Contacts of the helix formed by residues 601 - 616 (chain A) in PDB entry 3RFU
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 MET 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A VAL* 3.8 16.8 - - + -
292A ILE* 4.0 22.0 - - + -
314A MET* 3.5 32.8 - - + -
317A ARG* 5.1 1.3 - - - +
600A ILE* 1.3 76.6 - - - +
602A PRO* 1.3 72.5 - - + +
603A GLU* 3.1 22.9 - - + +
604A ASP* 2.5 39.4 + - - +
605A LYS* 3.3 6.6 + - - +
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Residues in contact with PRO 602 (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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275A MET 4.8 0.2 - - - +
276A VAL* 3.7 24.0 - - + -
314A MET* 3.3 26.2 - - + -
318A ILE* 4.1 16.6 - - + -
600A ILE 4.6 0.2 - - - +
601A MET* 1.3 89.8 - - + +
603A GLU* 1.3 59.5 + - - +
605A LYS* 3.4 20.9 + - + +
606A SER 3.5 4.7 + - - -
626A VAL 5.2 0.2 - - - +
627A ASN* 3.8 14.1 - - + -
628A ASP 3.7 21.3 + - - +
630A PRO* 3.3 26.0 - - + +
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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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314A MET* 4.6 1.3 - - + -
317A ARG* 2.8 43.4 + - - +
321A MET* 3.5 34.7 - - + +
601A MET* 3.9 21.7 - - + +
602A PRO* 1.3 81.0 - - - +
604A ASP* 1.3 65.5 + - + +
606A SER* 3.1 8.7 + - - -
607A ARG* 3.0 50.0 + - + +
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Residues in contact with ASP 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 ILE* 3.0 33.1 - - - +
601A MET* 2.5 47.5 + - - +
603A GLU* 1.3 78.0 - - + +
605A LYS* 1.3 62.4 + - - +
607A ARG* 3.0 36.7 + - - +
608A ILE* 2.8 39.8 + - + +
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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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426A ASP* 4.3 3.7 + - - -
576A LEU* 2.9 60.8 + - + +
577A THR* 3.0 11.9 - - - +
578A GLY 4.6 0.4 - - - +
600A ILE* 3.5 14.7 - - + +
601A MET 3.4 12.6 - - - +
602A PRO* 3.5 10.3 - - + +
603A GLU 3.1 0.4 - - - -
604A ASP* 1.3 80.6 + - - +
606A SER* 1.3 65.8 + - - +
608A ILE* 3.1 4.0 + - - +
609A VAL* 3.0 27.4 + - - +
621A MET* 4.0 8.7 - - - -
627A ASN* 4.4 7.6 - - - +
628A ASP* 3.2 44.0 - - + +
631A ALA* 4.0 12.1 - - + -
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Residues in contact with SER 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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321A MET* 4.7 7.2 + - - +
325A ALA* 5.8 0.5 - - - +
602A PRO 3.5 2.0 + - - -
603A GLU* 3.1 11.5 + - - -
605A LYS* 1.3 78.9 - - - +
607A ARG* 1.3 55.9 + - - +
609A VAL* 3.9 2.2 - - - +
610A SER* 3.0 29.1 + - - -
630A PRO* 3.6 39.7 + - - +
631A ALA* 4.1 11.6 - - - +
634A LYS* 3.9 11.0 - - - +
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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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321A MET* 6.3 0.7 - - - -
603A GLU* 3.0 48.9 + - - +
604A ASP* 3.0 33.8 + - - +
605A LYS 3.1 0.2 - - - -
606A SER* 1.3 76.0 - - - +
608A ILE* 1.3 69.6 + - + +
610A SER* 3.3 7.1 + - - -
611A GLU* 3.0 23.8 + - - +
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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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424A VAL* 6.0 0.9 - - + -
574A VAL* 5.5 3.8 - - + -
576A LEU* 3.7 34.5 - - + -
597A VAL* 5.6 13.5 - - + -
