Contacts of the helix formed by residues 120 - 127 (chain N) in PDB entry 3J0S
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 120 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N GLY* 4.3 10.3 - - - +
5N VAL* 3.2 35.8 - - - +
40N LEU* 5.0 1.5 - - - +
47N ILE* 4.3 3.6 - - - +
82N TYR* 3.0 23.6 + - - -
116N ILE* 2.9 17.8 + - - -
117N TYR* 3.2 0.8 + - - -
119N SER* 1.3 75.1 - - - +
121N LYS* 1.3 58.1 + - - +
122N ASP 3.3 2.7 - - - -
123N ALA* 3.1 4.8 + - - +
124N ILE* 2.7 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 4.7 0.4 - - + -
146C GLY 5.1 2.5 - - - +
148C THR* 2.9 42.9 - - - +
149C THR* 4.6 4.4 + - - +
167C GLU* 4.6 7.4 + - - -
82N TYR* 4.6 0.4 - - - -
103N PHE* 3.4 31.6 - - + -
117N TYR* 3.5 8.4 + - + +
118N ALA* 3.5 10.1 + - - +
119N SER 3.4 2.8 - - - -
120N SER* 1.3 76.2 - - - +
122N ASP* 1.3 63.9 + - - +
124N ILE* 3.1 10.5 - - - +
125N LYS* 3.0 30.2 + - + +
134N GLU* 3.0 40.6 + - - -
136N GLN* 3.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 2.7 31.3 + - - +
148C THR* 4.1 18.8 + - - +
167C GLU* 4.1 18.0 - - - +
168C GLY* 4.2 12.3 - - - -
375C PHE* 4.4 15.6 - - + -
2N ALA 3.1 25.3 - - - +
3N SER* 4.6 2.2 - - - -
120N SER 3.3 0.8 - - - -
121N LYS* 1.3 77.2 - - - +
123N ALA* 1.3 56.2 + - - +
125N LYS* 3.6 8.6 - - - +
126N LYS* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N SER* 3.5 25.3 - - - +
4N GLY 3.6 1.6 - - - +
5N VAL* 3.1 45.6 - - + +
7N VAL* 5.1 2.8 - - - +
47N ILE* 5.3 1.9 - - - +
120N SER* 3.1 10.1 + - - +
122N ASP* 1.3 77.3 - - - +
124N ILE* 1.3 64.5 + - - +
126N LYS* 3.2 17.8 + - - +
127N LYS* 3.6 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N PHE* 6.0 1.6 - - + -
47N ILE* 4.3 11.7 - - + -
82N TYR* 3.4 37.7 - - + +
101N PHE* 3.1 36.1 - - + -
103N PHE* 3.6 14.8 - - + -
120N SER* 2.7 19.1 + - - +
121N LYS* 3.1 14.8 - - - +
123N ALA* 1.3 73.9 - - - +
125N LYS* 1.3 62.3 + - - +
127N LYS* 2.9 52.2 - - - +
128N LEU* 3.3 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 2.9 41.8 + - - +
103N PHE* 4.9 3.8 - - + -
121N LYS* 3.0 31.7 + - + +
122N ASP* 3.6 13.0 - - - +
124N ILE* 1.3 75.3 - - + +
126N LYS* 1.3 63.4 + - - +
127N LYS 3.2 2.2 - - - -
128N LEU* 2.9 37.7 + - + +
129N THR 3.2 8.8 + - - -
130N GLY* 3.8 16.0 + - - -
131N ILE* 4.8 20.9 - - + +
134N GLU* 5.6 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C MET* 5.4 3.4 - - - +
3N SER* 3.8 30.1 + - - +
5N VAL 5.7 1.8 - - - +
122N ASP 2.9 18.5 + - - +
123N ALA* 3.2 10.5 - - + +
124N ILE 3.2 0.2 - - - -
125N LYS* 1.3 79.3 - - - +
127N LYS* 1.3 59.7 + - - +
129N THR* 3.5 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 3.2 44.6 - - + -
11N VAL* 3.1 43.7 - - + +
12N ILE* 5.2 16.1 - - + +
38N PHE* 5.6 0.2 - - - -
47N ILE* 3.9 16.6 - - + -
101N PHE* 5.3 0.2 - - - -
123N ALA 3.6 3.3 + - - +
124N ILE* 2.9 56.7 + - - +
126N LYS* 1.3 74.8 - - - +
128N LEU* 1.3 64.6 + - - +
129N THR* 3.1 14.0 + - - -
----------------------------------------------------------
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