Contacts of the helix formed by residues 57 - 62 (chain C) in PDB entry 5NJ8
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 57 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.7 24.5 - - - +
56C PHE* 1.3 93.6 - - + +
58C GLN* 1.3 67.6 + - - +
59C ASP* 2.9 12.6 + - + +
60C VAL* 3.1 12.0 + - + -
61C ILE* 3.0 20.1 + - - +
149C GLN* 5.7 2.0 - - - +
150C GLN* 5.9 1.1 - - - +
156D PRO* 3.4 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 3.2 31.6 + - - +
144A ASP* 3.6 17.8 + - - +
56C PHE 3.7 0.6 + - - -
57C PRO* 1.3 72.1 - - - +
59C ASP* 1.3 64.1 + - - +
61C ILE* 3.6 13.0 - - + -
62C ASN* 3.4 21.3 + - - +
149D SER* 4.5 17.8 + - - +
151D ASP* 5.2 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 3.4 32.7 - - - +
59A ASP* 4.1 23.5 - - + +
60A VAL* 5.7 5.2 - - + -
143A GLN* 3.2 11.5 + - - +
149A GLN* 2.7 37.6 + - - +
57C PRO* 2.9 7.8 + - + +
58C GLN* 1.3 78.9 - - - +
60C VAL* 1.3 60.7 + - - +
62C ASN* 4.1 4.9 + - - +
63C LYS* 4.1 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 5.1 6.7 - - + +
63A LYS* 4.2 18.8 - - - +
56C PHE* 3.5 24.7 - - + -
57C PRO* 3.5 19.7 - - + +
59C ASP* 1.3 75.2 - - + +
61C ILE* 1.3 61.4 + - - +
62C ASN 3.0 2.7 - - - -
63C LYS* 2.6 31.0 + - + -
64C LEU* 3.3 22.7 + - + +
149C GLN* 4.7 13.9 - - + +
151C SER* 3.6 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA* 3.3 37.1 - - + +
52C SER* 3.9 15.5 - - - +
54C LEU* 3.7 36.1 - - + +
56C PHE* 4.1 13.2 - - + +
57C PRO 3.0 18.6 + - - +
58C GLN* 3.6 19.1 - - + +
60C VAL* 1.3 78.8 - - - +
62C ASN* 1.3 63.4 + - + +
63C LYS 3.2 3.8 + - - -
64C LEU* 3.8 21.3 + - + +
69C VAL* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 4.5 9.0 - - + +
147A GLY* 2.6 43.2 + - - +
227A LEU* 4.5 19.7 + - - +
228A LEU* 4.8 5.1 - - - +
58C GLN 3.4 17.0 + - - +
59C ASP 4.4 2.9 - - - +
60C VAL 2.9 1.8 + - - -
61C ILE* 1.3 81.4 - - + +
63C LYS* 1.3 61.1 + - - +
64C LEU 3.9 0.4 - - - -
----------------------------------------------------------
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