Contacts of the helix formed by residues 630 - 646 (chain B) in PDB entry 1PKG
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 HIS 630 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628B SER 5.7 2.4 + - - -
629B ALA* 1.3 78.1 - - - +
631B LEU* 1.3 65.5 + - - +
632B THR* 3.3 6.5 - - - +
633B GLU* 3.0 36.9 + - - +
634B ARG* 3.5 7.0 + - - +
830B ARG* 5.5 9.6 + - - -
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Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A ASP* 4.3 18.2 - - - +
912A LEU* 6.5 1.3 - - + -
630B HIS* 1.3 71.4 - - - +
632B THR* 1.3 75.4 + - - +
634B ARG* 2.8 24.6 + - + +
635B GLU* 3.0 39.5 + - + +
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Residues in contact with THR 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B PHE* 3.9 23.1 - - + -
630B HIS* 4.5 4.5 - - - +
631B LEU* 1.3 86.7 - - - +
633B GLU* 1.3 73.4 + - - +
635B GLU* 3.6 4.8 + - - +
636B ALA* 3.1 24.5 + - + +
813B LEU* 6.0 0.9 - - + -
830B ARG* 5.5 15.7 + - + +
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Residues in contact with GLU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B ALA 3.8 16.0 - - - +
600B PHE* 4.1 23.4 - - + +
625B LEU* 3.2 22.2 - - + +
626B LYS* 5.7 2.4 + - - +
628B SER 5.3 0.5 - - - +
629B ALA* 3.7 20.2 - - + +
630B HIS* 3.0 41.8 + - - +
632B THR* 1.3 90.6 - - - +
634B ARG* 1.3 66.3 + - - +
636B ALA* 3.7 8.8 - - - +
637B LEU* 3.3 13.0 + - - +
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Residues in contact with ARG 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A PRO* 6.4 0.2 - - - +
912A LEU* 5.7 9.0 - - - -
625B LEU* 3.2 39.2 - - + +
629B ALA* 4.5 7.9 + - - +
630B HIS 3.5 16.5 + - - +
631B LEU* 2.8 16.6 + - + +
633B GLU* 1.3 81.0 - - - +
635B GLU* 1.3 65.3 + - + +
637B LEU* 3.2 12.0 + - - +
638B MET* 3.6 12.2 + - - +
665B PRO* 5.6 9.9 - - - +
666B THR 5.9 1.4 - - - +
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Residues in contact with GLU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A ASP* 5.2 3.3 - - - +
631B LEU* 3.0 42.3 + - + +
632B THR* 4.0 4.5 - - - +
634B ARG* 1.3 78.2 - - + +
636B ALA* 1.3 56.7 + - - +
638B MET* 3.5 9.0 + - - +
639B SER* 3.0 28.6 + - - -
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Residues in contact with ALA 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B PHE* 3.6 30.1 - - + +
632B THR 3.1 18.6 + - - +
633B GLU* 4.0 4.3 - - - +
634B ARG 3.2 0.4 - - - -
635B GLU* 1.3 74.0 - - - +
637B LEU* 1.3 60.3 + - - +
639B SER* 4.2 3.4 - - - -
640B GLU* 3.1 26.0 + - - +
812B GLY* 3.4 32.2 - - - +
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Residues in contact with LEU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B PHE 4.9 6.0 + - - +
623B LYS* 3.7 36.6 - - + +
624B MET 5.1 0.4 - - - -
625B LEU* 4.1 29.4 - - + +
633B GLU 3.3 10.7 + - - +
634B ARG 3.2 10.1 + - - +
636B ALA* 1.3 75.7 - - - +
638B MET* 1.3 61.7 + - - +
640B GLU* 3.2 6.3 - - + +
641B LEU* 3.0 27.7 + - - +
666B THR* 3.6 41.1 - - + +
668B VAL* 3.6 25.5 - - + +
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Residues in contact with MET 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B ARG 3.6 7.2 + - - +
635B GLU* 3.5 10.6 + - - +
637B LEU* 1.3 79.0 - - - +
639B SER* 1.3 50.9 + - - +
641B LEU* 3.2 25.1 + - + +
642B LYS* 2.8 36.2 + - - +
