Contacts of the helix formed by residues 643 - 656 (chain A) in PDB entry 4N78
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 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A TRP* 3.5 1.0 - - - -
624A ARG* 3.0 28.6 + - - +
639A PRO 3.7 0.8 + - - -
640A ILE* 3.0 17.0 + - - -
641A GLU 3.4 0.2 - - - -
642A MET* 1.3 76.8 - - - +
644A MET* 1.3 55.1 + - - +
645A PRO* 3.4 11.8 - - - +
646A TRP* 3.0 5.2 + - - +
647A ILE* 2.8 32.9 + - - +
694A GLU* 2.5 32.5 + - - -
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Residues in contact with MET 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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412A TYR* 3.8 22.0 - - + -
435A TYR* 5.1 2.2 + - - +
439A THR* 3.9 24.0 - - + -
443A TYR* 3.8 43.7 - - + +
451A LEU* 4.7 3.4 - - + -
621A LEU* 3.6 31.0 + - + +
624A ARG* 4.9 0.6 - - - +
642A MET 3.6 2.4 + - - +
643A SER* 1.3 70.3 - - - +
645A PRO* 1.3 71.3 - - + +
647A ILE* 3.0 12.4 + - + +
648A LEU* 2.9 61.2 + - + +
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Residues in contact with PRO 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A LEU* 4.1 9.9 - - + +
622A TRP* 4.0 28.5 - - + +
643A SER* 3.4 11.0 - - - +
644A MET* 1.3 94.9 - - + +
646A TRP* 1.3 52.8 + - - +
648A LEU* 3.6 2.3 + - + +
649A THR* 2.6 36.3 + - - -
667A SER 4.2 2.2 - - - +
670A LEU* 4.3 33.2 - - + -
671A TYR* 3.4 30.3 - - + -
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Residues in contact with TRP 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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640A ILE* 3.4 49.3 - - + +
641A GLU* 4.5 4.0 - - - -
643A SER* 3.0 6.2 + - - +
645A PRO* 1.3 77.5 - - - +
647A ILE* 1.3 60.0 + - - +
649A THR* 4.1 23.6 - - + -
650A ASP* 2.7 69.4 + - + +
653A LEU* 4.2 11.0 - - + -
668A LEU* 5.2 5.4 - - + -
671A TYR* 3.5 15.0 + - - +
698A CYS* 3.4 48.0 - - + -
701A GLN* 3.7 32.7 - - + +
702A PHE* 4.1 9.0 - + + -
705A LYS* 4.9 1.1 - - + -
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Residues in contact with ILE 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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439A THR* 4.0 5.6 - - - +
440A ARG* 3.7 33.2 - - + +
443A TYR* 5.6 1.8 - - + -
448A LYS* 3.8 27.5 + - + +
640A ILE 4.5 0.2 - - - +
641A GLU* 3.4 28.7 - - - +
642A MET 3.6 19.5 - - - +
643A SER 2.8 22.0 + - - +
644A MET* 3.4 18.2 - - + +
646A TRP* 1.3 73.8 - - - +
648A LEU* 1.3 64.8 + - + +
650A ASP* 4.5 2.1 - - - +
651A HIS* 3.3 23.6 + - - +
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Residues in contact with LEU 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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448A LYS* 3.8 43.6 - - + +
451A LEU* 4.3 17.7 - - + -
452A VAL* 3.7 16.4 - - + +
455A ILE* 4.0 27.1 - - + -
621A LEU* 4.8 4.5 - - + -
644A MET* 2.9 40.4 + - + +
645A PRO* 4.1 3.4 - - + +
647A ILE* 1.3 76.6 - - + +
649A THR* 1.3 62.6 + - - +
651A HIS* 3.9 7.6 + - - +
652A ILE* 3.7 19.6 + - - +
667A SER* 4.3 5.8 - - - -
670A LEU* 4.3 10.3 - - + -
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Residues in contact with THR 649 (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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645A PRO 2.6 23.6 + - - -
646A TRP* 4.0 17.7 - - + -
648A LEU* 1.3 75.1 - - - +
650A ASP* 1.3 66.1 + - - +