600A ILE* 6.5 1.3 - - + -
604A ASP* 2.8 28.5 + - + +
605A LYS* 3.1 4.5 + - - +
607A ARG* 1.3 77.4 - - + +
609A VAL* 1.3 63.8 + - - +
611A GLU* 3.1 17.0 + - - +
612A LEU* 2.9 43.2 + - + +
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Residues in contact with VAL 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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424A VAL* 4.0 30.5 - - + -
576A LEU* 4.9 1.3 - - + -
605A LYS 3.0 20.3 + - - +
606A SER* 3.9 5.6 - - - +
608A ILE* 1.3 76.1 - - + +
610A SER* 1.3 63.4 + - - +
612A LEU* 3.1 10.7 + - - +
613A LYS* 3.0 23.5 + - + +
619A VAL* 4.2 11.0 - - + -
621A MET* 4.8 0.9 - - + -
631A ALA* 4.0 21.5 - - + +
634A LYS* 4.3 5.2 - - + -
635A ALA* 3.8 38.6 - - + +
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Residues in contact with SER 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 SER 3.0 21.3 + - - -
607A ARG* 3.3 7.4 + - - -
609A VAL* 1.3 75.7 - - - +
611A GLU* 1.3 54.5 + - - +
613A LYS* 3.3 6.2 + - - +
614A ASP* 2.7 43.3 + - - +
634A LYS* 3.4 32.6 + - - +
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Residues in contact with GLU 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 3.0 11.8 + - - +
608A ILE* 3.4 22.3 - - - +
610A SER* 1.3 73.3 - - - +
612A LEU* 1.3 70.9 + - + +
613A LYS 3.1 1.8 - - - -
614A ASP* 2.9 22.9 + - + +
615A LYS* 3.0 35.1 + - + +
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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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422A THR* 4.5 22.7 - - + +
424A VAL* 5.9 4.5 - - + -
574A VAL* 5.5 14.1 - - + -
595A LYS* 5.8 5.4 - - - +
608A ILE* 2.9 46.8 + - + +
609A VAL* 3.4 11.2 - - - +
611A GLU* 1.3 83.5 - - + +
613A LYS* 1.3 51.2 + - - +
615A LYS* 4.4 16.2 - - - -
616A GLY* 2.6 44.4 + - - +
619A VAL* 4.6 19.1 - - + -
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Residues in contact with LYS 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 VAL* 3.0 15.0 + - + +
610A SER 3.4 8.0 + - - +
612A LEU* 1.3 73.1 - - - +
614A ASP* 1.3 66.7 + - - +
615A LYS 4.1 0.2 - - - -
616A GLY 2.5 20.4 - - - +
617A LEU* 4.1 10.4 - - - +
618A ILE 5.5 2.0 - - - +
619A VAL* 3.4 28.0 - - + +
634A LYS* 3.8 46.0 - - - +
635A ALA* 4.2 3.1 - - - -
636A ASP* 2.8 32.5 - - - +
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Residues in contact with ASP 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 SER* 2.7 29.7 + - - +
611A GLU* 2.9 13.7 + - + +
613A LYS* 1.3 84.7 + - - +
615A LYS* 1.3 59.4 + - - +
617A LEU* 5.1 1.6 - - - +
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Residues in contact with LYS 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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595A LYS* 5.6 5.9 - - - +
611A GLU* 3.0 36.9 + - + +
612A LEU* 4.0 18.2 - - - +
614A ASP* 1.3 77.7 - - + +
616A GLY* 1.3 75.1 + - - +
617A LEU* 3.2 14.4 - - - +
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Residues in contact with GLY 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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422A THR* 6.0 2.9 - - - -
612A LEU* 2.6 21.9 + - - +
613A LYS 2.5 29.6 - - - +
615A LYS* 1.3 83.7 - - - +
617A LEU* 1.3 58.0 + - - +
619A VAL* 6.4 0.2 - - - -
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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