Contacts of the helix formed by residues 898 - 903 (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 PRO 898 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B PHE* 3.7 29.4 - - + -
888B LEU* 3.6 25.6 - - + +
889B ALA* 3.5 27.8 - - - +
892B TYR* 4.4 7.4 - - + -
894B SER* 3.3 19.5 - - - +
896B SER 3.3 3.6 - - - +
897B ILE* 1.3 93.9 - - + +
899B PHE* 1.3 59.9 + - - +
901B VAL* 3.1 12.7 + - - +
902B MET* 3.0 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 899 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B PHE* 3.7 13.9 - + - -
895B TRP 3.6 17.3 - - - -
896B SER* 3.0 29.0 + - - +
898B PRO* 1.3 74.6 - - - +
900B SER* 1.3 65.2 + - - +
902B MET* 3.7 30.3 - - + -
903B LEU* 3.1 37.4 + - + +
1029B VAL* 4.6 9.4 - - + -
1033B PHE* 5.2 10.8 - + + -
1105B D10 3.8 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 900 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B ILE 2.9 17.0 + - - -
899B PHE* 1.3 78.0 - - - +
901B VAL* 1.3 62.0 + - - +
903B LEU* 4.4 1.3 - - - -
946B VAL* 3.6 22.7 - - - +
1022B VAL* 4.5 9.5 - - - +
1025B PHE* 3.5 33.5 - - - +
1026B PHE* 3.9 32.8 - - - -
1029B VAL* 4.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 901 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B LEU* 4.5 11.9 - - + -
892B TYR* 3.5 37.2 - - + +
897B ILE 4.4 0.4 - - - +
898B PRO 3.1 9.4 + - - +
900B SER* 1.3 88.3 + - - +
902B MET* 1.3 66.1 + - - +
903B LEU 3.2 1.8 - - - -
904B VAL* 2.9 30.0 + - - +
939B ALA* 4.0 17.0 - - + +
942B ALA* 4.2 10.8 - - + +
943B ILE* 3.7 26.5 - - + -
946B VAL* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 902 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881B LEU* 4.4 20.4 - - + -
884B VAL* 4.1 18.4 - - + -
885B PHE* 3.6 49.6 - - + -
888B LEU* 4.1 7.9 - - + -
898B PRO 3.0 18.1 + - - +
899B PHE* 3.3 24.1 + - + +
901B VAL* 1.3 76.6 - - - +
903B LEU* 1.3 59.7 + - + +
904B VAL 2.7 7.8 + - - -
905B VAL* 3.0 29.8 + - + +
906B PRO* 4.6 0.2 - - - +
1105B D10 5.0 4.9 - - + -
1116B D10 5.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 903 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B TYR* 2.6 52.0 + - + +
899B PHE* 3.1 25.8 + - + +
900B SER* 4.5 0.7 - - - -
901B VAL 3.1 0.6 + - - -
902B MET* 1.3 76.9 - - + +
904B VAL* 1.3 61.2 + - - +
905B VAL 3.1 0.2 - - - -
906B PRO* 3.1 6.7 - - - +
907B LEU* 4.5 0.2 - - - +
1025B PHE* 3.6 42.1 - - + -
1028B VAL* 6.2 1.6 - - + -
1029B VAL* 4.9 8.7 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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