Contacts of the helix formed by residues 642 - 653 (chain A) in PDB entry 6M0X
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 642 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A LEU* 4.8 0.2 - - - -
635A ASP* 3.8 11.7 - - - +
640A ALA 4.0 0.6 + - - -
641A TRP* 1.3 81.6 - - - +
643A PHE* 1.3 64.1 + - - +
644A ARG* 3.4 21.5 + - - -
645A GLU* 2.5 49.6 + - - +
646A LEU 3.2 8.7 + - - -
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Residues in contact with PHE 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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630A PRO 4.1 5.2 - - - +
631A TYR* 3.6 62.6 - + + +
634A LEU* 4.2 22.0 - - + +
635A ASP* 2.9 30.7 + - - +
641A TRP 3.8 0.6 + - - -
642A SER* 1.3 72.9 - - - +
644A ARG* 1.3 59.3 + - - +
646A LEU* 3.3 3.4 + - + +
647A LYS* 2.8 54.7 + - + +
664A LEU 4.0 5.8 - - - -
665A LEU* 3.8 41.1 - - + -
667A GLU* 4.4 9.2 - - + -
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Residues in contact with ARG 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ASP* 4.7 0.4 + - - -
642A SER* 3.1 24.5 + - - +
643A PHE* 1.3 79.0 - - - +
645A GLU* 1.3 86.0 + - - +
647A LYS* 3.1 15.3 + - + +
648A ALA* 2.9 23.1 + - + +
900A GLU* 6.3 2.7 - - - -
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Residues in contact with GLU 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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641A TRP* 3.9 39.0 - - + +
642A SER* 2.5 38.8 + - - +
644A ARG* 1.3 99.6 + - - +
646A LEU* 1.3 63.2 + - - +
648A ALA* 3.2 8.5 + - - +
649A PHE* 2.9 23.6 + - - +
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Residues in contact with LEU 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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577A LEU* 2.8 46.2 - - + +
578A TYR* 5.0 0.9 - - + -
630A PRO* 4.4 4.7 - - + -
634A LEU* 4.0 22.0 - - + -
641A TRP* 3.7 20.7 - - + +
642A SER 3.2 4.0 + - - +
643A PHE* 3.6 11.0 - - + +
644A ARG 3.2 0.2 - - - -
645A GLU* 1.3 77.9 - - - +
647A LYS* 1.3 63.2 + - - +
649A PHE* 3.2 2.4 + - + +
650A VAL* 2.9 32.2 + - + +
664A LEU* 3.5 23.1 - - + +
665A LEU* 3.4 26.7 - - + -
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Residues in contact with LYS 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 PHE* 2.8 55.9 + - + +
644A ARG* 3.1 11.2 + - - +
646A LEU* 1.3 74.7 - - - +
648A ALA* 1.3 64.2 + - - +
650A VAL* 3.2 2.3 + - - +
651A ARG* 3.0 62.9 + - - +
665A LEU* 3.9 25.4 - - + +
667A GLU* 4.4 11.8 + - - +
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Residues in contact with ALA 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 ARG* 2.9 13.6 + - + +
645A GLU* 3.4 12.1 - - - +
647A LYS* 1.3 77.5 - - - +
649A PHE* 1.3 63.1 + - - +
651A ARG* 3.9 7.5 - - - +
652A GLU* 2.9 34.9 + - - +
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Residues in contact with PHE 649 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A GLN 3.7 26.5 - - - -
573A GLY* 4.6 6.7 - - - -
575A ARG* 2.9 35.9 - - - -
577A LEU* 4.2 16.8 - - + -
641A TRP* 3.3 28.0 - + + -
645A GLU 2.9 16.3 + - - +
646A LEU* 3.6 4.5 - - + +
648A ALA* 1.3 78.2 - - - +
650A VAL* 1.3 67.8 + - + +
652A GLU* 3.3 7.2 + - - +
653A SER* 3.2 38.0 + - - -
655A THR* 5.3 2.0 - - - -
656A LEU* 4.7 9.4 - - + -
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Residues in contact with VAL 650 (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 LEU* 5.1 2.0 - - + -
646A LEU* 2.9 35.4 + - + +
647A LYS 3.9 3.1 - - - +
649A PHE* 1.3 80.7 - - + +
651A ARG* 1.3 63.7 + - - +
653A SER 3.8 5.4 + - - +
656A LEU* 3.8 23.8 - - + +
661A LYS* 3.5 56.5 + - + +
664A LEU* 4.5 13.5 - - + -
665A LEU* 4.2 16.2 - - + -
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Residues in contact with ARG 651 (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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647A LYS* 3.0 59.9 + - - +
648A ALA* 4.0 5.4 - - - +
650A VAL* 1.3 80.4 - - - +
652A GLU* 1.3 65.7 + - - +
653A SER 3.5 5.9 + - - +
661A LYS* 4.5 9.4 + - - +
665A LEU* 5.2 6.2 - - - +
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Residues in contact with GLU 652 (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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648A ALA* 2.9 26.4 + - - +
649A PHE* 3.7 6.6 - - - +
651A ARG* 1.3 78.5 - - - +
653A SER* 1.3 65.1 + - - +
654A LYS* 5.7 1.2 - - - +
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Residues in contact with SER 653 (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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649A PHE* 3.2 35.5 + - - -
650A VAL 3.8 4.4 + - - +
651A ARG 3.4 3.4 - - - +
652A GLU* 1.3 84.6 - - - +
654A LYS* 1.3 66.4 + - - +
655A THR* 3.7 19.3 - - - -
656A LEU* 5.0 5.4 - - - -
661A LYS* 3.7 20.3 + - - -
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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