Contacts of the helix formed by residues 651 - 665 (chain A) 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 VAL 651 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A ILE* 5.6 5.4 - - + -
646A TYR 4.0 1.8 - - - +
647A PHE* 3.0 36.9 + - + +
650A ASN* 1.4 80.3 - - + +
652A ILE* 1.4 69.8 + - + +
653A ASP 3.6 1.1 - - - -
654A LYS* 3.5 3.6 + - - +
655A GLU* 3.0 24.8 + - - +
682A ASN* 3.4 24.9 + - - +
683A ILE* 5.4 7.0 - - + -
686A ASN* 3.8 41.7 - - + +
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Residues in contact with ILE 652 (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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427A LEU* 5.2 9.0 - - + +
429A TYR* 4.8 27.6 - - + -
585A ILE* 4.1 29.2 - - + -
589A GLN* 4.1 14.1 - - - +
647A PHE* 3.8 35.0 - - + +
648A ASN* 3.2 16.3 + - + +
651A VAL* 1.4 82.2 - - + +
653A ASP* 1.3 70.8 + - - +
655A GLU* 3.3 3.3 + - - +
656A VAL* 2.9 45.0 + - + +
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Residues in contact with ASP 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TYR* 4.5 20.0 - - - -
648A ASN* 2.8 46.1 + - - +
649A GLN* 3.6 15.9 - - + +
652A ILE* 1.3 74.9 - - - +
654A LYS* 1.4 62.7 + - - +
656A VAL* 3.3 11.2 - - - +
657A TYR* 3.1 25.5 + - - +
247C TYR* 5.3 1.6 + - - -
329C ARG* 5.5 7.7 - - - -
359C ARG* 4.1 13.3 - - - +
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Residues in contact with LYS 654 (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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649A GLN 3.2 13.4 + - - +
650A ASN* 3.7 22.9 - - - +
651A VAL 3.6 7.2 - - - +
653A ASP* 1.4 79.9 - - - +
655A GLU* 1.4 61.7 + - - +
657A TYR* 3.4 5.8 + - - +
658A SER* 2.9 29.6 + - - +
682A ASN* 5.2 9.0 - - - +
329C ARG* 4.4 32.9 - - - +
330C GLN* 4.2 19.8 + - - +
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Residues in contact with GLU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A VAL 3.0 18.0 + - - +
652A ILE* 3.3 3.5 + - - +
654A LYS* 1.4 76.4 - - - +
656A VAL* 1.4 60.4 + - + +
658A SER* 3.3 10.9 + - - -
659A LEU* 3.0 23.6 + - + +
675A GLU* 3.6 20.6 - - - +
678A GLY* 3.2 28.2 - - - +
679A GLY* 4.3 8.1 + - - +
681A THR 4.6 2.0 - - - +
682A ASN* 3.5 30.7 - - + +
683A ILE 5.8 0.2 - - - +
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Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 5.2 8.7 - - + +
427A LEU* 4.1 26.7 - - + -
429A TYR* 5.6 14.4 - - + -
652A ILE* 2.9 32.6 + - + +
653A ASP* 3.3 22.7 - - - +
655A GLU* 1.4 75.1 - - + +
657A TYR* 1.4 64.6 + - - +
659A LEU* 3.3 8.7 + - + +
660A GLU* 3.1 35.2 + - + +
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Residues in contact with TYR 657 (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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653A ASP 3.1 19.4 + - - +
654A LYS* 3.7 7.0 - - - +
655A GLU 3.3 0.2 - - - -
656A VAL* 1.4 76.4 - - + +
658A SER* 1.4 65.0 + - - +
660A GLU* 3.5 15.8 + - + +
661A LYS* 3.3 21.0 + - + +
664A ARG* 5.5 13.1 + - - -
326C VAL* 4.6 21.7 - - + +
328C PRO* 6.6 0.4 - - + -
329C ARG* 5.0 15.9 - - - +
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Residues in contact with SER 658 (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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654A LYS* 2.9 17.7 + - - +
655A GLU* 3.3 19.3 - - - -
657A TYR* 1.4 79.7 - - - +
659A LEU* 1.3 63.9 + - - +
661A LYS* 3.3 11.0 + - - +
662A CYS* 3.1 22.2 + - - +
675A GLU* 4.1 2.2 - - - +
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Residues in contact with LEU 659 (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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419A LEU* 5.4 10.1 - - + -
423A GLN* 3.5 30.7 - - + +
427A LEU* 4.8 17.5 - - + -
655A GLU* 3.0 18.9 + - + +
656A VAL* 3.3 10.3 + - + +
658A SER* 1.3 76.1 - - - +
660A GLU* 1.4 69.6 + - + +
662A CYS* 3.2 5.4 + - - +
663A TYR* 3.1 29.1 + - + -
675A GLU* 3.1 40.9 - - + +
679A GLY* 5.5 6.5 - - - -
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Residues in contact with GLU 660 (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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423A GLN* 4.6 8.1 - - - +
656A VAL* 3.1 25.6 + - + +
657A TYR* 3.7 20.6 - - + +
658A SER 3.2 0.2 - - - -
659A LEU* 1.4 77.4 - - + +
661A LYS* 1.3 67.1 + - - +
663A TYR* 3.2 32.3 + - + +
664A ARG* 3.1 45.4 + - - +
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Residues in contact with LYS 661 (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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657A TYR* 3.3 12.0 + - + +
658A SER* 3.3 12.6 + - - +
660A GLU* 1.3 80.6 - - - +
662A CYS* 1.4 86.4 + - - +
664A ARG* 3.2 18.2 + - - +
665A ASN* 3.1 49.1 + - + +
666A PRO* 4.7 9.5 - - - +
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Residues in contact with CYS 662 (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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658A SER 3.1 7.1 + - - +
659A LEU 3.2 2.2 + - - +
661A LYS* 1.4 95.2 - - - +
663A TYR* 1.4 63.4 + - - +
666A PRO* 3.2 31.3 - - - +
671A ALA* 3.4 30.9 - - - +
674A ASN* 4.4 9.4 - - - -
675A GLU* 3.2 33.0 - - - +
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Residues in contact with TYR 663 (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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416A ILE* 4.9 23.5 - - + +
419A LEU* 4.8 22.4 - - + -
420A LYS* 6.0 2.5 - - + +
423A GLN* 5.4 5.8 - - - -
659A LEU* 3.1 22.1 + - + +
660A GLU* 3.2 48.1 + - + +
662A CYS* 1.4 77.2 - - - +
664A ARG* 1.4 83.7 + - + +
666A PRO 3.1 15.0 - - - +
667A THR* 3.7 11.8 - - + +
671A ALA* 5.0 5.6 - - - -
672A ILE* 6.1 5.8 - - + -
675A GLU* 5.2 5.7 - - + +
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Residues in contact with ARG 664 (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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657A TYR* 5.5 13.9 + - - -
660A GLU* 3.1 47.3 + - - +
661A LYS* 3.2 18.2 + - - +
663A TYR* 1.4 104.1 + - + +
665A ASN* 1.3 77.3 + - - +
667A THR* 3.6 18.8 + - - +
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Residues in contact with ASN 665 (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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661A LYS* 3.1 36.4 + - + +
664A ARG* 1.3 97.4 + - - +
666A PRO* 1.3 72.0 - - + +
667A THR* 3.6 2.8 + - - -
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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