Contacts of the helix formed by residues 629 - 644 (chain A) in PDB entry 4QUN
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 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A ASP* 1.3 90.5 + - - +
630A LEU* 1.3 64.1 + - - +
631A GLU* 3.5 11.9 + - - +
632A GLY* 2.8 24.1 + - - -
633A SER* 3.0 22.2 + - - -
865A ASN* 5.8 1.8 - - - -
867A PRO* 4.1 1.8 - - - -
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Residues in contact with LEU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A THR* 1.3 72.4 - - - +
631A GLU* 1.3 64.4 + - - +
633A SER* 2.8 28.4 + - - +
634A MET* 3.0 25.8 + - + +
862A THR* 3.6 29.6 - - - +
865A ASN* 3.6 33.5 + - - +
866A LEU 3.3 23.6 - - - +
867A PRO* 3.9 7.8 - - - +
868A ILE* 3.8 19.1 - - + -
902A TYR* 3.6 28.9 - - + -
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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
----------------------------------------------------------
629A THR* 3.2 10.9 + - - +
630A LEU* 1.3 78.7 - - - +
632A GLY* 1.3 63.9 + - - +
634A MET* 3.3 2.9 + - - +
635A ALA* 3.1 21.8 + - + +
865A ASN* 5.1 1.2 + - - -
902A TYR* 3.3 25.4 + - + +
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Residues in contact with GLY 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASP* 3.3 23.7 - - - +
629A THR* 2.8 18.2 + - - -
631A GLU* 1.3 79.2 - - - +
633A SER* 1.3 60.6 + - - +
635A ALA* 3.3 7.7 + - - +
636A GLN* 3.1 21.7 + - - +
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Residues in contact with SER 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASP* 3.7 1.8 + - - -
629A THR 3.0 11.8 + - - -
630A LEU* 2.8 20.7 + - - +
632A GLY* 1.3 75.7 - - - +
634A MET* 1.3 64.6 + - - +
636A GLN* 3.4 6.1 + - - +
637A LEU* 2.9 27.5 + - - +
867A PRO* 3.6 2.2 - - - +
868A ILE 3.2 38.3 + - - +
869A TYR* 3.8 28.0 - - - -
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Residues in contact with MET 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 3.0 28.7 + - + +
631A GLU 3.7 4.5 - - - +
632A GLY 3.2 0.2 - - - -
633A SER* 1.3 82.6 - - - +
635A ALA* 1.3 59.3 + - - +
637A LEU* 3.9 22.2 - - + -
638A LYS* 2.9 30.7 + - - +
868A ILE* 3.7 36.1 - - + +
898A ILE* 4.0 11.9 - - + -
899A LEU* 3.6 19.1 - - + +
902A TYR* 3.5 52.0 - - + -
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Residues in contact with ALA 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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631A GLU* 3.1 13.8 + - + +
632A GLY* 3.3 11.2 + - - +
634A MET* 1.3 76.4 - - - +
636A GLN* 1.3 62.9 + - - +
638A LYS* 3.4 5.6 + - - +
639A LYS* 3.0 25.6 + - - +
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Residues in contact with GLN 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASP* 5.1 5.8 - - - +
632A GLY 3.1 13.5 + - - +
633A SER* 3.6 8.5 - - - +
635A ALA* 1.3 78.7 - - - +
637A LEU* 1.3 58.2 + - - +
639A LYS* 3.4 6.3 + - - +
640A GLY* 2.8 26.9 + - - -
646A VAL* 4.9 1.0 - - - +
869A TYR* 3.8 32.5 + - - -
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER 2.9 17.9 + - - +
634A MET* 3.6 26.2 - - + +
635A ALA 3.4 0.2 - - - -
636A GLN* 1.3 77.2 - - - +
638A LYS* 1.3 57.8 + - - +
640A GLY* 3.2 1.2 + - - -
641A LEU* 2.9 37.2 + - + +
646A VAL* 4.3 18.4 - - + -
868A ILE 5.5 0.4 - - - +
870A PRO* 4.3 20.0 - - + -
891A TYR* 5.6 0.4 - - - +
895A CYS* 3.8 48.5 - - + +
898A ILE* 4.2 8.5 - - + -
899A LEU* 3.9 14.1 - - + -
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Residues in contact with LYS 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 MET 2.9 18.1 + - - +
635A ALA* 3.8 6.1 - - - +
637A LEU* 1.3 75.3 - - - +
639A LYS* 1.3 63.0 + - - +
641A LEU* 3.2 5.2 + - - +
642A GLU* 3.0 53.2 + - + +
899A LEU* 3.9 24.8 - - + +
903A GLU* 6.2 0.2 - - - +
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Residues in contact with LYS 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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635A ALA 3.0 18.4 + - - +
636A GLN* 3.7 6.5 - - - +
638A LYS* 1.3 75.8 - - - +
640A GLY* 1.3 58.5 + - - +
642A GLU* 3.4 14.6 + - - +
643A SER* 3.1 36.5 + - - +
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Residues in contact with GLY 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 GLN 2.8 13.2 + - - -
637A LEU 3.2 1.1 + - - -
639A LYS* 1.3 76.6 - - - +
641A LEU* 1.3 59.3 + - - +
643A SER* 3.6 6.1 - - - -
644A GLY* 2.9 31.7 - - - -
645A THR* 3.2 8.2 + - - -
646A VAL* 3.2 28.9 + - - +
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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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637A LEU* 2.9 18.2 + - + +
638A LYS 3.6 6.7 - - - +
640A GLY* 1.3 75.9 - - - +
642A GLU* 1.3 66.1 + - + +
643A SER 3.5 0.2 + - - -
644A GLY* 3.9 5.9 - - - -
646A VAL* 4.0 16.4 - - + -
647A LEU* 4.4 14.8 - - + -
892A LYS* 4.6 18.9 - - + -
895A CYS* 4.0 29.4 - - + -
896A GLU* 4.0 19.1 - - + +
899A LEU* 3.6 31.0 - - + -
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Residues in contact with GLU 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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638A LYS* 3.0 49.5 + - + +
639A LYS* 3.4 15.9 + - - +
641A LEU* 1.3 79.2 - - + +
643A SER* 1.3 62.7 + - - +
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Residues in contact with SER 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A LYS* 3.1 27.2 + - - +
640A GLY* 3.3 2.8 + - - -
642A GLU* 1.3 78.7 - - - +
644A GLY* 1.3 47.5 + - - +
645A THR* 3.0 36.8 + - - +
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Residues in contact with GLY 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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640A GLY 2.9 17.0 - - - -
641A LEU 3.9 8.1 - - - -
642A GLU 3.9 0.2 + - - -
643A SER* 1.3 68.7 + - - -
645A THR* 1.3 64.4 + - - +
646A VAL 3.1 4.4 + - - -
647A LEU* 3.3 15.9 + - - +
648A ILE* 3.7 12.4 + - - +
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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