Contacts of the helix formed by residues 659 - 672 (chain A) in PDB entry 4UDC
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 659 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A TRP* 3.8 2.7 - - - -
614A ARG* 5.8 0.7 - - - +
657A GLN 4.5 0.2 - - - -
658A VAL* 1.3 74.1 - - - +
660A TYR* 1.3 57.9 + - - +
661A GLU* 3.7 7.1 + - - +
662A GLU* 3.0 34.2 + - - +
663A TYR* 3.0 29.6 + - - +
700A ALA 4.9 1.2 + - - -
704A ARG* 3.3 26.7 - - - +
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Residues in contact with TYR 660 (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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537A GLU* 2.8 45.3 + - + +
540A GLU* 3.7 20.6 - - + +
610A TRP* 3.5 36.6 - + + -
614A ARG* 5.7 0.2 - - - +
659A SER* 1.3 72.2 - - - +
661A GLU* 1.3 61.6 + - + +
663A TYR* 3.4 12.0 + + - +
664A LEU* 3.0 51.2 + - + +
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Residues in contact with GLU 661 (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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533A VAL* 3.7 39.4 - - + +
659A SER* 3.3 6.1 + - - +
660A TYR* 1.3 79.6 - - + +
662A GLU* 1.4 62.8 + - - +
664A LEU* 3.5 4.7 + - + -
665A CYS* 3.2 27.9 + - - -
700A ALA* 4.0 18.7 - - + +
703A LYS* 3.4 39.1 + - - +
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Residues in contact with GLU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A VAL* 3.6 5.2 - - + -
659A SER* 3.0 25.0 + - - +
661A GLU* 1.4 74.1 - - - +
663A TYR* 1.4 52.6 + - - +
665A CYS* 3.3 4.1 + - - +
666A MET* 2.9 40.2 + - - +
697A LEU* 3.7 5.4 - - + +
700A ALA* 3.9 20.9 - - + -
701A ILE* 3.6 17.6 - - + +
704A ARG* 2.9 21.9 + - - -
714A ARG* 2.9 43.9 + - - -
718A LEU* 3.7 22.4 - - + +
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Residues in contact with TYR 663 (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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540A GLU* 3.3 25.0 + - - -
606A PHE* 3.4 39.5 - + - -
607A ALA* 3.6 15.6 + - - +
610A TRP* 3.4 63.9 - + + +
653A LEU* 5.3 1.8 - - + -
658A VAL* 4.0 9.3 - - + +
659A SER 3.0 17.6 + - - +
660A TYR* 3.4 14.4 - + - +
662A GLU* 1.4 76.1 - - - +
664A LEU* 1.4 57.4 + - + +
666A MET* 3.2 6.8 + - - +
667A LYS* 2.8 62.9 + - + +
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A VAL* 4.3 17.7 - - + -
536A LEU* 3.7 27.5 - - + +
537A GLU* 3.7 34.1 - - + +
540A GLU* 3.6 35.0 - - + +
577A TRP* 5.7 0.4 - - - +
660A TYR* 3.0 43.8 + - + +
661A GLU* 3.8 6.3 - - + +
662A GLU 3.4 0.2 - - - -
663A TYR* 1.4 79.3 - - + +
665A CYS* 1.3 60.6 + - - +
667A LYS* 4.2 6.2 + - - +
668A THR* 3.4 25.1 + - - -
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Residues in contact with CYS 665 (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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533A VAL* 4.0 13.0 - - - -
536A LEU* 4.4 8.5 - - - -
661A GLU 3.2 19.9 + - - -
662A GLU 3.7 6.7 - - - +
664A LEU* 1.3 74.2 - - - +
666A MET* 1.3 58.7 + - - +
668A THR* 3.3 5.1 + - - +
669A LEU* 3.0 33.3 + - - +
693A TYR* 4.4 6.4 - - + +
696A GLU* 3.5 42.8 - - + -
697A LEU* 3.8 23.3 - - + +
700A ALA* 4.7 2.9 - - - -
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Residues in contact with MET 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A PHE* 3.6 27.8 - - + -
653A LEU* 5.1 0.2 - - + -
658A VAL* 4.3 11.9 - - - -
662A GLU 2.9 25.7 + - - +
663A TYR 3.5 4.0 - - - +
