Contacts of the helix formed by residues 650 - 660 (chain A) in PDB entry 4NC6
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 GLY 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A ASP* 2.9 16.3 + - - -
612A ARG* 4.1 9.4 - - - +
649A GLN* 1.3 71.5 - - - +
651A GLN* 1.3 64.0 + - - +
652A SER 3.1 2.9 - - - -
653A PHE* 3.1 34.6 + - - +
654A LEU* 3.9 2.4 + - - +
726A GLN* 5.3 0.7 - - - -
729A LEU 5.9 0.7 - - - -
730A THR* 4.1 20.9 - - - +
733A THR* 4.5 1.2 + - - -
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Residues in contact with GLN 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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635A CYS* 4.9 0.9 - - - -
638A TYR* 3.4 38.4 - - - -
647A TYR* 3.4 22.0 + - + -
648A CYS* 2.8 43.1 + - + +
649A GLN 3.3 1.6 + - - -
650A GLY* 1.3 76.8 - - - +
652A SER* 1.3 57.2 - - - +
654A LEU* 3.1 12.7 + - + +
655A ALA* 2.9 28.7 + - - +
671A LEU* 3.8 17.1 - - + +
675A MET* 3.6 33.9 - - - +
680A LEU* 5.9 1.3 - - + -
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Residues in contact with SER 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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609A ASP* 3.3 15.7 - - - +
610A ILE* 4.0 16.4 - - - -
613A THR* 2.7 28.4 + - - +
631A LEU* 3.5 4.8 - - - +
635A CYS* 3.8 23.6 - - - -
647A TYR* 3.1 14.4 + - - -
651A GLN* 1.3 78.2 - - - +
653A PHE* 1.3 61.4 + - - +
655A ALA* 4.3 0.7 - - - -
656A ALA* 2.9 30.7 + - - +
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Residues in contact with PHE 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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612A ARG* 3.4 67.5 - - + -
613A THR* 3.8 19.5 - - + -
614A PHE* 3.8 22.2 - + + -
650A GLY* 3.1 15.2 + - - +
652A SER* 1.3 84.9 + - - +
654A LEU* 1.3 61.4 + - - +
656A ALA* 3.3 2.8 + - - +
657A VAL* 3.0 27.7 + - - +
733A THR* 3.3 36.3 - - - +
734A ALA* 3.9 28.0 - - + -
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Residues in contact with LEU 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 GLY 3.9 0.6 + - - +
651A GLN* 3.1 14.2 + - + +
653A PHE* 1.3 76.2 - - - +
655A ALA* 1.3 68.7 + - - +
657A VAL* 3.2 5.6 + - + +
658A LEU* 3.1 32.7 + - + +
671A LEU* 3.7 22.9 - - + -
674A ILE* 3.9 41.3 - - + -
675A MET* 4.8 3.4 - - - -
680A LEU* 4.1 18.2 - - + -
730A THR* 5.0 3.6 - - - +
731A LEU* 4.3 6.3 - - + -
733A THR* 3.5 19.1 + - + +
745A ILE* 4.1 24.9 - - + -
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Residues in contact with ALA 655 (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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631A LEU* 3.7 20.4 - - + -
634A ILE* 4.0 27.1 - - + -
635A CYS* 4.3 4.9 - - - -
651A GLN 2.9 16.0 + - - +
652A SER* 3.8 2.5 - - - +
654A LEU* 1.3 78.1 - - - +
656A ALA* 1.3 56.1 + - - +
658A LEU* 3.3 12.8 + - - +
659A LEU* 2.9 32.2 + - - +
667A ALA* 4.7 1.3 - - - +
671A LEU* 4.4 9.8 - - + +
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Residues in contact with ALA 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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613A THR* 3.6 17.7 - - + -
614A PHE* 3.9 9.4 - - + -
620A PHE* 3.6 25.6 - - + -
631A LEU* 3.7 7.6 - - + +
652A SER 2.9 18.6 + - - +
653A PHE 3.5 5.2 - - - +
654A LEU 3.2 0.2 - - - -
655A ALA* 1.3 72.9 - - - +
657A VAL* 1.4 59.5 + - - +
659A LEU* 3.2 3.6 + - - +
660A LEU* 2.9 37.5 + - - +
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Residues in contact with VAL 657 (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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576A TRP* 3.8 24.4 - - + -
614A PHE* 4.2 5.2 - - + -
653A PHE 3.0 19.0 + - - +
654A LEU* 3.2 11.2 + - + +
656A ALA* 1.4 74.9 - - - +
658A LEU* 1.3 60.3 + - + +
660A LEU* 3.4 9.8 + - - +
661A HIS* 2.8 31.9 + - - -
733A THR* 4.2 6.3 - - + -
738A LEU* 4.2 19.7 - - + -
741A VAL* 4.0 21.1 - - + -
742A PHE* 3.8 12.6 - - + -
745A ILE* 4.2 17.7 - - + -
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Residues in contact with LEU 658 (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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576A TRP* 3.8 26.2 - - + -
654A LEU* 3.1 18.6 + - + +
655A ALA* 3.5 7.9 - - - +
657A VAL* 1.3 76.5 - - + +
659A LEU* 1.3 58.1 + - - +
661A HIS* 3.0 18.4 + - - +
662A MET* 3.0 21.8 + - + +
667A ALA* 3.6 34.3 - - + +
670A VAL* 3.7 22.9 - - + -
671A LEU* 3.7 30.1 - - + +
674A ILE* 4.5 12.6 - - + -
745A ILE* 4.9 6.3 - - + -
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Residues in contact with LEU 659 (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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619A TYR* 4.1 28.1 + - + +
620A PHE* 4.5 4.3 - - + -
627A GLY 4.1 4.7 - - - +
630A SER* 3.9 12.1 - - - -
631A LEU* 3.5 44.9 - - + +
634A ILE* 3.5 25.8 - - + -
655A ALA 2.9 20.5 + - - +
656A ALA* 3.2 4.9 + - - +
658A LEU* 1.3 76.8 - - - +
660A LEU* 1.3 60.8 + - - +
661A HIS 3.1 1.5 + - - -
662A MET 3.5 14.1 + - - +
664A GLU* 3.6 26.0 - - - +
667A ALA* 3.8 4.5 - - + -
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Residues in contact with LEU 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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569A GLU* 5.0 2.4 - - - +
614A PHE* 5.2 2.0 - - + -
617A HIS* 3.5 39.5 - - + +
619A TYR* 3.7 23.8 - - + -
620A PHE* 3.9 13.5 - - + -
656A ALA 2.9 21.9 + - - +
657A VAL 3.6 8.3 - - - +
658A LEU 3.1 1.2 - - - -
659A LEU* 1.3 77.1 - - - +
661A HIS* 1.3 72.1 + - + +
738A LEU* 4.3 13.5 - - + -
742A PHE* 4.1 20.4 - - + -
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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