Contacts of the helix formed by residues 601 - 616 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B VAL* 3.8 18.4 - - + -
292B ILE* 4.0 21.8 - - + -
314B MET* 3.5 33.0 - - + -
317B ARG* 5.1 1.1 - - - +
600B ILE* 1.3 76.2 - - - +
602B PRO* 1.3 73.6 - - + +
603B GLU* 3.1 23.1 - - + +
604B ASP* 2.5 40.7 + - - +
605B LYS* 3.3 6.4 + - - +
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Residues in contact with PRO 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B MET 4.8 0.2 - - - +
276B VAL* 3.7 24.0 - - + -
277B THR 5.5 0.2 - - - +
314B MET* 3.3 26.7 - - + -
318B ILE* 4.1 16.4 - - + -
600B ILE 4.6 0.2 - - - +
601B MET* 1.3 90.1 - - + +
603B GLU* 1.3 58.3 + - - +
605B LYS* 3.4 20.8 + - + +
606B SER 3.5 4.3 + - - -
627B ASN* 3.8 13.5 - - + -
628B ASP 3.7 21.3 + - - +
630B PRO* 3.3 25.9 - - + +
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Residues in contact with GLU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B MET* 4.6 1.6 - - + -
317B ARG* 2.8 42.8 + - - +
321B MET* 3.5 34.2 - - + +
601B MET* 3.9 21.5 - - + +
602B PRO* 1.3 81.4 - - - +
604B ASP* 1.3 66.5 - - + +
606B SER* 3.1 8.5 + - - -
607B ARG* 3.0 48.9 + - - +
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Residues in contact with ASP 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B ILE* 3.0 32.7 - - - +
601B MET* 2.5 47.3 + - - +
603B GLU* 1.3 78.5 - - + +
605B LYS* 1.3 62.6 + - - +
607B ARG* 3.0 37.0 + - + +
608B ILE* 2.8 41.1 + - + +
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Residues in contact with LYS 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASP* 4.2 3.9 + - - -
576B LEU* 2.9 59.7 + - + +
577B THR* 3.0 11.5 - - - +
578B GLY 4.6 0.4 - - - +
600B ILE* 3.5 14.4 - - + +
601B MET 3.4 13.7 - - - +
602B PRO* 3.5 10.1 - - + +
603B GLU 3.1 0.2 - - - -
604B ASP* 1.3 82.7 + - - +
606B SER* 1.3 64.6 + - - +
608B ILE* 3.1 4.2 + - - +
609B VAL* 3.0 26.9 + - - +
621B MET* 4.0 9.0 - - - -
627B ASN* 4.4 7.7 - - - +
628B ASP* 3.2 42.8 - - + +
631B ALA* 4.0 12.8 - - + -
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Residues in contact with SER 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B MET* 4.7 7.6 - - - +
325B ALA* 5.8 0.9 - - - +
602B PRO 3.5 2.4 + - - -
603B GLU* 3.1 10.9 + - - -
605B LYS* 1.3 81.0 - - - +
607B ARG* 1.3 57.6 + - - +
609B VAL* 3.9 3.1 - - - +
610B SER* 3.0 29.3 + - - -
630B PRO* 3.6 39.7 + - - +
631B ALA* 4.1 11.3 - - - +
634B LYS* 3.9 11.3 - - - +
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Residues in contact with ARG 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B MET* 6.3 1.1 - - - -
603B GLU* 3.0 49.5 + - - +
604B ASP* 3.0 34.4 + - - +
605B LYS 3.1 0.4 - - - -
606B SER* 1.3 75.4 - - - +
608B ILE* 1.3 70.3 + - + +
610B SER* 3.3 6.5 + - - -
611B GLU* 3.0 23.5 + - - +
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Residues in contact with ILE 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B VAL* 6.0 1.1 - - + -
574B VAL* 5.5 4.0 - - + -
576B LEU* 3.7 34.5 - - + -
597B VAL* 5.6 13.2 - - + -
600B ILE* 6.5 1.3 - - + -
604B ASP* 2.8 29.3 + - + +