665A CYS* 1.3 72.8 - - - +
667A LYS* 1.4 58.6 + - - +
669A LEU* 3.2 8.8 + - - +
670A LEU* 2.9 31.0 + - - +
697A LEU* 3.7 14.8 - - + -
718A LEU* 3.5 45.5 - - + +
721A LEU* 3.9 23.8 - - + -
722A LEU* 3.5 24.5 - - + +
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Residues in contact with LYS 667 (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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540A GLU* 3.0 27.3 + - - -
541A PRO* 4.9 3.4 - - - +
577A TRP* 3.2 33.0 - - + +
603A LEU* 3.3 43.8 - - + +
606A PHE* 3.7 21.0 - - + -
607A ALA* 4.2 15.3 - - + -
663A TYR* 2.8 54.9 + - + +
664A LEU* 4.2 6.4 + - - +
666A MET* 1.4 67.2 - - - +
668A THR* 1.3 65.1 + - - +
670A LEU* 3.2 10.6 + - - +
671A LEU 3.3 0.7 + - - -
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Residues in contact with THR 668 (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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536A LEU* 3.5 19.5 - - - +
577A TRP* 3.8 20.8 - - - -
581A ILE* 4.0 21.5 - - + +
664A LEU 3.4 16.1 + - - -
665A CYS 3.3 5.9 + - - -
667A LYS* 1.3 76.1 - - - +
669A LEU* 1.3 60.2 + - - +
671A LEU* 3.2 18.7 + - + +
672A LEU* 3.5 12.9 - - + +
693A TYR* 3.7 38.1 - - + -
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Residues in contact with LEU 669 (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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665A CYS 3.0 20.6 + - - +
666A MET* 3.2 8.2 + - - +
668A THR* 1.3 73.0 - - - +
670A LEU* 1.4 64.6 + - - +
672A LEU* 3.1 18.4 + - + +
673A SER* 3.2 13.0 + - - -
690A ARG* 3.8 26.8 + - + +
693A TYR* 3.8 25.6 - - + +
694A ILE* 3.8 27.8 - - + -
697A LEU* 3.8 29.8 - - + -
722A LEU* 3.9 19.5 - - + -
774A PHE* 4.6 7.9 - - + -
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Residues in contact with LEU 670 (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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599A SER* 3.4 11.7 - - - -
602A SER* 3.6 29.0 + - - +
603A LEU* 4.3 8.5 - - + -
606A PHE* 3.3 50.0 - - + -
666A MET 2.9 15.8 + - - +
667A LYS* 3.2 9.3 + - - +
669A LEU* 1.4 72.8 - - - +
671A LEU* 1.3 63.1 + - - +
673A SER* 2.7 31.4 + - - +
722A LEU* 3.7 26.2 - - + +
725A MET* 3.8 20.9 - - + -
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Residues in contact with LEU 671 (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 TRP* 4.2 4.0 - - + -
578A ALA* 4.1 7.4 - - + -
581A ILE* 3.5 31.2 - - + -
584A PHE* 3.7 26.5 - - + -
595A LEU* 3.7 33.6 - - + +
596A LEU* 4.0 21.5 - - + +
599A SER* 3.4 27.7 + - - +
603A LEU* 3.9 16.5 - - + +
667A LYS 3.3 6.1 + - - +
668A THR* 3.2 12.3 + - + +
670A LEU* 1.3 75.7 - - - +
672A LEU* 1.4 63.7 + - + +
673A SER 3.5 2.0 + - - -
674A SER 5.0 1.2 + - - +
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Residues in contact with LEU 672 (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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581A ILE* 6.4 0.2 - - + -
584A PHE* 4.9 6.1 - - + -
587A LEU* 5.1 1.8 - - + -
595A LEU* 4.0 16.8 - - + -
668A THR* 3.5 20.9 - - + +
669A LEU* 3.1 13.4 + - + +
671A LEU* 1.4 89.6 - - + +
673A SER* 1.3 56.1 + - - +
674A SER 3.6 2.2 - - - -
686A PHE* 3.5 39.9 - - + -
689A ILE* 4.3 20.0 - - + -
690A ARG* 3.1 52.0 + - + -
693A TYR* 4.4 11.4 - - + -
772A LEU* 3.5 2.8 - - - +
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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