Contacts of the helix formed by residues 599 - 619 (chain A) in PDB entry 5SY1
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 LYS 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A ASN* 1.3 75.6 - - - +
600A VAL* 1.3 63.2 + - + +
602A ASN* 3.3 13.6 + - + +
603A ALA* 3.1 23.7 + - - +
124C GLU* 5.4 13.5 - - - +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ASN* 3.1 18.5 + - - +
599A LYS* 1.3 78.8 - - + +
601A SER* 1.3 63.8 + - - +
603A ALA* 3.1 18.2 + - + +
604A LYS* 3.3 9.0 + - - +
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ASN* 2.6 44.2 + - - -
600A VAL* 1.3 70.9 - - - +
602A ASN* 1.3 58.5 + - - +
603A ALA 3.2 0.2 - - - -
604A LYS* 3.2 13.1 + - - +
605A ARG* 2.8 43.5 + - - +
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Residues in contact with ASN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ASN 2.9 19.2 + - - +
599A LYS* 3.4 15.7 - - + +
600A VAL 3.2 0.4 - - - -
601A SER* 1.3 74.1 - - - +
603A ALA* 1.3 53.6 + - - +
605A ARG* 3.3 29.7 + - - +
606A ALA* 2.4 36.6 + - - +
121C GLU* 3.1 30.0 + - - +
124C GLU* 4.1 27.3 + - - +
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Residues in contact with ALA 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A LYS 3.1 11.7 + - - +
600A VAL* 3.1 14.3 + - + +
602A ASN* 1.3 74.1 - - - +
604A LYS* 1.3 59.6 + - - +
606A ALA* 3.9 7.9 - - - -
607A ARG* 2.9 11.1 + - - +
124C GLU 5.8 0.4 - - - -
128C GLU* 2.9 48.8 - - + +
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Residues in contact with LYS 604 (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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600A VAL 3.3 4.3 + - - +
601A SER* 3.2 18.8 + - - +
603A ALA* 1.3 79.0 - - - +
605A ARG* 1.3 56.9 - - + +
607A ARG* 3.3 22.7 + - - +
608A ALA* 2.8 26.6 + - + +
55C GLU* 5.9 4.5 - - - -
75C ARG* 5.3 16.2 - - - +
128C GLU* 5.2 0.2 - - - -
148C SER 4.0 19.2 + - - -
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Residues in contact with ARG 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ASN 3.1 28.7 + - - +
601A SER* 2.8 34.6 + - - +
602A ASN* 3.0 36.0 + - - +
604A LYS* 1.3 70.5 - - + +
606A ALA* 1.3 56.9 + - - +
608A ALA* 3.4 10.3 - - + +
609A HIS* 2.7 50.0 + - + +
57C ASP 6.1 0.7 - - - -
58C ALA* 5.2 14.1 - - + +
121C GLU* 5.0 2.0 + - - -
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Residues in contact with ALA 606 (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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602A ASN* 2.4 20.5 + - - +
603A ALA* 3.2 6.0 + - - +
605A ARG* 1.3 72.3 - - - +
607A ARG* 1.3 60.1 + - - +
609A HIS* 3.9 2.1 + - - +
610A TRP* 3.3 31.2 + - - -
124C GLU 4.1 6.5 - - - +
125C MET* 3.8 35.9 - - + +
128C GLU* 3.2 19.7 - - + +
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Residues in contact with ARG 607 (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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603A ALA 2.9 13.5 + - - +
604A LYS* 3.5 28.3 - - - +
605A ARG 3.2 0.2 - - - -
606A ALA* 1.3 77.7 - - - +
608A ALA* 1.3 56.8 + - - +
610A TRP* 3.3 8.5 + - - +
611A GLN* 2.9 40.0 + - + +
128C GLU* 3.3 12.7 + - - +
144C THR* 4.0 7.5 + - - -
145C MET* 3.3 60.8 + - + +
148C SER* 2.7 54.9 + - - -
