Contacts of the helix formed by residues 599 - 610 (chain A) in PDB entry 5FWP
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 THR 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A THR* 4.6 3.5 + - - +
519A GLU* 2.7 29.9 + - - +
535A SER* 5.7 0.7 - - - +
537A THR* 4.4 12.6 - - - +
538A LYS* 4.4 17.0 - - - -
593A THR* 3.6 25.8 - - - +
597A GLY 5.3 1.3 - - - +
598A TRP* 1.3 76.9 - - - +
600A ALA* 1.3 55.4 + - - +
601A ASN* 3.5 4.2 + - - +
602A MET* 2.9 22.1 + - + +
603A GLU* 2.7 33.3 + - - +
668A PHE* 5.2 0.4 - - - -
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Residues in contact with ALA 600 (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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593A THR* 3.7 8.7 - - + +
599A THR* 1.3 74.5 - - - +
601A ASN* 1.3 57.1 + - - +
603A GLU* 3.5 7.0 + - - +
604A ARG* 3.1 26.2 + - - +
666A SER 3.4 24.2 - - - +
667A GLY* 3.6 23.6 - - - +
668A PHE* 3.9 27.0 - - + +
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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
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487A THR* 4.3 6.8 - - - +
488A GLY* 3.6 34.7 + - - +
489A GLU* 4.2 2.1 - - + +
514A THR 5.2 0.2 + - - -
515A GLU 4.6 4.9 + - - -
519A GLU* 2.9 28.1 + - - +
599A THR* 3.1 3.9 + - - +
600A ALA* 1.3 77.8 - - - +
602A MET* 1.3 58.8 + - - +
604A ARG* 2.8 40.0 + - - +
605A ILE* 2.9 47.9 + - - +
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Residues in contact with MET 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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519A GLU* 3.1 29.1 - - + +
520A TYR* 5.8 1.1 - - + -
522A VAL* 5.4 2.2 - - + -
523A GLN* 3.6 47.3 - - + +
538A LYS* 6.3 0.9 - - - +
597A GLY 4.3 4.5 - - - +
598A TRP* 3.2 36.6 - - + -
599A THR* 2.9 30.7 + - + +
601A ASN* 1.3 77.2 - - - +
603A GLU* 1.3 57.0 + - - +
605A ILE* 3.4 3.6 + - + +
606A MET* 2.8 44.9 + - + +
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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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598A TRP* 3.4 37.5 - - + +
599A THR 2.7 23.6 + - - +
600A ALA* 3.7 8.0 - - - +
602A MET* 1.3 69.1 - - - +
604A ARG* 1.3 60.5 + - - +
607A LYS* 2.8 68.2 + - + +
621A MET 5.1 0.4 - - - +
622A ALA* 3.6 25.1 - - - +
623A LYS 4.5 1.2 + - - +
668A PHE* 4.6 16.8 - - - -
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Residues in contact with ARG 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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488A GLY 4.5 4.6 + - - -
489A GLU* 3.1 39.1 + - - +
514A THR 4.9 1.0 + - - -
516A PRO* 4.2 10.3 - - - +
600A ALA 3.1 12.6 + - - +
601A ASN* 2.8 37.7 + - - +
603A GLU* 1.3 80.7 - - - +
605A ILE* 1.3 79.4 + - - +
607A LYS* 4.5 1.5 - - - +
608A ALA* 3.3 26.5 + - + +
667A GLY 5.8 2.9 - - - +
604B ARG* 4.7 14.1 + - + +
607B LYS* 2.9 33.9 + - - +
608B ALA* 3.5 12.9 - - + +
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Residues in contact with ILE 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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516A PRO* 3.5 37.2 - - + -
519A GLU* 3.6 15.7 - - + -
520A TYR* 3.5 26.5 - - + +
601A ASN* 2.9 41.8 + - - +
602A MET* 3.6 4.7 - - + +
604A ARG* 1.3 91.4 - - - +
606A MET* 1.3 58.9 + - + +
609A GLN* 2.8 38.8 + - - +
608B ALA* 3.7 17.9 - - - +
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Residues in contact with MET 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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520A TYR* 3.1 38.8 - - - +
523A GLN* 5.9 0.2 - - - -
598A TRP* 3.5 46.2 - - + +
602A MET* 2.8 33.4 + - + +
605A ILE* 1.3 72.3 - - + +
607A LYS* 1.3 61.9 + - - +
610A ALA* 3.0 50.9 + - + +
617A MET* 4.9 2.0 - - - -
87K ILE* 3.8 34.1 - - + -
88K LYS 5.8 0.2 - - - +
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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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598A TRP* 3.9 19.7 - - + -
603A GLU* 2.8 63.5 + - + +
604A ARG* 4.5 1.6 - - - +
606A MET* 1.3 73.7 - - - +
608A ALA* 1.3 58.3 + - - +
610A ALA 4.3 6.6 - - - +
618A GLY* 5.0 11.6 + - - -
622A ALA* 4.8 9.1 - - - +
489B GLU* 5.5 7.3 - - - +
516B PRO* 4.3 9.9 - - - +
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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 ARG* 3.3 18.6 + - + +
607A LYS* 1.3 80.2 - - - +
609A GLN* 1.3 63.1 + - - +
610A ALA 4.3 0.4 - - - +
611A LEU* 5.9 0.9 - - - +
489B GLU* 5.2 8.3 - - - +
516B PRO* 3.7 24.3 - - - +
604B ARG* 5.0 3.1 - - + +
605B ILE* 3.9 30.8 - - + +
608B ALA* 3.6 16.2 - - + -
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Residues in contact with GLN 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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520A TYR* 4.1 16.5 + - - +
605A ILE* 2.8 29.9 + - + +
606A MET* 4.9 0.7 - - - -
608A ALA* 1.3 74.8 - - - +
610A ALA* 1.3 63.3 + - - +
611A LEU* 3.4 14.0 + - - +
605B ILE 5.5 1.1 - - - -
608B ALA* 2.9 15.6 - - - +
609B GLN* 3.5 38.0 - - - +
610B ALA* 2.9 34.0 + - - +
611B LEU* 5.9 0.6 - - - +
89K VAL* 6.2 2.2 - - - +
90K THR 4.9 14.8 + - - +
91K LEU* 4.9 3.8 - - - +
92K VAL* 5.1 3.8 - - - +
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Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TRP* 6.4 0.2 - - + -
606A MET* 3.0 36.7 + - + +
607A LYS 4.3 9.0 - - - +
608A ALA 4.3 2.9 - - - +
609A GLN* 1.3 80.3 - - - +
611A LEU* 1.3 62.5 + - - +
612A ARG* 4.0 20.0 - - + +
516B PRO* 4.8 7.4 - - - +
88K LYS 6.2 0.2 - - - +
90K THR* 5.2 4.0 - - - -
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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