Contacts of the helix formed by residues 628 - 638 (chain A) in PDB entry 5FZ9
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 SER 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A CYS* 6.1 0.4 - - - -
627A PHE* 1.3 81.6 - - - +
629A HIS* 1.3 63.2 + - - +
630A ASP* 3.6 4.2 + - - +
631A GLU* 3.1 38.5 + - - +
632A MET* 3.2 15.9 + - - +
687A ASP* 5.5 0.2 + - - -
690A ARG* 4.2 3.8 - - - -
698A THR* 4.0 31.1 + - - +
700A PHE* 3.4 15.2 - - - +
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Residues in contact with HIS 629 (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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503A HIS* 5.4 1.0 + - - +
607A TRP* 4.0 8.9 - + - -
608A LEU* 3.5 26.2 + - + -
611A GLY* 3.7 16.2 - - - -
612A ARG* 3.6 40.0 + - - +
615A VAL* 3.9 25.8 - - + +
627A PHE* 3.6 16.3 + - + -
628A SER* 1.3 69.6 + - - +
630A ASP* 1.3 68.4 + - - +
632A MET* 3.2 25.1 + - + +
633A ILE* 3.0 29.6 + - + +
654A ASP* 3.0 20.4 + - - -
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Residues in contact with ASP 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ARG* 3.1 32.7 + - - -
628A SER* 3.4 5.0 + - - +
629A HIS* 1.3 78.7 - - - +
631A GLU* 1.3 62.1 + - - +
633A ILE* 3.2 6.7 + - - +
634A CYS* 3.0 31.3 + - - -
700A PHE* 3.9 18.5 - - + -
1763A EDO 2.5 28.1 + - - -
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Residues in contact with GLU 631 (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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476A THR* 5.4 3.1 + - - -
477A ALA* 4.8 15.1 + - - +
628A SER* 3.1 26.5 + - - +
629A HIS 3.2 0.2 - - - -
630A ASP* 1.3 76.5 - - - +
632A MET* 1.3 57.8 + - - +
634A CYS* 3.4 1.4 + - - +
635A LYS* 2.9 29.2 + - + +
683A GLU* 3.4 25.5 - - - +
690A ARG* 3.1 32.4 + - - -
700A PHE* 3.6 27.7 - - + -
1758A DMS 3.9 9.7 + - - +
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Residues in contact with MET 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A VAL* 4.1 24.9 - - - +
472A LEU* 5.0 1.8 - - - -
474A HIS 6.3 0.2 - - - -
475A ILE* 4.1 32.1 - - + +
607A TRP* 3.9 7.9 - - + -
608A LEU* 3.6 30.3 - - + -
627A PHE* 4.2 14.8 - - + -
628A SER 3.2 9.4 + - - +
629A HIS* 3.2 36.2 + - + +
631A GLU* 1.3 79.9 - - - +
633A ILE* 1.3 68.5 + - + +
635A LYS* 3.4 6.3 + - - +
636A MET* 3.1 34.9 + - + +
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Residues in contact with ILE 633 (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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608A LEU* 3.9 26.9 - - + -
612A ARG* 4.3 7.0 - - - +
629A HIS* 3.0 22.0 + - + +
630A ASP* 3.5 9.2 - - - +
632A MET* 1.3 80.6 - - + +
634A CYS* 1.3 60.9 + - - +
636A MET* 3.3 14.7 + - + +
637A ALA* 3.0 27.4 + - + +
651A VAL* 4.2 20.5 - - + +
654A ASP* 3.2 37.2 - - + +
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Residues in contact with CYS 634 (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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630A ASP* 3.0 21.6 + - - +
631A GLU 4.0 1.6 - - - +
633A ILE* 1.3 76.9 - - - +
635A LYS* 1.3 66.2 + - - +
637A ALA* 3.4 8.5 + - - +
638A SER* 3.0 24.6 + - - -
700A PHE* 3.9 27.1 - - + -
1758A DMS 3.6 9.1 - - + +
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Residues in contact with LYS 635 (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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474A HIS* 3.4 31.2 - - + +
475A ILE* 5.2 2.2 - - - -
476A THR* 4.1 29.8 + - + +
631A GLU* 2.9 20.1 + - + +
632A MET* 3.6 8.3 - - - +
633A ILE 3.3 0.2 - - - -
634A CYS* 1.3 78.3 - - - +
636A MET* 1.3 60.5 + - - +
638A SER* 2.9 20.8 + - - +
639A LYS* 3.4 36.8 + - + +
1758A DMS 3.6 32.4 - - - +
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Residues in contact with MET 636 (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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471A VAL* 3.8 21.8 - - + +
474A HIS* 3.5 45.1 - - + +
608A LEU* 4.8 1.8 - - + -
632A MET* 3.1 37.6 + - + +
633A ILE* 3.3 19.0 + - + +
635A LYS* 1.3 74.3 - - - +
637A ALA* 1.3 60.6 + - - +
639A LYS* 2.8 24.7 + - - +
640A ALA 3.2 8.0 + - - -
643A LEU* 3.6 21.2 - - + +
647A VAL* 4.4 6.7 - - - -
651A VAL* 3.7 28.9 - - + -
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Residues in contact with ALA 637 (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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633A ILE* 3.0 18.4 + - + +
634A CYS* 3.7 9.4 - - - +
636A MET* 1.3 74.1 - - - +
638A SER* 1.3 62.2 + - - +
639A LYS 3.2 1.0 + - - -
640A ALA* 3.2 18.7 + - - +
651A VAL* 4.7 0.6 - - - +
745A MET 5.3 7.6 - - - +
747A ALA* 4.8 5.7 - - - +
748A LEU* 3.9 32.3 - - + +
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Residues in contact with SER 638 (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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634A CYS 3.0 15.6 + - - -
635A LYS* 2.9 15.8 + - - +
636A MET 3.1 0.6 - - - -
637A ALA* 1.3 74.7 - - - +
639A LYS* 1.3 75.9 + - - +
640A ALA 3.5 0.7 - - - -
641A ASP* 4.8 2.1 - - - +
1758A DMS 3.9 16.4 - - - +
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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