Contacts of the helix formed by residues 656 - 671 (chain B) in PDB entry 5FLZ
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 ILE 656 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652B TYR* 3.4 37.1 + - + +
655B CYS* 1.3 82.7 - - + +
657B ILE* 1.4 66.0 + - + +
658B GLU 3.6 0.2 - - - -
660B ASN* 2.8 51.3 + - - +
735B ILE* 4.2 20.6 - - + +
738B HIS* 3.0 48.2 - - + +
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Residues in contact with ILE 657 (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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478B LYS* 5.7 7.4 - - + -
482B LEU* 4.2 24.5 - - + +
590B LEU* 4.0 27.8 - - + -
652B TYR* 3.9 10.8 - - + +
653B LEU* 3.2 37.7 + - + +
656B ILE* 1.4 80.8 - - + +
658B GLU* 1.3 66.8 + - - +
660B ASN 3.1 1.9 + - - -
661B PHE* 3.0 23.3 + - + +
731B PHE* 3.3 33.4 - - + -
735B ILE* 4.9 11.7 - - + -
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Residues in contact with GLU 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LYS* 5.8 8.7 + - - +
653B LEU* 3.0 22.7 + - + +
654B ASN* 3.8 10.8 - - - +
657B ILE* 1.3 73.5 - - - +
659B GLU* 1.3 71.3 + - - +
661B PHE* 3.6 4.4 + - - +
662B LYS* 3.1 55.6 + - + +
249D TYR* 3.3 36.7 + - - -
329D ARG* 4.4 4.9 + - - +
359D ARG* 3.2 23.4 + - - -
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Residues in contact with GLU 659 (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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654B ASN 2.7 22.5 + - - +
655B CYS 3.8 17.5 - - - +
656B ILE 4.2 0.2 - - - +
657B ILE 3.3 0.4 - - - -
658B GLU* 1.3 84.0 - - - +
660B ASN* 1.4 63.6 + - - +
662B LYS* 3.3 5.8 + - - +
663B GLU* 3.2 22.3 + - - +
329D ARG* 3.1 36.2 - - + +
330D GLN* 4.2 23.8 - - + +
333D ARG* 3.4 27.7 - - + +
359D ARG* 3.8 7.9 + - - -
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Residues in contact with ASN 660 (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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655B CYS 4.8 0.7 - - - +
656B ILE* 2.8 37.3 + - - +
657B ILE 3.1 1.8 + - - -
659B GLU* 1.4 76.1 - - - +
661B PHE* 1.4 62.9 + - - +
663B GLU* 3.3 15.6 + - - +
664B MET* 3.1 30.6 + - - +
731B PHE* 3.4 30.1 + - + -
734B ASN* 3.2 43.1 + - - +
738B HIS* 6.0 0.3 - - - -
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Residues in contact with PHE 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B VAL* 4.2 21.3 - - + -
475B PHE* 4.8 15.5 - + - -
478B LYS* 3.8 43.3 - - + -
482B LEU* 6.0 0.2 - - + -
657B ILE* 3.0 16.6 + - + +
658B GLU* 4.0 4.7 - - - +
660B ASN* 1.4 74.4 - - - +
662B LYS* 1.3 68.3 + - - +
664B MET* 3.3 23.5 + - + +
665B THR* 3.0 35.3 + - + +
727B VAL* 6.4 0.2 - - + -
731B PHE* 3.6 29.3 - + + -
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Residues in contact with LYS 662 (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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658B GLU* 3.1 44.6 + - + +
659B GLU* 3.6 6.5 - - - +
660B ASN 3.3 0.2 - - - -
661B PHE* 1.3 80.8 - - + +
663B GLU* 1.3 63.2 + - - +
665B THR* 3.2 16.2 - - + +
666B ARG* 3.1 52.5 + - - +
326D VAL* 5.5 1.6 - - - +
329D ARG* 3.7 40.7 - - + +
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Residues in contact with GLU 663 (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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659B GLU 3.2 8.4 + - - +
660B ASN* 3.4 21.6 - - - +
662B LYS* 1.3 77.4 - - - +
664B MET* 1.3 66.6 + - + +
