Contacts of the helix formed by residues 590 - 607 (chain A) in PDB entry 6DWY
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 590 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ARG* 3.9 7.4 - - - -
588A ARG 3.1 6.2 + - - -
589A ILE* 1.3 76.2 - - - +
591A GLN* 1.3 79.1 + - - +
592A GLN 3.4 0.4 + - - -
593A THR* 3.1 25.2 + - - -
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Residues in contact with GLN 591 (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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189A ARG* 3.4 35.4 - - - +
191A PHE* 4.7 9.1 - - - -
211A LEU 4.9 3.7 - - - +
213A SER* 2.7 27.3 + - - +
215A ASP* 2.5 27.1 + - - +
590A GLY* 1.3 75.8 - - - -
592A GLN* 1.3 62.4 + - + +
594A VAL* 2.7 33.3 + - - +
595A ASP* 3.1 9.1 + - - -
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Residues in contact with GLN 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A THR* 4.9 11.1 - - + +
156A LYS* 4.1 18.4 + - - -
590A GLY 3.4 0.8 + - - -
591A GLN* 1.3 84.2 + - + +
593A THR* 1.3 53.9 + - - +
595A ASP* 3.5 12.4 - - + +
596A SER* 2.7 42.6 + - - +
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Residues in contact with THR 593 (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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148A SER* 5.0 17.5 + - - +
151A VAL* 5.8 3.6 - - + -
152A THR* 4.7 12.6 + - - +
589A ILE* 3.6 22.0 - - + -
590A GLY 3.1 15.1 + - - -
591A GLN 3.0 0.6 + - - -
592A GLN* 1.3 78.2 - - - +
594A VAL* 1.3 57.8 + - - +
596A SER* 3.9 5.1 - - - -
597A LEU* 3.0 44.0 + - + +
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Residues in contact with VAL 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 5.7 0.9 - - - +
191A PHE* 5.4 9.2 - - + -
211A LEU* 4.2 24.9 - - + -
578A ALA* 4.6 4.7 - - + +
581A ILE* 3.6 28.9 - - + -
582A ILE* 5.1 12.8 - - + -
589A ILE* 3.4 27.6 - - + +
590A GLY 4.4 1.1 - - - +
591A GLN* 2.7 21.1 + - - +
593A THR* 1.3 70.8 - - - +
595A ASP* 1.3 64.5 + - - +
596A SER 3.2 0.2 - - - -
598A LEU* 2.9 34.2 + - + +
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Residues in contact with ASP 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 5.0 12.6 + - - +
208A ILE* 5.7 0.2 - - - +
209A LEU 4.9 2.6 - - - +
210A GLY* 3.3 11.7 - - - -
211A LEU* 2.9 48.0 + - - +
212A LYS* 3.9 14.6 - - + +
234A GLN* 5.0 9.6 + - - +
591A GLN 3.1 4.2 + - - -
592A GLN* 3.1 20.1 + - + +
594A VAL* 1.3 77.1 - - - +
596A SER* 1.3 62.4 + - - +
598A LEU* 4.2 2.3 - - - +
599A PHE* 3.3 24.1 + - - +
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Residues in contact with SER 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.6 18.9 + - - -
152A THR* 4.1 11.0 + - - +
155A ALA* 3.6 27.8 - - - +
159A LYS* 5.6 1.6 + - - +
592A GLN* 2.7 26.1 + - - +
593A THR* 3.9 5.6 - - - -
595A ASP* 1.3 73.7 + - - +
597A LEU* 1.3 66.3 + - - +
599A PHE* 3.1 4.2 + - - +
600A LEU* 3.0 30.1 + - - +
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Residues in contact with LEU 597 (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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151A VAL* 3.6 30.1 - - + -
581A ILE* 3.6 28.7 - - + -
586A ARG* 3.9 21.3 - - - +
589A ILE* 4.6 0.4 - - + -
593A THR* 3.0 37.1 + - + +
594A VAL 4.1 0.2 - - - +
596A SER* 1.3 77.2 - - - +
598A LEU* 1.3 64.2 + - + +
600A LEU* 4.6 2.9 - - + +
601A ASN* 3.5 22.2 + - - +
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Residues in contact with LEU 598 (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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208A ILE* 4.1 16.6 - - + +
211A LEU* 3.9 26.9 - - + +
574A THR* 3.5 40.8 - - + +
577A LEU* 4.2 16.4 - - + +
578A ALA* 4.0 10.1 - - + +
581A ILE* 3.9 28.3 - - + -
594A VAL* 2.9 18.7 + - + +
595A ASP* 4.2 2.9 - - - +
597A LEU* 1.3 80.2 - - + +
599A PHE* 1.3 64.8 + - - +
601A ASN* 3.5 4.3 + - - +