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Residues in contact with ALA 608 (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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604A LYS* 2.8 17.7 + - + +
605A ARG* 3.0 12.7 + - + +
607A ARG* 1.3 78.3 - - - +
609A HIS* 1.3 59.0 + - - +
611A GLN* 3.4 4.1 + - - +
612A LEU* 3.1 31.5 + - - +
55C GLU 6.1 0.7 - - - +
58C ALA* 4.3 18.1 - - + +
75C ARG* 4.2 23.3 + - - +
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Residues in contact with HIS 609 (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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605A ARG* 2.7 34.4 + - + +
606A ALA* 4.3 6.0 - - - +
608A ALA* 1.3 72.6 - - - +
610A TRP* 1.3 63.1 + - - +
612A LEU* 3.6 14.7 + - + +
613A LEU* 3.4 24.9 + - - +
58C ALA* 3.2 38.3 + - + +
59C ASP* 5.1 1.0 - - - -
117C LEU* 3.4 37.0 - - + +
121C GLU* 4.1 23.7 + - + +
125C MET* 3.7 25.7 - - + +
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Residues in contact with TRP 610 (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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606A ALA 3.3 14.1 + - - -
607A ARG* 3.3 7.3 + - - +
608A ALA 3.2 0.4 - - - -
609A HIS* 1.3 77.8 - - - +
611A GLN* 1.3 60.1 + - - +
613A LEU* 2.9 17.6 + - + +
614A TYR* 2.8 27.5 + - - +
106C LEU* 4.6 11.0 - - + +
125C MET* 3.1 65.9 - - + -
126C ILE* 3.8 14.4 - - + -
128C GLU* 4.6 4.3 - - - -
129C ALA* 3.7 26.9 - - + -
137C VAL* 5.5 3.6 - - + -
141C GLU* 5.1 2.7 - - + -
142C PHE* 5.2 19.4 - + + -
145C MET* 3.6 39.0 - - + -
146C MET* 4.5 12.9 - - + +
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Residues in contact with GLN 611 (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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607A ARG* 2.9 31.8 + - + +
608A ALA* 4.0 4.8 - - - +
609A HIS 3.4 0.2 - - - -
610A TRP* 1.3 73.6 - - - +
612A LEU* 1.3 63.9 + - - +
614A TYR* 3.8 7.8 - - + +
615A THR* 3.1 25.8 + - - -
2C ALA* 5.5 2.7 - - + +
71C THR* 3.9 11.3 - - + +
75C ARG* 2.6 50.7 + - - +
145C MET 3.4 20.0 + - - -
146C MET* 4.0 27.6 + - + +
148C SER 4.7 5.9 - - - -
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Residues in contact with LEU 612 (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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608A ALA 3.1 15.1 + - - +
609A HIS* 3.6 20.0 - - + +
610A TRP 3.2 0.4 - - - -
611A GLN* 1.3 79.5 - - - +
613A LEU* 1.3 63.9 + - + +
615A THR* 3.6 2.5 + - - -
616A LEU* 3.3 32.2 + - + +
626A ARG* 4.5 27.1 - - - +
58C ALA* 3.9 28.7 - - + -
59C ASP* 5.3 2.0 - - + +
67C PRO* 4.3 23.8 - - + +
68C GLU* 4.5 19.7 - - + +
71C THR* 4.5 9.0 - - + +
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Residues in contact with LEU 613 (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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609A HIS 3.4 14.8 + - - +
610A TRP* 2.9 19.5 + - + +
612A LEU* 1.3 79.2 - - + +
614A TYR* 1.3 59.1 + - - +
616A LEU* 3.2 9.1 + - + +
617A VAL* 3.0 36.5 + - + +
93C PHE* 4.5 18.2 - - + -
106C LEU* 4.4 23.3 - - + -
109C VAL* 5.0 7.0 - - + -
110C MET* 4.8 21.5 - - + -
113C LEU* 4.6 22.7 - - + -
125C MET* 5.6 5.2 - - + -
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Residues in contact with TYR 614 (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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610A TRP 2.8 15.0 + - - +
