Contacts of the helix formed by residues 589 - 600 (chain r) in PDB entry 6FF7
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 589 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541r ILE* 5.3 0.2 - - - -
542r ALA 3.4 13.5 - - - -
543r PRO 5.0 7.9 - - - -
544r MET 5.8 4.7 - - - -
545r ARG* 5.9 2.0 - - - -
548r VAL* 5.5 2.8 - - - +
588r CYS* 1.3 75.4 - - - +
590r PRO* 1.3 66.4 - - - +
591r GLU* 4.4 7.9 - - - -
592r LYS* 2.9 23.3 + - - +
593r TRP* 3.2 8.9 + - - +
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Residues in contact with PRO 590 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541r ILE* 4.9 14.3 - - + -
542r ALA 4.2 4.8 - - - -
543r PRO* 5.8 1.5 - - + -
588r CYS 3.9 1.4 - - - -
589r THR* 1.3 70.6 - - - +
591r GLU* 1.3 64.7 + - - +
593r TRP* 3.3 10.9 + - + +
594r ASP* 2.9 21.5 + - - +
627r VAL* 4.5 18.0 - - + +
628r LEU* 4.6 16.6 - - + +
631r LEU* 5.6 6.9 - - + +
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Residues in contact with GLU 591 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589r THR* 3.0 6.3 + - - -
590r PRO* 1.3 78.4 - - - +
592r LYS* 1.3 56.6 + - - +
594r ASP* 2.6 28.5 + - - +
595r ILE* 2.9 14.9 + - - +
627r VAL* 4.8 8.2 - - + +
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Residues in contact with LYS 592 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569r LEU* 4.5 13.0 - - + +
588r CYS* 4.1 15.7 - - + -
589r THR* 2.9 18.4 + - - +
591r GLU* 1.3 75.9 - - - +
593r TRP* 1.3 64.6 + - - +
595r ILE* 3.5 4.6 + - - +
596r ILE* 3.0 29.1 + - - +
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Residues in contact with TRP 593 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588r CYS* 4.8 7.3 - - + +
589r THR 3.2 6.7 + - - +
590r PRO* 3.5 12.3 - - + +
591r GLU 3.2 0.6 - - - -
592r LYS* 1.3 80.2 - - - +
594r ASP* 1.3 56.8 + - - +
596r ILE* 3.8 3.9 - - - +
597r THR* 2.9 31.2 + - - -
602r GLU* 5.5 0.7 - - - +
631r LEU* 5.9 6.1 - - + -
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Residues in contact with ASP 594 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590r PRO 2.9 12.0 + - - +
591r GLU* 2.6 18.3 + - - +
593r TRP* 1.3 68.7 - - - +
595r ILE* 1.3 65.2 + - - +
597r THR* 3.3 5.3 + - - -
598r ARG* 2.9 22.3 + - - +
627r VAL* 5.3 14.8 - - + +
630r ALA* 5.7 6.5 - - + -
631r LEU* 5.8 6.3 - - + +
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Residues in contact with ILE 595 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591r GLU 2.9 13.7 + - - +
592r LYS* 4.1 6.7 - - - +
594r ASP* 1.3 71.3 - - - +
596r ILE* 1.3 58.0 + - - +
598r ARG* 2.7 28.8 + - - +
599r LYS* 2.9 14.6 + - - +
989r SER 5.5 2.0 - - - -
990r HIS 4.7 14.4 - - - +
992r TYR* 5.3 12.8 - - + -
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Residues in contact with ILE 596 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592r LYS 3.0 19.4 + - - +
593r TRP* 4.2 3.8 - - - +
595r ILE* 1.3 77.7 - - - +
597r THR* 1.3 55.6 + - - +
599r LYS* 3.7 5.5 + - - +
600r GLY 3.2 4.2 + - - -
601r GLY* 2.9 34.5 + - - -
602r GLU* 3.5 7.4 + - + +
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Residues in contact with THR 597 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593r TRP 2.9 20.0 + - - -
594r ASP* 3.8 5.4 - - - -
596r ILE* 1.3 76.1 - - - +
598r ARG* 1.3 63.6 + - - +
599r LYS 3.2 0.4 - - - -
600r GLY* 3.2 12.6 + - - -
602r GLU* 3.8 22.1 - - - +
907r LEU* 5.7 3.6 - - - +
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Residues in contact with ARG 598 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594r ASP 2.9 12.6 + - - +
595r ILE* 2.7 17.0 + - - +
597r THR* 1.3 73.5 - - - +
599r LYS* 1.3 59.0 + - - +
903r ALA* 5.1 13.7 - - + +
906r VAL* 5.8 4.4 - - + +
907r LEU* 5.6 9.9 - - - +
989r SER* 4.2 31.4 - - - +
990r HIS* 4.8 5.5 + - - +
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Residues in contact with LYS 599 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573r HIS* 5.6 10.3 - - + -
595r ILE 2.9 13.3 + - - +
596r ILE* 4.1 7.4 - - - +
598r ARG* 1.3 78.2 - - - +
600r GLY* 1.3 58.3 + - - +
601r GLY* 3.6 2.9 - - - +
990r HIS* 5.3 14.8 - - + +
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Residues in contact with GLY 600 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596r ILE 3.2 0.8 + - - -
597r THR 3.2 14.6 + - - -
599r LYS* 1.3 80.8 - - - +
601r GLY* 1.3 57.5 + - - +
602r GLU 2.9 6.5 - - - -
603r ARG* 2.9 32.7 + - - +
604r THR* 3.8 4.5 + - - -
1537r THR* 4.8 13.2 - - - -
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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