661B THR* 4.4 15.7 - - + -
666B THR* 4.1 26.2 - - - +
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Residues in contact with SER 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635B GLU 3.0 19.0 + - - -
636B ALA* 4.2 6.3 - - - -
638B MET* 1.3 71.1 - - - +
640B GLU* 1.3 60.9 + - - +
642B LYS* 3.9 6.0 - - - +
643B VAL* 2.9 35.9 + - - +
811B PHE 3.5 12.6 + - - -
812B GLY 3.8 9.3 + - - -
814B ALA 3.9 13.5 + - - -
815B ARG* 4.5 6.0 + - - -
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Residues in contact with GLU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B PHE* 6.1 0.2 - - - +
623B LYS* 2.9 35.7 + - - -
636B ALA 3.1 20.4 + - - +
637B LEU* 3.2 11.7 - - + +
639B SER* 1.3 76.2 + - - +
641B LEU* 1.3 66.3 + - - +
643B VAL* 3.8 0.7 - - - +
644B LEU* 2.8 54.5 + - + +
654B VAL* 5.3 0.5 - - - +
668B VAL* 4.4 11.9 - - + -
810B ASP* 3.8 4.2 + - - +
811B PHE* 2.9 46.4 + - - +
812B GLY* 3.7 5.9 + - - -
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B HIS* 4.9 16.8 - - + -
582B TRP* 4.9 7.9 - - + -
637B LEU 3.0 9.1 + - - +
638B MET* 3.4 30.7 - - + +
640B GLU* 1.3 80.8 - - - +
642B LYS* 1.3 63.1 + - - +
644B LEU* 3.4 5.6 + - - +
645B SER* 3.1 21.7 + - - -
656B LEU* 4.3 15.8 - - + +
659B ALA* 3.6 32.5 - - + -
661B THR* 4.4 9.0 - - + -
666B THR* 4.5 4.5 - - + -
668B VAL* 4.1 22.2 - - + -
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Residues in contact with LYS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B MET 2.8 19.7 + - - +
639B SER* 3.9 7.0 - - - +
641B LEU* 1.3 71.7 - - - +
643B VAL* 1.3 69.2 + - - +
645B SER* 3.0 20.4 + - - -
646B TYR* 3.5 41.4 + - + +
816B ASP* 6.3 1.6 - - - +
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Residues in contact with VAL 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B SER* 2.9 26.8 + - - +
640B GLU 3.9 1.6 - - - +
642B LYS* 1.3 77.2 - - + +
644B LEU* 1.3 60.8 + - - +
645B SER 3.3 0.7 + - - -
646B TYR* 3.4 14.2 + - - +
647B LEU* 3.4 17.6 - - + +
788B CYS* 4.3 16.6 - - - -
811B PHE* 3.6 35.9 - - + -
814B ALA* 4.0 25.8 - - + +
815B ARG* 5.0 4.9 - - - +
816B ASP* 5.7 3.6 - - + +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B TRP* 5.1 0.5 - - - -
640B GLU* 2.8 53.3 + - + +
641B LEU* 3.8 4.5 - - - +
643B VAL* 1.3 72.9 - - - +
645B SER* 1.3 59.6 + - - +
646B TYR 3.3 0.2 - - - -
647B LEU* 4.0 4.2 - - + +
648B GLY* 3.5 19.8 + - - -
653B ILE* 5.0 2.7 - - + -
654B VAL* 3.4 33.0 - - + +
656B LEU* 3.9 26.4 + - + +
668B VAL* 4.4 14.6 - - + -
670B THR* 4.5 15.0 - - + -
811B PHE* 3.6 27.6 - - + -
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Residues in contact with SER 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B LYS* 5.1 5.5 + - - -
582B TRP* 3.0 38.8 + - - -
641B LEU* 3.1 14.3 + - - -
642B LYS* 3.0 13.8 + - - -
644B LEU* 1.3 78.0 - - - +
646B TYR* 1.3 77.5 + - - +
647B LEU 3.3 4.0 + - - -
648B GLY* 4.9 1.0 + - - -
656B LEU* 3.8 9.9 - - - -
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Residues in contact with TYR 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642B LYS* 3.5 39.2 + - + +
643B VAL* 3.4 9.0 + - - +
644B LEU 3.3 0.4 - - - -
645B SER* 1.3 98.6 - - - +
647B LEU* 1.3 72.0 + - + +
650B HIS* 5.6 0.2 + - - -
786B LYS* 4.5 12.5 + - - +
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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