Contacts of the helix formed by residues 620 - 630 (chain A) in PDB entry 4FM9
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 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A LEU* 3.4 6.5 - - - +
611A LYS* 6.3 0.9 - - - +
618A THR 4.8 4.5 - - - +
619A SER* 1.3 77.9 - - - +
621A SER* 1.3 60.4 + - - +
622A LYS* 3.6 10.9 + - - +
623A GLU* 3.0 39.3 + - - +
624A ALA 2.9 21.0 + - - -
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Residues in contact with SER 621 (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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467A THR* 5.7 1.6 - - - +
468A LEU* 4.4 3.2 - - - +
471A SER* 3.2 27.4 + - - -
620A THR* 1.3 71.8 - - - +
622A LYS* 1.3 61.9 + - - +
624A ALA* 3.0 9.3 + - - +
625A LYS* 2.8 43.5 + - - +
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Residues in contact with LYS 622 (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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620A THR* 3.6 9.8 + - - +
621A SER* 1.3 77.4 - - - +
623A GLU* 1.3 67.5 + - + +
624A ALA 3.0 0.5 + - - -
625A LYS* 3.0 17.1 + - + +
626A GLU* 2.8 50.2 + - + +
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Residues in contact with GLU 623 (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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579A LYS* 2.4 35.9 + - - +
611A LYS* 5.2 2.6 + - - -
613A TYR* 2.8 28.9 + - - -
618A THR 4.2 1.7 - - - +
619A SER* 3.4 6.3 - - - -
620A THR* 3.0 43.0 + - - +
622A LYS* 1.3 81.8 - - + +
624A ALA* 1.3 57.1 + - - +
626A GLU* 3.4 15.1 - - - +
627A TYR* 2.8 43.3 + - - +
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Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 3.5 40.2 - - + +
472A GLY* 4.1 4.3 - - - +
620A THR 2.9 13.7 + - - +
621A SER* 3.1 11.7 - - - +
622A LYS 3.0 0.4 - - - -
623A GLU* 1.3 75.1 - - - +
625A LYS* 1.3 65.5 + - - +
627A TYR* 3.1 13.4 + - + +
628A PHE* 2.9 33.5 + - + -
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Residues in contact with LYS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A SER* 3.3 23.8 - - - +
472A GLY* 4.1 4.9 - - - -
474A GLY* 5.8 2.7 - - - -
475A VAL* 3.7 25.7 - - + +
621A SER* 2.8 32.0 + - - +
622A LYS* 3.5 12.2 - - - +
624A ALA* 1.3 71.9 - - - +
626A GLU* 1.3 52.8 + - + +
628A PHE* 3.2 2.4 + - - -
629A ALA* 2.8 34.0 + - - +
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Residues in contact with GLU 626 (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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579A LYS* 5.2 4.2 + - - -
586A GLU* 4.5 13.1 - - - +
622A LYS* 2.8 49.2 + - + +
623A GLU* 3.4 18.9 - - - +
625A LYS* 1.3 74.3 - - + +
627A TYR* 1.3 69.9 + - + +
629A ALA* 3.0 22.7 - - - +
630A ASP* 3.2 6.8 + - - +
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Residues in contact with TYR 627 (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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468A LEU* 5.1 2.7 - - + -
573A PHE* 3.9 12.6 - + + -
575A THR* 4.1 20.5 - - + -
576A PRO* 3.5 29.6 + - + +
579A LYS* 3.3 30.1 + - - -
590A TYR* 5.5 0.2 - - - -
613A TYR* 4.3 4.0 - - - -
619A SER* 3.3 38.4 - - - -
623A GLU* 2.8 31.6 + - + -
624A ALA* 3.3 14.6 - - + +
626A GLU* 1.3 73.4 - - + +
628A PHE* 1.3 65.5 + + + +
630A ASP 3.0 12.5 + - - -
631A MET* 4.3 0.2 - - - -
634A HIS* 2.9 47.9 - + + +
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Residues in contact with PHE 628 (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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458A ILE* 5.4 2.0 - - + -
468A LEU* 4.4 4.0 - - + -
469A ALA* 3.9 29.2 - - + -
472A GLY* 3.5 32.1 - - - +
473A LEU* 4.2 17.9 - - + -
475A VAL* 4.6 5.1 - - + +
476A VAL* 4.0 20.9 - - + +
481A TYR* 6.0 1.3 - + - -
537A MET* 4.7 10.8 - - + -
539A MET* 4.8 10.1 - - + -
573A PHE* 3.9 32.5 - + - -
624A ALA* 2.9 31.8 + - + +
625A LYS 3.7 3.4 - - - +
627A TYR* 1.3 79.3 - + + +
629A ALA* 1.3 63.3 + - - +
631A MET* 3.4 39.5 + - + +
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Residues in contact with ALA 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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475A VAL* 4.4 13.9 - - + +
625A LYS 2.8 12.9 + - - +
626A GLU* 3.0 16.4 + - - +
628A PHE* 1.3 77.6 - - - +
630A ASP* 1.3 58.0 + - + +
631A MET* 2.8 10.4 + - - +
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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
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626A GLU 3.2 5.3 + - - +
627A TYR* 3.0 10.4 + - - +
629A ALA* 1.3 73.8 - - + +
631A MET* 1.3 64.0 + - - +
632A LYS* 4.1 5.0 + - - +
633A ARG* 3.1 33.7 + - - +
634A HIS* 3.1 21.0 + - + +
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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