Contacts of the helix formed by residues 592 - 611 (chain A) in PDB entry 2W8D
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 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A LYS* 6.2 0.2 - - - +
576A TYR* 3.5 28.6 - - - +
587A GLU* 3.8 42.7 + - - -
590A VAL* 3.3 17.9 + - - +
591A ASP* 1.3 69.3 + - - +
593A SER* 1.3 63.3 + - - +
594A GLU 3.2 1.9 + - - -
595A ASP* 3.2 17.1 + - + +
596A SER* 3.1 27.1 + - - +
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Residues in contact with SER 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ASP* 2.8 24.9 + - - -
592A LYS* 1.3 78.2 - - - +
594A GLU* 1.3 69.9 + - - +
596A SER* 3.7 7.7 + - - -
597A LEU* 3.2 30.3 + - - +
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Residues in contact with GLU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A VAL* 3.6 26.2 - - + +
564A PHE* 3.6 20.7 - - + -
566A SER* 2.6 34.5 + - - -
567A PRO* 5.7 0.5 - - - +
568A LYS* 3.9 14.6 - - - +
569A TYR* 3.6 23.0 - - + -
591A ASP* 3.9 3.3 + - + +
592A LYS 3.2 1.2 - - - -
593A SER* 1.3 84.7 + - - +
595A ASP* 1.3 68.7 + - - +
597A LEU* 3.1 11.3 + - + +
598A VAL* 3.0 25.8 + - - +
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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
----------------------------------------------------------
562A GLY 4.9 3.8 - - - +
564A PHE* 3.6 19.0 - - + -
571A LYS* 2.9 30.4 + - - +
576A TYR* 3.4 19.9 + - - +
591A ASP 4.9 0.4 + - - -
592A LYS* 3.2 20.6 + - + +
594A GLU* 1.3 78.7 - - - +
596A SER* 1.3 57.4 + - - +
598A VAL* 3.2 5.5 + - - +
599A LYS* 3.0 60.0 + - - +
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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
----------------------------------------------------------
592A LYS* 3.1 16.4 + - - +
593A SER* 3.9 10.8 - - - -
595A ASP* 1.3 74.2 + - - +
597A LEU* 1.3 64.8 + - - +
599A LYS* 3.4 21.5 + - - +
600A LYS* 3.1 44.6 + - - +
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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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226A TYR* 4.3 10.1 + - + +
230A ASN* 5.2 12.1 - - - +
554A ARG* 6.4 1.6 - - + -
556A VAL* 4.7 19.1 - - + -
593A SER* 3.2 21.1 + - - +
594A GLU* 3.1 16.2 + - + +
596A SER* 1.3 77.3 - - - +
598A VAL* 1.3 57.4 + - - +
600A LYS* 3.6 9.0 + - + +
601A GLU* 2.9 31.4 + - - +
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Residues in contact with VAL 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A VAL* 3.6 15.5 - - + +
558A PRO* 3.9 31.2 - - + -
562A GLY* 4.0 20.2 - - - +
563A ASP 4.3 0.4 - - - +
564A PHE* 3.6 33.7 - - + -
594A GLU 3.0 17.2 + - - +
595A ASP* 3.2 8.5 + - - +
597A LEU* 1.3 72.8 - - - +
599A LYS* 1.3 68.2 + - + +
601A GLU* 3.1 7.8 + - - +
602A LEU* 2.9 33.5 + - + +
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Residues in contact with LYS 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ASP* 3.0 41.1 + - - +
596A SER* 3.4 22.9 + - - +
598A VAL* 1.3 77.9 - - + +
600A LYS* 1.3 51.8 + - - +
602A LEU* 3.3 6.9 + - - +
603A GLU* 2.8 38.7 + - - +
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Residues in contact with LYS 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 3.9 26.0 - - + -
596A SER* 3.1 32.1 + - - +
597A LEU* 3.8 9.6 - - + +
599A LYS* 1.3 76.0 - - + +
601A GLU* 1.3 65.0 + - - +
603A GLU* 3.7 18.1 - - - +
604A MSE 3.0 34.8 + - + +
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Residues in contact with GLU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 3.5 17.8 + - + +
309A TYR* 2.6 34.8 + - + +
524A VAL* 4.1 0.3 - - - +
544A SER* 3.6 21.3 + - - +
554A ARG* 2.8 45.6 + - - +
556A VAL 4.5 0.7 - - - +
558A PRO* 3.8 12.8 - - + +
597A LEU 2.9 22.0 + - - +
598A VAL* 3.1 4.6 + - - +
600A LYS* 1.3 74.2 - - - +
602A LEU* 1.3 62.6 + - - +
604A MSE 3.6 2.6 + - - +
605A SER* 3.4 19.2 + - - -
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 3.6 42.8 - - + -
558A PRO* 4.1 8.5 - - + -
559A PHE 3.7 22.4 - - - +
560A ARG* 4.1 28.0 + - - +
562A GLY* 4.1 17.0 - - - -
598A VAL* 2.9 25.8 + - + +
599A LYS* 3.7 5.6 - - - +
601A GLU* 1.3 76.8 - - - +
603A GLU* 1.3 56.8 + - - +
605A SER* 3.4 6.0 + - - -