611A GLN* 4.1 5.2 - - + +
612A LEU 3.4 0.2 - - - -
613A LEU* 1.3 75.8 - - - +
615A THR* 1.3 61.0 + - - +
617A VAL* 4.0 2.5 + - + +
618A ASN* 3.6 31.9 + - - -
2C ALA* 3.3 37.2 - - + +
3C ASP* 2.5 29.9 + - - -
78C LYS* 5.0 7.5 + - - -
85C GLU* 4.3 2.9 - - - +
86C ILE* 3.6 29.3 + - + +
89C ALA* 3.8 20.6 - - + -
93C PHE* 4.8 6.7 - + - -
142C PHE* 3.8 28.7 - + + -
146C MET* 3.6 27.4 - - + -
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Residues in contact with THR 615 (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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611A GLN 3.1 17.7 + - - -
612A LEU* 3.9 3.6 - - - -
613A LEU 3.2 0.4 - - - -
614A TYR* 1.3 79.0 - - - +
616A LEU* 1.3 62.0 + - + +
618A ASN* 3.3 2.6 + - - +
619A ASN* 3.0 45.6 + - + +
622A LEU* 5.0 4.3 - - + -
2C ALA* 3.7 26.7 - - - +
67C PRO* 5.6 5.2 - - + -
70C LEU* 3.9 24.5 - - + -
71C THR* 3.5 18.9 - - + +
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Residues in contact with LEU 616 (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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612A LEU* 3.3 22.6 + - + +
613A LEU* 3.2 11.4 + - + +
615A THR* 1.3 76.5 - - + +
617A VAL* 1.3 64.0 + - - +
619A ASN 3.0 19.3 - - - +
620A PRO* 4.0 2.1 - - - +
622A LEU* 4.3 15.9 - - + +
623A VAL* 3.8 40.9 - - + +
626A ARG* 3.7 35.9 - - + +
67C PRO* 4.7 9.9 - - + -
113C LEU* 4.1 26.6 - - + +
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Residues in contact with VAL 617 (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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613A LEU 3.0 21.7 + - - +
614A TYR* 4.4 4.0 - - + +
615A THR 3.3 0.2 - - - -
616A LEU* 1.3 80.0 - - - +
618A ASN* 1.3 71.1 + - - +
619A ASN 3.2 1.3 + - - -
620A PRO* 4.3 10.0 - - - +
89C ALA* 5.2 7.2 - - + +
92C VAL* 4.2 33.2 - - + -
93C PHE* 3.9 27.8 - - + -
109C VAL* 4.5 17.5 - - + -
113C LEU* 4.6 7.6 - - + -
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Residues in contact with ASN 618 (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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614A TYR* 3.6 47.7 + - - +
615A THR 3.3 3.3 + - - +
617A VAL* 1.3 84.3 - - - +
619A ASN* 1.3 66.5 + - - +
620A PRO* 3.9 6.7 - - - +
2C ALA 4.0 3.0 + - - -
3C ASP* 3.8 8.6 + - - +
4C GLN* 3.5 40.6 - - + +
85C GLU* 4.9 10.1 + - - +
88C GLU* 5.4 6.8 - - - +
89C ALA* 4.9 6.0 - - - +
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Residues in contact with ASN 619 (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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615A THR* 3.0 33.7 + - - +
616A LEU* 3.0 18.1 - - - +
617A VAL 3.2 1.0 - - - -
618A ASN* 1.3 84.6 - - - +
620A PRO* 1.3 67.2 - - - +
621A SER* 3.5 3.1 + - - +
622A LEU* 3.7 33.9 + - + +
623A VAL* 4.1 1.4 - - - +
2C ALA* 4.8 0.6 - - - +
3C ASP 3.0 19.0 + - - -
4C GLN* 4.5 0.2 - - - +
5C LEU* 3.3 27.2 + - - +
10C ILE* 4.2 11.9 - - + +
70C LEU* 4.6 4.4 - - - +
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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
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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