
321A LEU* 3.4 17.8 - - + +
572A PHE* 3.9 23.1 - + - +
631A ALA* 3.1 24.4 + - - +
632A LEU 3.0 4.2 + - - +
634A ALA* 1.3 78.1 - - + +
636A ILE* 1.3 59.2 + - - +
637A GLY 3.5 0.7 - - - -
647A ILE* 4.0 16.8 - - + -
648A GLY 2.5 35.9 + - - -
649A PRO* 3.3 10.2 - - + +
650A ILE* 4.2 16.8 - - + -
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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