Contacts of the helix formed by residues 836 - 849 (chain B) in PDB entry 5NC5
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 836 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831B ALA* 3.5 4.5 - - - +
834B GLY 4.3 0.6 + - - -
835B LYS* 1.3 76.9 - - - +
837B THR* 1.3 64.7 + - - +
838B GLY* 3.3 6.4 + - - -
839B GLU* 3.1 42.4 + - - +
840B ALA 3.2 9.2 + - - -
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Residues in contact with THR 837 (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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677B ALA 2.9 29.2 - - - +
678B THR* 3.0 27.1 - - - +
679B GLY 4.1 9.0 - - - +
680B PHE* 5.5 1.7 - - - -
831B ALA* 4.0 8.3 - - + -
835B LYS 4.0 0.6 + - - +
836B SER* 1.3 73.3 - - - +
838B GLY* 1.3 55.7 + - - +
840B ALA* 3.1 4.0 + - - +
841B MET* 2.7 44.9 + - - +
866B GLU* 3.5 25.7 + - - +
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Residues in contact with GLY 838 (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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836B SER* 3.2 8.1 + - - -
837B THR* 1.3 83.8 + - - +
839B GLU* 1.3 56.0 + - - +
841B MET* 3.6 8.2 + - - +
842B GLU* 3.1 30.5 + - - +
866B GLU* 4.5 8.4 + - - -
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Residues in contact with GLU 839 (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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712B MET* 4.0 17.6 - - + +
834B GLY 4.6 1.4 - - - +
835B LYS* 3.6 30.5 + - - +
836B SER* 3.1 38.1 + - - +
838B GLY* 1.3 74.4 - - - +
840B ALA* 1.3 65.8 + - - +
842B GLU* 3.1 16.3 + - - +
843B LEU* 3.0 21.8 + - - +
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Residues in contact with ALA 840 (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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680B PHE* 4.2 10.3 - - + -
712B MET* 4.0 7.9 - - - +
713B LEU* 3.4 27.1 - - + +
831B ALA* 3.8 31.4 - - + +
836B SER 3.2 2.4 + - - -
837B THR* 3.1 7.9 + - - +
839B GLU* 1.3 77.0 - - - +
841B MET* 1.3 63.5 + - - +
843B LEU* 3.1 4.3 + - - +
844B MET* 2.9 26.5 + - - +
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Residues in contact with MET 841 (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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679B GLY 4.8 2.5 - - - +
680B PHE* 4.2 11.9 - - + -
837B THR* 2.7 32.6 + - - +
838B GLY* 3.7 6.5 - - - +
840B ALA* 1.3 72.0 - - - +
842B GLU* 1.3 64.8 + - - +
844B MET* 3.2 3.7 + - - +
845B GLU* 2.9 30.1 + - - +
859B TRP* 3.7 40.5 - - + +
863B SER* 3.6 28.9 - - - +
866B GLU* 3.7 38.6 - - + +
867B ARG* 5.3 8.1 - - - -
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Residues in contact with GLU 842 (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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838B GLY 3.1 16.8 + - - +
839B GLU* 3.1 16.0 + - - +
841B MET* 1.3 79.2 - - - +
843B LEU* 1.3 62.8 + - - +
845B GLU* 3.4 16.3 + - - +
846B GLN* 3.1 41.5 + - - +
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Residues in contact with LEU 843 (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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709B HIS* 3.7 27.6 - - + +
712B MET* 3.3 35.4 - - + -
713B LEU* 3.4 24.2 - - + -
839B GLU 3.0 12.9 + - - +
840B ALA 3.1 8.0 + - - +
842B GLU* 1.3 74.2 - - - +
844B MET* 1.3 56.5 + - - +
846B GLN* 2.8 26.2 + - + +
847B LEU* 2.7 51.4 + - + +
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Residues in contact with MET 844 (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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680B PHE* 3.6 36.3 - - + -
682B PHE* 4.2 22.4 - - + -
702B LEU* 3.7 32.5 - - + -
706B ALA* 4.4 4.9 - - - -
713B LEU* 4.2 16.4 - - + -
716B VAL* 3.9 20.4 - - + -
827B ILE* 4.6 4.5 - - + -
840B ALA 2.9 15.2 + - - +
841B MET 3.5 8.5 - - - +
843B LEU* 1.3 74.6 - - - +
845B GLU* 1.3 56.1 + - - +
847B LEU* 3.3 7.5 + - - +
848B ALA* 2.9 30.4 + - - +
859B TRP* 3.9 13.9 - - + -
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Residues in contact with GLU 845 (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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682B PHE* 5.1 0.2 - - - -
841B MET* 2.9 21.6 + - - +
842B GLU* 3.6 18.7 - - - +
844B MET* 1.3 75.0 - - - +
846B GLN* 1.3 64.4 + - + +
848B ALA* 3.1 5.6 + - - +
849B SER* 3.0 22.9 + - - -
857B TYR* 3.3 34.4 + - + +
859B TRP* 2.9 35.0 + - + +
867B ARG* 5.5 3.1 - - - -
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Residues in contact with GLN 846 (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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842B GLU* 3.1 36.4 + - - +
843B LEU* 2.8 30.9 + - + +
845B GLU* 1.3 78.5 - - + +
847B LEU* 1.3 62.3 - - + +
849B SER* 2.4 27.8 + - - -
850B LYS* 3.8 7.3 - - - +
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Residues in contact with LEU 847 (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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702B LEU* 3.5 18.3 - - + +
705B GLU* 3.9 22.8 - - + +
706B ALA* 3.7 34.3 - - + +
709B HIS* 4.3 15.3 - - + +
713B LEU* 3.9 18.4 - - + -
843B LEU* 2.7 35.1 + - + +
844B MET* 3.7 6.7 - - - +
846B GLN* 1.3 73.4 - - + +
848B ALA* 1.3 62.3 + - - +
850B LYS* 3.3 21.8 + - - +
851B LEU* 3.9 7.4 - - - +
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Residues in contact with ALA 848 (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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682B PHE* 3.8 24.9 - - + -
702B LEU* 3.8 3.3 - - + +
844B MET 2.9 18.0 + - - +
845B GLU* 3.4 6.3 - - - +
847B LEU* 1.3 72.9 - - - +
849B SER* 1.3 59.2 + - - +
850B LYS 3.1 5.4 - - - -
851B LEU* 3.1 39.0 + - + +
855B VAL 4.9 5.4 - - - +
857B TYR* 3.9 18.9 - - + -
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Residues in contact with SER 849 (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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845B GLU 3.0 10.9 + - - -
846B GLN* 2.4 26.2 + - - -
848B ALA* 1.3 74.6 - - - +
850B LYS* 1.3 67.5 + - - +
851B LEU 3.4 4.8 + - - +
857B TYR* 5.3 4.4 - - - -
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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