Contacts of the strand formed by residues 73 - 77 (chain C) in PDB entry 3NJ4
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 GLU 73 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ALA 3.0 14.4 + - - +
49C ARG* 3.2 20.4 - - + -
50C ILE 2.9 27.0 + - - -
71C GLY 4.2 1.0 + - - -
72C ALA* 1.3 71.8 - - - +
74C VAL* 1.3 60.7 + - - +
120C PHE* 3.0 35.6 - - + +
121C LYS* 5.6 1.1 - - - -
122C ASP* 3.4 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 3.4 14.8 - - + +
64C ILE* 4.2 12.1 - - + +
67C LEU* 4.0 27.4 - - + -
68C VAL* 4.1 15.6 - - + +
72C ALA* 3.6 16.9 + - + +
73C GLU* 1.3 82.8 - - - +
75C GLN* 1.3 68.4 + - - +
76C TRP* 3.4 36.3 - - + -
97C ILE* 3.2 21.4 - - + +
98C PRO* 3.3 10.9 - - - +
120C PHE* 3.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS* 3.7 13.7 + - - -
50C ILE 3.3 3.3 + - - +
51C ALA* 3.7 3.8 - - - -
52C GLY 3.3 22.2 + - - -
74C VAL* 1.3 78.0 - - - +
76C TRP* 1.3 60.5 + - - +
98C PRO* 3.3 34.4 - - + +
116C GLN 4.0 1.0 - - - +
117C THR* 2.8 47.0 + - + +
119C TYR 2.8 30.5 + - - +
120C PHE* 3.2 35.3 - - + +
121C LYS 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 5.1 1.1 - - + -
52C GLY* 3.7 20.6 - - - -
54C LEU* 2.9 48.8 + - + +
56C MET* 4.1 20.4 - - - -
60C THR* 3.4 18.0 - - + +
63C LEU* 4.3 8.7 - - + -
64C ILE* 3.7 29.4 - - + -
67C LEU* 4.0 12.1 - - + -
74C VAL* 3.4 30.3 - - + -
75C GLN* 1.3 72.7 - - - +
77C SER* 1.3 81.4 + - - +
78C SER 4.6 0.2 - - - -
97C ILE* 5.0 1.7 - - + +
98C PRO 2.8 13.5 + - - +
99C VAL* 4.7 6.5 - - + -
100C TYR* 3.0 25.2 + - - -
117C THR* 3.3 12.4 - - - +
129C LEU* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY 3.2 11.4 + - - -
53C CYS* 3.0 18.5 - - - +
54C LEU 2.9 24.3 + - - +
76C TRP* 1.3 85.7 - - - +
78C SER* 1.3 62.7 + - - +
100C TYR 3.5 15.7 - - - -
101C ALA* 4.5 1.1 - - - -
113C CYS* 4.1 24.0 - - - -
114C ILE* 3.9 14.6 - - - +
117C THR* 4.1 4.5 + - - -
135C LEU* 5.7 0.3 - - - +
----------------------------------------------------------
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