666B ARG* 3.3 15.1 - - + +
667B LYS* 3.1 57.4 + - + +
730B THR* 5.4 6.2 - - - +
734B ASN* 5.2 5.0 + - - -
330D GLN* 5.4 8.1 + - - +
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Residues in contact with MET 664 (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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660B ASN* 3.1 22.5 + - - +
661B PHE* 3.3 33.0 - - + +
663B GLU* 1.3 86.1 - - + +
665B THR* 1.4 56.1 - - - +
667B LYS* 3.5 6.6 + - - +
668B LEU* 3.1 35.0 + - + +
727B VAL* 3.1 62.3 - - + +
728B HIS* 4.1 1.8 - - - +
730B THR* 4.9 8.3 - - + -
731B PHE* 4.0 27.6 - - + -
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Residues in contact with THR 665 (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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475B PHE* 4.5 14.5 - - + -
661B PHE* 3.0 30.4 + - + +
662B LYS* 3.2 33.7 - - + +
664B MET* 1.4 74.3 - - - +
666B ARG* 1.3 61.0 - - + +
668B LEU* 3.4 10.8 + - - +
669B GLN* 2.9 49.6 + - - +
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Residues in contact with ARG 666 (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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662B LYS* 3.1 48.8 + - - +
663B GLU* 3.3 21.0 - - - +
665B THR* 1.3 75.4 - - + +
667B LYS* 1.3 59.6 + - + +
669B GLN* 2.9 15.9 + - - +
670B ARG* 2.7 38.6 + - - +
328D PRO* 5.8 9.9 - - - +
329D ARG* 5.3 9.9 - - - +
330D GLN* 5.6 4.4 + - - +
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Residues in contact with LYS 667 (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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663B GLU* 3.1 43.7 + - + +
664B MET* 3.6 6.5 - - - +
665B THR 3.2 0.2 - - - -
666B ARG* 1.3 81.1 - - + +
668B LEU* 1.3 61.0 + - + +
670B ARG* 3.6 12.3 + - - +
671B THR* 3.7 16.8 + - - +
727B VAL* 6.3 1.3 - - + -
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Residues in contact with LEU 668 (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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471B ARG* 5.7 1.7 + - - +
664B MET 3.1 22.6 + - - +
665B THR* 3.6 10.5 - - - +
666B ARG 3.3 0.2 - - - -
667B LYS* 1.3 75.1 - - + +
669B GLN* 1.3 61.7 + - + +
671B THR* 3.0 19.7 + - - +
723B GLU* 4.3 29.6 - - + +
724B LEU* 5.8 3.4 - - + -
727B VAL* 4.2 33.2 - - + -
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Residues in contact with GLN 669 (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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471B ARG* 3.8 38.0 - - - +
475B PHE* 5.0 9.1 - - - -
665B THR* 2.9 43.7 + - - +
666B ARG* 2.9 17.2 + - - +
668B LEU* 1.3 73.5 - - + +
670B ARG* 1.3 55.9 + - - +
671B THR 2.6 19.8 - - - +
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Residues in contact with ARG 670 (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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474A PRO* 3.2 46.0 + - - +
666B ARG 2.7 20.4 + - - +
667B LYS* 3.9 7.6 - - - +
668B LEU 3.4 0.2 - - - -
669B GLN* 1.3 68.2 - - - +
671B THR* 1.4 72.7 - - + +
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Residues in contact with THR 671 (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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667B LYS 3.7 11.4 + - - +
668B LEU* 3.0 23.1 + - - +
669B GLN 2.6 23.6 - - - +
670B ARG* 1.4 81.8 - - + +
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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