Contacts of the helix formed by residues 635 - 648 (chain A) in PDB entry 1QZJ
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 GLU 635 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A LEU* 3.1 30.5 + - + +
632A THR* 3.6 8.3 + - - +
634A ARG* 1.3 104.1 + - - +
636A ALA* 1.3 57.7 + - - +
637A LEU 3.3 0.9 - - - -
638A MET* 3.4 31.5 + - - +
639A SER* 2.9 33.4 + - - +
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Residues in contact with ALA 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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600A PHE* 4.3 15.3 - - + -
632A THR 3.2 12.3 + - - +
633A GLU* 3.4 19.7 - - - +
634A ARG 3.1 1.4 - - - -
635A GLU* 1.3 77.1 - - - +
637A LEU* 1.3 55.7 + - - +
639A SER* 3.5 8.8 - - - -
640A GLU* 3.1 23.0 + - - +
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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
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600A PHE* 6.4 1.1 - - + -
623A LYS* 3.7 34.1 - - + +
624A MET 3.5 39.9 - - - +
625A LEU* 3.8 20.9 - - + -
633A GLU 4.6 0.4 + - - -
634A ARG 3.5 2.9 + - - +
635A GLU 3.3 0.6 - - - -
636A ALA* 1.3 73.0 - - - +
638A MET* 1.3 63.7 + - - +
639A SER 3.3 0.2 - - - -
640A GLU* 3.4 23.8 - - + +
641A LEU* 3.3 15.4 + - - +
666A THR 3.6 21.8 - - - +
668A VAL* 3.7 18.9 - - + +
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Residues in contact with MET 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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578A TYR* 5.9 4.3 - - + -
634A ARG 4.2 2.2 + - - -
635A GLU* 3.4 33.7 + - - +
637A LEU* 1.3 76.5 - - - +
639A SER* 1.3 61.2 + - - +
641A LEU* 3.3 16.1 + - - +
642A LYS* 3.3 49.9 + - + +
661A THR* 4.1 17.7 - - + +
666A THR* 3.8 36.4 + - + +
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Residues in contact with SER 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 GLU* 2.9 20.0 + - - +
636A ALA* 3.5 10.5 - - - -
637A LEU 3.3 0.2 - - - -
638A MET* 1.3 76.6 - - - +
640A GLU* 1.3 60.4 + - - +
642A LYS* 3.3 8.0 + - - +
643A VAL* 3.1 33.0 + - - +
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Residues in contact with GLU 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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623A LYS* 2.9 32.9 + - + +
636A ALA 3.1 14.3 + - - +
637A LEU* 3.4 27.0 - - + +
638A MET 3.3 0.2 - - - -
639A SER* 1.3 75.5 - - - +
641A LEU* 1.3 61.9 + - - +
643A VAL* 3.4 13.3 - - - +
644A LEU* 3.1 47.5 + - + +
668A VAL* 5.3 3.4 - - + -
810A ASP* 4.4 18.2 + - - +
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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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578A TYR 5.1 8.3 - - - +
582A TRP* 4.4 8.7 - - + -
583A GLU* 5.0 1.3 - - - +
637A LEU 3.3 8.9 + - - +
638A MET* 3.3 19.6 + - - +
640A GLU* 1.3 78.3 - - - +
642A LYS* 1.3 64.5 + - + +
644A LEU* 3.5 3.9 + - - +
645A SER* 2.9 38.1 + - - +
656A LEU* 3.8 28.3 - - + -
659A ALA* 3.8 25.4 - - + -
661A THR* 3.7 30.7 - - + +
668A VAL* 4.0 14.8 - - + +
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Residues in contact with LYS 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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577A PRO 5.3 3.4 + - - -
578A TYR* 4.3 18.6 + - - +
638A MET* 3.3 38.8 + - + +
639A SER* 3.3 9.6 + - - +
641A LEU* 1.3 83.4 - - + +
643A VAL* 1.3 57.9 + - + +
645A SER* 3.5 8.2 + - - +
646A TYR* 3.1 27.5 + - - +
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Residues in contact with VAL 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 SER* 3.1 19.3 + - - +
640A GLU* 3.4 26.7 - - - +
642A LYS* 1.3 74.1 - - + +
644A LEU* 1.3 62.0 + - + +
646A TYR* 3.6 10.5 + - + +
647A LEU* 3.0 31.0 + - - +
788A CYS* 4.9 10.8 - - - -
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Residues in contact with LEU 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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582A TRP* 5.7 0.3 - - - -
623A LYS* 6.5 0.4 - - + -
640A GLU* 3.1 42.8 + - + +
641A LEU 3.8 4.3 - - - +
643A VAL* 1.3 76.3 - - + +
645A SER* 1.3 59.0 + - - +
647A LEU* 3.7 19.8 + - + +
648A GLY* 3.2 27.9 + - - +
649A ASN* 4.9 0.3 - - - +
653A ILE* 4.6 7.0 - - + -
654A VAL* 4.3 19.3 - - + +
656A LEU* 4.0 37.1 - - + +
668A VAL* 4.5 4.9 - - + -
670A THR* 4.4 16.2 - - + -
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Residues in contact with SER 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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582A TRP* 3.2 33.4 + - - +
641A LEU* 2.9 23.8 + - - +
642A LYS* 3.6 9.7 - - - +
643A VAL 3.4 0.2 - - - -
644A LEU* 1.3 77.0 - - - +
646A TYR* 1.3 61.4 + - - +
648A GLY* 3.6 11.1 + - - -
656A LEU* 3.5 7.8 - - - +
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Residues in contact with TYR 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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642A LYS 3.1 17.3 + - - +
643A VAL* 3.7 13.0 - - + +
644A LEU 3.4 0.2 - - - -
645A SER* 1.3 75.4 - - - +
647A LEU* 1.3 64.9 + - - +
648A GLY* 3.5 0.7 + - - -
786A LYS* 3.4 25.6 - - + +
787A ASN* 3.3 27.6 + - + +
788A CYS* 4.2 13.2 - - - -
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Residues in contact with LEU 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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643A VAL 3.0 19.2 + - - +
644A LEU* 3.8 17.0 - - + +
646A TYR* 1.3 79.8 - - - +
648A GLY* 1.3 66.3 + - - +
653A ILE* 3.8 24.0 - - + -
782A PHE* 3.5 32.3 - - + -
783A LEU* 3.6 35.4 - - + -
786A LYS* 3.6 35.9 - - + +
788A CYS* 4.2 11.4 - - - -
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Residues in contact with GLY 648 (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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644A LEU 3.2 14.1 + - - +
645A SER 3.6 7.3 + - - -
646A TYR 3.3 3.2 - - - -
647A LEU* 1.3 83.1 - - - +
649A ASN* 1.3 68.8 + - - +
650A HIS 3.9 0.2 + - - -
653A ILE* 3.8 18.0 - - - +
782A PHE* 4.4 2.9 - - - -
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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