Contacts of the helix formed by residues 836 - 849 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560C PRO* 3.7 12.0 - - - +
561C SER 3.1 15.5 + - - -
562C SER* 4.6 1.6 - - - -
831C ALA* 3.5 6.9 - - - +
834C GLY 4.3 0.4 + - - -
835C LYS* 1.3 74.8 - - - +
837C THR* 1.3 64.2 + - - +
838C GLY* 3.1 3.3 + - - -
839C GLU* 2.7 41.1 + - - +
840C ALA 3.1 10.0 + - - -
922C THR* 3.7 27.1 - - - +
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Residues in contact with THR 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C SER* 3.7 13.7 - - - -
563C PHE* 4.3 1.7 + - - +
678C THR* 6.2 0.2 - - - +
679C GLY* 4.7 24.5 - - - +
680C PHE* 5.7 3.3 - - - +
831C ALA* 4.4 13.5 - - + +
836C SER* 1.3 71.2 - - - +
838C GLY* 1.3 66.9 + - - +
839C GLU 3.2 0.2 + - - -
840C ALA* 3.2 4.4 + - - +
841C MET* 2.9 29.3 + - - +
866C GLU* 2.4 38.4 + - - -
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Residues in contact with GLY 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C SER* 2.8 37.5 + - - -
837C THR* 1.3 80.7 + - - +
839C GLU* 1.3 60.5 + - - +
841C MET* 3.4 6.5 + - - +
842C GLU* 3.1 24.6 + - - +
866C GLU* 4.0 8.3 - - - -
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Residues in contact with GLU 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C PRO* 3.9 24.9 - - + +
712C MET* 3.9 28.4 - - + +
834C GLY 4.3 2.3 - - - +
835C LYS* 3.2 26.3 + - - +
836C SER* 2.7 41.6 + - - +
838C GLY* 1.3 73.7 - - - +
840C ALA* 1.3 61.4 + - - +
842C GLU* 3.3 11.8 + - - +
843C LEU* 3.2 20.4 + - - +
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Residues in contact with ALA 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C PHE* 4.2 15.0 - - + -
712C MET* 4.4 6.8 - - - +
713C LEU* 3.6 25.5 - - + +
831C ALA* 4.0 20.9 - - + +
836C SER 3.1 9.2 + - - +
837C THR* 3.2 7.4 + - - +
839C GLU* 1.3 75.8 - - - +
841C MET* 1.3 67.0 + - - +
843C LEU* 3.1 4.2 + - - +
844C MET* 3.0 26.6 + - - +
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Residues in contact with MET 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C PHE* 4.3 10.5 - - + -
837C THR 2.9 16.8 + - - +
838C GLY* 3.6 6.1 - - - +
840C ALA* 1.3 73.0 - - - +
842C GLU* 1.3 59.1 + - - +
844C MET* 3.1 5.2 + - - +
845C GLU* 2.9 36.9 + - - +
859C TRP* 3.4 62.0 - - + +
863C SER* 3.8 21.5 - - - +
866C GLU* 2.9 37.7 - - + +
867C ARG* 4.6 11.9 - - + +
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Residues in contact with GLU 842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838C GLY 3.1 14.4 + - - +
839C GLU* 3.6 9.0 - - - +
840C ALA 3.2 0.2 - - - -
841C MET* 1.3 78.9 - - - +
843C LEU* 1.3 63.8 + - - +
845C GLU* 3.3 18.4 + - - +
846C GLN* 3.0 42.2 + - + +
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Residues in contact with LEU 843 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709C HIS* 3.7 39.3 - - + +
712C MET* 3.6 32.8 - - + -
713C LEU* 4.1 10.1 - - + -
839C GLU 3.2 8.9 + - - +
840C ALA* 3.1 8.1 + - - +
842C GLU* 1.3 80.5 + - - +
844C MET* 1.3 52.5 + - - +
846C GLN* 3.0 23.8 + - + +
847C LEU* 2.8 55.3 + - + +
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Residues in contact with MET 844 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680C PHE* 3.7 35.4 - - + -
682C PHE* 3.9 35.1 - - + -
702C LEU* 4.2 24.0 - - + +
706C ALA* 4.8 9.0 - - - -
713C LEU* 3.8 21.8 - - + -
716C VAL* 5.0 4.0 - - + -
827C ILE* 4.8 7.9 - - + -
840C ALA 3.0 17.8 + - - +
841C MET 3.2 9.2 - - - +
843C LEU* 1.3 75.7 - - - +
845C GLU* 1.3 57.6 + - - +
847C LEU* 3.6 7.3 + - - +
848C ALA* 2.9 29.2 + - - +
859C TRP* 3.8 12.6 - - + -
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Residues in contact with GLU 845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C MET* 2.9 22.4 + - - +
842C GLU* 3.4 19.1 - - - +
844C MET* 1.3 75.0 - - - +
846C GLN* 1.3 66.0 + - - +
848C ALA* 3.2 3.5 + - - +
849C SER* 3.0 21.5 + - - -
857C TYR* 2.9 41.6 + - + +
859C TRP* 3.0 27.1 + - + +
867C ARG* 4.8 8.5 + - - +
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Residues in contact with GLN 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C GLU* 3.0 43.0 + - - +
843C LEU* 3.4 27.6 - - + +
845C GLU* 1.3 75.9 - - - +
847C LEU* 1.3 62.3 + - + +
849C SER* 2.6 27.4 + - - -
850C LYS* 3.8 6.6 - - - +
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Residues in contact with LEU 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C LEU* 3.6 18.4 - - + -
705C GLU* 3.7 33.2 - - + +
706C ALA* 3.9 33.7 - - + +
709C HIS* 4.2 13.7 - - + +
713C LEU* 4.6 4.5 - - + -
843C LEU* 2.8 44.0 + - + +
844C MET* 3.9 3.1 - - - +
846C GLN* 1.3 74.9 - - + +
848C ALA* 1.3 62.0 + - - +
850C LYS* 3.2 21.2 + - + +
851C LEU* 3.7 12.3 - - - +
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Residues in contact with ALA 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682C PHE* 3.7 16.2 - - + -
702C LEU* 4.0 3.1 - - + +
844C MET 2.9 19.0 + - - +
845C GLU* 3.2 6.0 + - - +
847C LEU* 1.3 79.6 - - - +
849C SER* 1.4 59.0 + - - +
850C LYS 3.1 0.7 - - - -
851C LEU* 3.1 35.5 + - + +
855C VAL 4.8 5.9 - - - +
856C GLY 6.1 0.4 - - - -
857C TYR* 3.7 28.6 - - + -
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Residues in contact with SER 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845C GLU 3.0 10.9 + - - -
846C GLN* 2.6 21.9 + - - -
847C LEU 3.1 0.2 - - - -
848C ALA* 1.4 75.1 - - - +
850C LYS* 1.3 71.1 + - - +
851C LEU 3.3 6.5 + - - +
857C TYR* 5.3 2.2 - - - -
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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