651A HIS 3.2 1.3 - - - -
652A ILE* 3.2 14.8 + - - +
653A LEU* 3.3 11.5 + - + +
664A VAL* 3.8 21.2 - - + +
667A SER* 2.8 31.9 + - - +
668A LEU* 3.7 13.1 + - + +
702A PHE* 4.2 19.3 - - + -
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Residues in contact with ASP 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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646A TRP* 2.7 53.4 + - + +
647A ILE* 4.6 2.2 - - - +
649A THR* 1.3 74.0 - - - +
651A HIS* 1.3 52.4 + - - +
653A LEU* 3.1 8.2 + - - +
654A GLU* 2.8 40.6 + - - +
701A GLN* 5.8 0.2 - - - -
705A LYS* 2.8 36.6 + - - +
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Residues in contact with HIS 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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445A SER* 2.9 39.2 + - - -
448A LYS* 3.2 44.8 + - + +
449A PHE* 3.2 33.4 - + - -
647A ILE 3.3 19.3 + - - +
648A LEU* 3.9 7.0 - - - +
649A THR 3.2 0.8 - - - -
650A ASP* 1.3 79.6 - - - +
652A ILE* 1.3 59.0 + - + +
654A GLU* 4.0 3.9 - - - +
655A THR* 2.8 48.6 + - + +
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Residues in contact with ILE 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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449A PHE* 4.3 13.0 - - + -
452A VAL* 3.9 31.2 - - + -
648A LEU 3.7 15.2 + - - +
649A THR 3.2 7.0 + - - +
650A ASP 3.2 0.6 - - - -
651A HIS* 1.3 74.3 - - - +
653A LEU* 1.3 61.1 + - - +
655A THR* 4.0 4.3 - - - -
656A LYS* 2.9 28.6 + - - -
657A GLU 3.6 2.7 + - - +
660A MET* 3.8 47.8 - - + +
661A MET* 4.1 14.7 - - + +
664A VAL* 3.9 27.4 - - + -
667A SER* 4.8 1.3 - - - +
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Residues in contact with LEU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TRP* 4.2 17.0 - - + -
649A THR 3.3 12.7 + - - +
650A ASP* 3.1 11.5 + - - +
652A ILE* 1.3 77.9 - - - +
654A GLU* 1.3 62.3 + - - +
656A LYS* 3.7 8.1 + - - +
661A MET* 5.2 5.6 - - - -
664A VAL* 4.3 8.1 - - + -
702A PHE* 3.6 54.1 - - + +
705A LYS* 4.4 17.1 - - + +
706A LEU* 4.5 23.1 - - + +
709A GLN* 2.9 35.2 + - - +
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Residues in contact with GLU 654 (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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650A ASP* 2.8 26.7 + - - +
651A HIS* 4.0 5.6 - - - +
653A LEU* 1.3 76.6 - - - +
655A THR* 1.3 63.8 + - + +
656A LYS* 3.6 16.1 + - - +
705A LYS* 3.2 31.3 + - - +
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Residues in contact with THR 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A SER* 4.9 1.8 - - - +
449A PHE* 3.3 22.4 - - + -
651A HIS* 2.8 44.5 + - + +
652A ILE 3.7 0.7 + - - -
654A GLU* 1.3 78.2 - - + +
656A LYS* 1.3 72.8 + - - +
657A GLU* 3.0 13.7 + - - +
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Residues in contact with LYS 656 (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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652A ILE 2.9 13.3 + - - -
653A LEU 3.7 13.3 + - - +
654A GLU* 3.3 14.1 + - - +
655A THR* 1.3 81.9 - - - +
657A GLU* 1.3 66.3 + - - +
658A ALA 3.0 1.4 + - - -
661A MET* 3.6 10.1 - - - -
709A GLN* 3.7 35.6 - - + +
744A ASN* 3.0 19.5 + - - +
746A TYR* 4.2 5.4 - - - +
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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