605B LYS* 3.6 4.0 - - - +
607B ARG* 1.3 77.8 - - + +
609B VAL* 1.3 64.0 + - - +
611B GLU* 3.1 17.0 + - - +
612B LEU* 2.9 42.9 + - + +
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Residues in contact with VAL 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 4.0 30.1 - - + -
576B LEU* 4.9 1.3 - - + -
605B LYS 3.0 20.3 + - - +
606B SER* 3.9 5.8 - - - +
608B ILE* 1.3 75.4 - - - +
610B SER* 1.3 64.3 + - - +
612B LEU* 3.1 10.8 + - - +
613B LYS* 3.0 22.0 + - + +
619B VAL* 4.2 11.4 - - + -
621B MET* 4.8 0.7 - - + -
631B ALA* 4.0 22.2 - - + +
634B LYS* 4.3 5.2 - - + -
635B ALA* 3.8 38.1 - - + +
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Residues in contact with SER 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B SER 3.0 20.1 + - - -
607B ARG* 3.3 7.8 + - - -
609B VAL* 1.3 76.1 - - - +
611B GLU* 1.3 53.9 + - - +
613B LYS* 3.3 6.4 + - - +
614B ASP* 2.7 42.1 + - - +
634B LYS* 3.4 32.7 + - - +
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Residues in contact with GLU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ARG 3.0 12.6 + - - +
608B ILE* 3.1 21.9 + - - +
610B SER* 1.3 72.0 - - - +
612B LEU* 1.3 72.6 + - - +
613B LYS 3.1 2.0 - - - -
614B ASP* 2.9 21.2 + - + +
615B LYS* 3.0 35.8 + - + +
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B THR* 4.5 22.5 - - + +
424B VAL* 5.9 4.7 - - + -
574B VAL* 5.5 13.9 - - + -
595B LYS* 5.8 5.4 - - - +
608B ILE* 2.9 47.5 + - + +
609B VAL* 3.4 11.7 - - - +
611B GLU* 1.3 83.9 - - + +
613B LYS* 1.3 52.1 + - - +
615B LYS* 4.4 16.6 - - - -
616B GLY* 2.6 43.5 + - - +
619B VAL* 4.6 18.4 - - + -
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Residues in contact with LYS 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B VAL* 3.0 15.5 + - + +
610B SER 3.4 6.9 + - - +
612B LEU* 1.3 73.3 - - - +
614B ASP* 1.3 66.5 + - - +
616B GLY 2.5 21.6 - - - +
617B LEU* 4.1 10.6 - - - +
618B ILE 5.5 2.0 - - - +
619B VAL* 3.4 28.0 - - + +
634B LYS* 3.8 44.6 - - - +
635B ALA* 4.2 2.9 - - - -
636B ASP* 2.8 31.9 - - - +
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Residues in contact with ASP 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B SER* 2.7 30.6 + - - +
611B GLU* 2.9 13.9 + - + +
613B LYS* 1.3 82.9 + - - +
615B LYS* 1.3 60.8 + - + +
617B LEU* 5.1 1.4 - - - +
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Residues in contact with LYS 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595B LYS* 5.6 5.9 - - - +
611B GLU* 3.0 36.9 + - + +
612B LEU* 4.0 17.3 - - - +
614B ASP* 1.3 76.8 - - - +
616B GLY* 1.3 74.4 + - - +
617B LEU* 3.2 14.0 - - - +
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Residues in contact with GLY 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B THR* 6.0 2.5 - - - -
612B LEU* 2.6 22.3 + - - +
613B LYS 2.5 30.0 - - - +
615B LYS* 1.3 83.5 - - - +
617B LEU* 1.3 59.3 + - - +
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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
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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