Contacts of the helix formed by residues 630 - 647 (chain A) in PDB entry 1MMG
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 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A PHE* 4.1 17.3 - - + -
587A LYS 3.3 23.8 - - - +
588A ASN* 3.0 17.9 + - - +
590A ASP* 3.6 24.2 - - + +
620A ARG* 3.7 20.6 - - - +
629A THR* 1.3 75.7 - - - +
631A ALA* 1.3 57.3 + - - +
633A GLN* 3.3 10.9 + - - +
634A TYR* 2.9 29.2 + - + +
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Residues in contact with ALA 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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466A PHE* 4.1 13.4 - - + -
470A CYS* 5.8 0.2 - - - -
526A LEU* 4.0 37.9 - - + +
529A LEU* 4.5 3.1 - - + -
530A ASP* 4.0 8.5 - - - +
588A ASN* 2.9 20.0 + - - +
629A THR* 3.9 3.1 - - - +
630A VAL* 1.3 78.7 - - - +
632A ALA* 1.3 52.8 + - - +
634A TYR* 3.3 5.6 + - - +
635A LYS* 2.9 33.5 + - - +
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Residues in contact with ALA 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ASP* 4.2 10.5 + - - +
628A LEU* 3.1 29.6 - - + -
629A THR* 2.9 20.5 + - + +
631A ALA* 1.3 73.2 - - - +
633A GLN* 1.3 66.1 + - - +
635A LYS* 3.3 9.1 + - - +
636A GLU* 3.0 24.6 + - - +
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Residues in contact with GLN 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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620A ARG* 3.6 37.8 - - - +
628A LEU* 3.5 21.5 - - + +
629A THR 2.9 17.4 + - - +
630A VAL* 3.7 14.6 + - - +
632A ALA* 1.3 76.8 - - - +
634A TYR* 1.3 60.7 + - - +
636A GLU* 3.2 5.8 + - - +
637A GLN* 2.9 58.4 + - + +
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Residues in contact with TYR 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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261A TYR* 5.4 11.6 - + + +
262A LEU* 3.6 36.7 - - + +
470A CYS* 3.2 48.0 + - + -
471A ILE* 3.6 7.8 + - - +
473A TYR* 4.0 21.1 - + - -
474A THR* 2.5 31.6 + - - -
526A LEU* 6.0 1.3 - - + -
630A VAL* 2.9 18.9 + - + +
631A ALA* 3.6 8.1 - - - +
633A GLN* 1.3 77.9 - - - +
635A LYS* 1.3 63.5 + - - +
637A GLN* 3.5 8.7 + - + +
638A LEU* 3.1 24.0 + - + +
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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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473A TYR* 3.6 27.3 + - + +
477A LYS* 5.6 0.8 + - - +
518A ASP* 2.8 46.0 + - + -
520A ARG* 4.4 21.0 - - - +
526A LEU* 4.8 8.5 - - + +
631A ALA 2.9 16.4 + - - +
632A ALA* 3.5 8.5 - - - +
633A GLN 3.2 0.2 - - - -
634A TYR* 1.3 76.3 - - - +
636A GLU* 1.3 67.9 + - - +
638A LEU* 3.4 2.1 + - - +
639A ALA* 3.0 24.2 + - + +
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Residues in contact with GLU 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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620A ARG 5.4 1.0 - - - +
628A LEU* 3.9 26.9 - - - +
632A ALA 3.0 16.3 + - - +
633A GLN* 3.3 8.6 - - - +
635A LYS* 1.3 81.5 - - - +
637A GLN* 1.3 69.1 + - + +
639A ALA* 3.2 7.9 + - - +
640A SER* 3.1 25.5 + - - +
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Residues in contact with GLN 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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259A GLN* 4.0 22.4 + - - +
260A SER 4.9 1.4 - - - +
261A TYR* 4.1 29.2 + - + -
633A GLN* 2.9 47.5 + - + +
634A TYR* 4.2 7.7 - - + +
636A GLU* 1.3 83.7 + - - +
638A LEU* 1.3 62.9 + - - +
640A SER* 3.9 8.3 + - - -
641A LEU* 3.1 22.9 + - - +
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Residues in contact with LEU 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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261A TYR* 6.0 0.4 - - - -
473A TYR* 3.6 31.4 - - + -
474A THR* 3.7 46.2 - - + +
477A LYS* 3.6 26.0 - - + +
634A TYR* 3.1 23.2 + - + +
635A LYS* 3.9 5.2 - - - +
636A GLU 3.2 0.4 - - - -
637A GLN* 1.3 77.8 - - - +
639A ALA* 1.3 59.8 + - - +
641A LEU* 3.3 11.2 + - + +