606A ASP* 2.9 35.4 + - - +
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Residues in contact with GLU 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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222A GLU* 5.0 0.9 - - - +
599A LYS* 2.8 20.4 + - - +
600A LYS* 3.2 20.6 + - - +
602A LEU* 1.3 74.4 - - - +
604A MSE 1.3 68.6 + - - +
606A ASP* 3.2 8.0 + - - +
607A LYS* 2.6 62.1 + - + +
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Residues in contact with MSE 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 3.6 18.6 - - - +
223A VAL* 3.7 33.7 - - + +
226A TYR* 3.5 43.3 - - + -
227A MSE 4.4 14.4 - - + -
600A LYS* 3.0 24.6 + - + +
601A GLU 4.1 3.6 - - - +
602A LEU 3.3 0.2 - - - -
603A GLU* 1.3 114.1 - - + +
605A SER* 1.3 65.7 + - - +
607A LYS* 3.3 21.6 + - + +
608A ILE* 3.3 21.8 + - - +
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Residues in contact with SER 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.7 14.2 - - - +
309A TYR* 2.9 48.0 + - - +
544A SER* 3.3 23.9 + - - -
601A GLU 3.4 4.8 + - - -
602A LEU 3.4 5.5 + - - -
603A GLU 3.3 0.2 - - - -
604A MSE 1.3 79.4 - - - +
606A ASP* 1.3 63.5 + - - +
608A ILE* 3.0 15.7 + - - +
609A ILE* 3.1 14.8 + - - +
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Residues in contact with ASP 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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309A TYR* 5.1 1.4 - - - +
312A ALA* 5.6 0.2 - - - +
560A ARG* 2.4 45.4 + - - -
602A LEU* 2.9 23.4 + - - +
603A GLU* 3.2 7.3 + - - +
605A SER* 1.3 72.8 + - - +
607A LYS* 1.3 57.9 + - - +
609A ILE* 4.5 1.0 - - - +
610A ASN* 2.8 49.1 + - - +
1638A PEG 2.9 24.9 + - - +
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Residues in contact with LYS 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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219A ASP 5.7 2.0 - - - +
222A GLU* 4.0 19.8 + - - +
223A VAL* 4.0 17.5 - - + -
603A GLU* 2.6 50.8 + - + +
604A MSE 3.5 26.8 - - + +
605A SER 3.2 0.2 - - - -
606A ASP* 1.3 76.0 - - - +
608A ILE* 1.3 64.2 + - - +
610A ASN* 4.9 2.5 - - - +
611A GLY* 3.0 19.3 + - - +
613A LEU* 3.4 16.4 - - + +
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Residues in contact with ILE 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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223A VAL* 3.5 19.7 - - + -
227A MSE 3.4 32.3 - - + -
308A LEU* 3.7 33.7 - - + -
323A ASN* 4.3 0.5 + - - -
542A LEU* 3.9 21.1 - - + -
604A MSE 3.3 7.8 + - - +
605A SER 3.0 8.3 + - - +
607A LYS* 1.3 76.3 - - - +
609A ILE* 1.3 59.3 + - + +
612A ASP* 2.9 24.4 + - - -
613A LEU* 3.0 27.1 + - + -
614A LEU* 4.1 21.8 - - + -
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Residues in contact with ILE 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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302A PHE* 4.0 16.8 - - + -
308A LEU* 3.5 43.7 - - + -
309A TYR 3.8 16.4 - - - +
311A LEU* 4.0 16.2 - - + -
316A VAL* 5.0 4.5 - - + -
320A LYS* 4.1 16.3 + - + -
323A ASN* 3.0 31.4 + - - +
325A LEU* 5.9 2.0 - - + -
605A SER* 3.1 17.1 + - - +
606A ASP* 4.8 0.7 - - - +
608A ILE* 1.3 75.9 - - + +
610A ASN* 1.3 64.4 + - - +
612A ASP 3.4 2.8 + - - -
1638A PEG 3.2 26.0 - - - +
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Residues in contact with ASN 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 4.6 0.9 - - - +
320A LYS* 4.7 13.6 + - - +
606A ASP* 2.8 35.7 + - - +
607A LYS* 4.5 2.2 - - - +
609A ILE* 1.3 77.5 - - - +
611A GLY* 1.3 58.9 + - - +
612A ASP* 3.7 0.9 + - - +
1638A PEG 2.7 36.2 + - - +
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Residues in contact with GLY 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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216A ASP 5.6 0.9 + - - -
607A LYS 3.0 15.6 + - - -
610A ASN* 1.3 77.5 - - - +
612A ASP* 1.4 71.5 + - - +
613A LEU* 3.1 17.7 + - - +
615A ARG* 3.1 16.4 + - - -
616A PHE* 4.6 0.3 - - - -
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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
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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