602A SER* 3.0 23.0 + - - -
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Residues in contact with PHE 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 4.0 7.2 - - + -
158A LYS* 3.5 23.8 - - + -
159A LYS* 3.7 28.5 - - + -
162A ILE* 3.5 31.6 - - + -
207A LEU* 5.8 7.0 - - + -
208A ILE* 3.2 33.6 - - + +
209A LEU* 4.6 7.0 - - + +
210A GLY* 5.7 0.2 - - - -
235A PHE* 4.1 19.7 - + - -
595A ASP* 3.3 19.5 + - - +
596A SER* 3.1 3.8 + - - +
598A LEU* 1.3 79.6 - - - +
600A LEU* 1.3 67.1 + - + +
602A SER* 3.2 4.0 + - - -
603A PHE* 2.7 40.5 + - + +
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Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.7 42.8 - - + +
154A ASP* 4.6 8.7 - - + +
155A ALA* 3.8 19.5 - - + +
158A LYS* 3.8 16.4 - - + -
596A SER 3.0 14.9 + - - +
597A LEU* 4.6 3.8 - - + +
599A PHE* 1.3 99.4 - - + +
601A ASN* 1.3 60.4 + - - +
603A PHE* 3.0 7.2 + - + +
604A TYR* 2.7 52.7 + - + +
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Residues in contact with ASN 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LEU* 4.5 17.4 - - - +
597A LEU 3.5 18.6 + - - +
598A LEU* 3.9 3.1 - - - +
599A PHE 3.4 0.4 - - - -
600A LEU* 1.3 77.8 - - - +
602A SER* 1.3 61.1 + - - +
604A TYR* 3.8 7.1 + - - +
605A LYS* 3.2 53.9 + - - +
4B G 5.1 6.0 + - - -
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP 5.2 0.4 - - - -
207A LEU* 3.1 33.9 - - - +
208A ILE* 3.1 24.0 + - - -
598A LEU 3.0 15.1 + - - -
599A PHE* 3.3 8.6 + - - -
601A ASN* 1.3 76.6 - - - +
603A PHE* 1.3 63.5 + - - +
605A LYS* 3.1 10.2 + - - +
606A ASN* 2.4 31.6 + - - +
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Residues in contact with PHE 603 (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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158A LYS* 3.5 40.2 - - + -
161A LEU* 4.8 10.5 - - + -
162A ILE* 3.5 25.8 - - + -
207A LEU* 5.8 1.6 - - - -
599A PHE* 2.7 32.6 + + + +
600A LEU* 3.5 7.9 - - + +
602A SER* 1.3 73.1 + - - +
604A TYR* 1.3 92.0 + + - +
606A ASN* 3.0 19.0 + - - -
607A PHE* 3.1 56.0 + + + +
608A CYS* 4.1 7.8 + - - -
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Residues in contact with TYR 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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154A ASP* 3.9 17.3 + - - -
158A LYS* 4.0 9.1 + - - -
600A LEU* 2.7 38.8 + - + +
601A ASN* 4.3 7.4 - - - +
603A PHE* 1.3 103.1 - + - +
605A LYS* 1.3 60.8 + - + +
608A CYS* 3.4 38.0 - - + +
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Residues in contact with LYS 605 (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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577A LEU* 4.3 10.7 - - - +
601A ASN* 3.2 47.3 + - - +
602A SER* 3.1 11.5 + - - +
604A TYR* 1.3 79.1 - - + +
606A ASN* 1.3 66.1 + - - +
608A CYS 3.8 8.5 - - - +
3B A 3.3 47.8 + - - +
4B G 5.1 5.6 - - - -
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Residues in contact with ASN 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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203A GLU* 4.8 4.5 - - - +
205A ARG* 3.3 39.5 + - + +
206A ASP 3.3 23.6 + - - +
207A LEU* 3.6 12.4 - - - +
602A SER* 2.4 46.6 + - - +
603A PHE* 3.0 4.2 + - - +
605A LYS* 1.3 85.5 - - - +
607A PHE* 1.3 81.4 + - + +
608A CYS 3.4 2.3 + - - +
609A LYS* 4.7 8.3 + - - -
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Residues in contact with PHE 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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162A ILE* 4.2 15.7 - - + -
165A GLU* 3.1 37.7 - - - -
166A ILE* 5.4 0.4 - - + -
198A TYR* 3.2 21.1 - + - -
205A ARG* 3.2 29.4 - - + +
207A LEU* 3.7 30.5 - - + -
603A PHE* 3.1 45.5 + + + -
606A ASN* 1.3 79.1 - - + +
608A CYS* 1.3 63.2 + - - +
609A LYS* 4.3 11.3 + - - +
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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