642A MET* 2.9 54.0 + - + +
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Residues in contact with ALA 639 (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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477A LYS* 4.9 12.5 - - - +
635A LYS* 3.0 18.2 + - + +
636A GLU* 3.6 7.4 - - - +
637A GLN 3.2 0.2 - - - -
638A LEU* 1.3 76.4 - - - +
640A SER* 1.3 59.7 + - - +
642A MET* 3.3 6.1 + - - +
643A ALA* 2.8 29.2 + - - +
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Residues in contact with SER 640 (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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636A GLU* 3.1 19.1 + - - +
637A GLN* 3.9 7.4 - - - -
638A LEU 3.3 0.4 - - - -
639A ALA* 1.3 73.8 - - - +
641A LEU* 1.3 69.1 + - - +
643A ALA* 2.9 9.6 + - - +
644A THR* 2.8 28.5 + - - -
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Residues in contact with LEU 641 (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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242A PHE* 4.1 31.6 - - + -
261A TYR* 3.8 26.9 - - + +
453A LEU* 4.1 24.2 - - + -
455A ILE* 5.7 0.9 - - + -
474A THR* 5.0 9.0 - - + -
478A LEU* 5.1 0.9 - - + -
637A GLN 3.1 17.4 + - - +
638A LEU* 3.5 19.7 - - + +
640A SER* 1.3 81.8 - - - +
642A MET* 1.3 68.0 + - - +
644A THR* 3.1 6.9 + - - -
645A LEU* 3.0 37.5 + - + +
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Residues in contact with MET 642 (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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477A LYS* 3.8 34.1 - - + +
478A LEU* 3.6 26.5 - - + -
481A PHE* 3.6 42.2 - - + -
638A LEU* 2.9 37.2 + - + +
639A ALA* 3.8 5.2 - - - +
641A LEU* 1.3 75.3 - - - +
643A ALA* 1.3 63.5 + - - +
645A LEU* 3.2 8.5 + - + -
646A GLU* 2.3 41.5 + - - +
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Residues in contact with ALA 643 (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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639A ALA 2.8 15.1 + - - +
640A SER* 2.9 13.9 + - - +
642A MET* 1.3 80.1 - - - +
644A THR* 1.3 65.1 + - - +
646A GLU* 3.1 14.6 + - - +
647A THR* 3.5 14.2 + - - +
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Residues in contact with THR 644 (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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242A PHE* 4.3 24.2 - - + -
244A GLU* 5.4 3.4 - - - +
449A PHE* 4.0 25.8 - - + -
640A SER* 2.8 13.2 + - - -
641A LEU* 3.4 10.9 - - - -
643A ALA* 1.3 77.6 - - - +
645A LEU* 1.3 65.0 + - - +
647A THR* 2.5 30.7 + - - +
648A THR* 3.5 3.6 - - + +
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Residues in contact with LEU 645 (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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174A SER* 3.6 30.1 - - - +
176A LEU* 4.4 17.3 - - + -
242A PHE* 4.0 23.3 - - + -
453A LEU* 4.9 3.6 - - + -
478A LEU* 3.9 27.8 - - + -
481A PHE* 3.5 24.7 - - + -
641A LEU* 3.0 29.2 + - + +
642A MET* 3.7 13.5 - - + +
644A THR* 1.3 81.4 - - - +
646A GLU* 1.3 57.3 + - - +
647A THR 3.0 0.2 - - - -
648A THR* 2.7 30.0 + - + +
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Residues in contact with GLU 646 (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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481A PHE* 3.9 28.4 - - + +
642A MET* 2.3 55.1 + - - +
643A ALA* 3.6 8.4 - - - +
644A THR 3.0 0.6 + - - -
645A LEU* 1.3 75.5 - - - +
647A THR* 1.3 59.1 + - + +
648A THR 3.7 4.4 + - - +
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Residues in contact with THR 647 (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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171A GLN* 4.2 12.1 + - - +
172A ASN* 4.3 13.2 + - - +
449A PHE* 4.3 10.6 - - - -
643A ALA 3.6 14.4 - - - +
644A THR* 2.5 21.4 + - - +
646A GLU* 1.3 77.6 - - - +
648A THR* 1.3 63.4 + - - +
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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