Contacts of the helix formed by residues 115 - 130 (chain G) in PDB entry 1N33
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 ARG 115 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1240A U 4.2 3.1 - - - +
49G ILE* 5.2 8.3 - - - +
114G ARG* 1.3 76.6 - - - +
116G ALA* 1.3 57.0 - - - +
117G ALA* 4.4 11.4 - - + +
118G VAL* 2.7 61.0 + - + +
119G ARG* 3.5 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1240A U 2.8 39.0 + - + +
42G ILE* 4.4 16.4 - - + -
114G ARG 2.8 7.1 + - - -
115G ARG* 1.3 68.6 - - - +
117G ALA* 1.3 61.9 + - - +
119G ARG* 3.0 50.9 + - - +
120G ILE* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ILE* 3.2 35.6 - - - +
45G ASP* 4.0 19.1 - - + +
46G ALA* 3.1 10.5 - - + +
49G ILE* 4.4 6.3 - - + -
115G ARG* 3.0 12.1 + - + +
116G ALA* 1.3 74.0 - - - +
118G VAL* 1.3 66.1 + - - +
120G ILE* 3.6 2.5 + - - +
121G ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ILE* 4.3 11.6 - - + +
113G GLU* 3.4 31.6 - - + +
115G ARG* 2.7 66.8 + - + +
117G ALA* 1.3 70.3 - - - +
119G ARG* 1.3 52.8 + - - +
121G ALA* 3.0 7.9 + - - +
122G HIS* 2.7 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1239A A 5.3 2.0 + - - +
1240A U 2.5 30.9 + - - -
108G ALA* 3.3 28.3 - - + +
109G ASN* 3.6 28.5 + - - +
111G ARG* 4.2 15.4 + - + +
113G GLU* 2.9 50.7 + - + -
114G ARG* 3.0 17.0 + - - +
115G ARG 4.5 0.4 - - - +
116G ALA* 3.0 26.2 + - - +
118G VAL* 1.3 80.7 - - - +
120G ILE* 1.3 56.0 + - + +
122G HIS* 2.9 1.9 + - - +
123G GLU* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1240A U 5.0 6.7 - - + +
26G PHE* 3.8 27.8 - - + -
30G ILE* 3.3 35.4 - - + -
42G ILE* 3.8 23.1 - - + -
43G PHE* 4.6 8.1 - - + -
46G ALA* 4.6 6.5 - - + -
105G VAL* 5.3 2.7 - - + -
108G ALA* 3.9 24.0 - - + +
109G ASN* 5.9 1.6 - - - +
116G ALA 3.5 7.5 + - - +
117G ALA 4.0 5.6 - - - +
118G VAL 3.5 0.2 - - - -
119G ARG* 1.3 79.7 - - + +
121G ALA* 1.3 56.7 + - - +
123G GLU* 3.1 2.2 + - - +
124G LEU* 2.8 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ALA* 3.5 22.0 - - + +
49G ILE* 3.9 28.7 - - + -
50G ILE* 5.0 1.1 - - - +
117G ALA 3.0 19.8 + - - +
118G VAL 3.1 4.5 - - - +
120G ILE* 1.3 79.1 - - - +
122G HIS* 1.3 63.8 + - - +
123G GLU 3.1 1.0 + - - -
124G LEU* 3.4 7.9 + - - +
125G MET* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ILE* 4.6 8.3 - - + +
53G LYS* 4.4 20.1 + - + +
111G ARG* 2.9 21.8 + - - +
113G GLU* 3.1 21.7 + - - +
118G VAL* 2.7 38.2 + - + +
119G ARG* 3.7 1.8 - - - +
121G ALA* 1.3 74.5 - - - +
123G GLU* 1.3 55.7 + - - +
125G MET* 3.3 28.7 - - + +
126G ASP* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G LEU* 4.2 14.8 - - + +
107G ALA* 3.3 17.3 - - - +
108G ALA* 4.0 22.7 - - + +
111G ARG* 2.6 40.7 + - - +
119G ARG 2.7 16.9 + - - +
120G ILE* 3.3 10.5 - - - +
121G ALA 3.0 0.2 - - - -
122G HIS* 1.3 73.6 - - - +
124G LEU* 1.3 69.5 + - + +
125G MET 3.1 1.3 - - - -
126G ASP* 3.4 3.0 + - - +
127G ALA* 2.8 23.6 + - - +
132G GLY* 4.7 0.7 - - - -
133G GLY 4.2 5.0 + - - -
134G ALA* 3.2 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 4.0 22.0 - - + -
43G PHE* 4.6 10.5 - - + -
46G ALA* 5.8 5.2 - - + +
47G CYS* 6.1 2.9 - - - -
50G ILE* 5.7 1.1 - - + -
61G VAL* 4.5 13.9 - - + +
62G PHE* 4.0 33.4 - - + -
65G ALA* 3.6 15.6 - - + +
104G LEU* 4.2 9.2 - - + -
120G ILE* 2.8 35.8 + - + +
121G ALA* 3.9 8.3 - - - +
123G GLU* 1.3 73.5 - - + +
125G MET* 1.3 54.3 + - + +
127G ALA* 2.9 7.4 - - - +
128G ALA* 2.6 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ILE* 4.1 17.3 - - + +
50G ILE* 3.2 33.2 - - + -
53G LYS* 4.1 22.9 - - + -
54G THR* 5.2 2.7 - - + -
61G VAL* 4.8 1.3 - - - +
121G ALA* 3.1 29.1 + - + +
122G HIS* 3.3 38.4 - - + +
123G GLU 3.1 0.2 - - - -
124G LEU* 1.3 73.1 - - - +
126G ASP* 1.3 70.2 + - - +
127G ALA 2.9 0.3 + - - -
128G ALA* 4.5 3.8 - - - +
129G GLU* 2.7 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ARG* 2.8 30.4 + - - +
122G HIS* 2.9 17.5 + - - +
123G GLU* 3.9 4.5 - - - +
125G MET* 1.3 79.2 - - - +
127G ALA* 1.3 57.7 + - - +
129G GLU* 3.6 5.8 - - - +
130G GLY 2.8 25.5 + - - -
131G LYS* 2.8 53.9 + - - +
132G GLY* 4.3 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ALA* 3.6 17.3 - - + -
68G ASN* 3.1 15.5 + - - -
69G VAL* 4.3 13.5 - - + -
104G LEU* 4.3 8.5 - - + -
123G GLU* 2.8 15.5 + - - +
124G LEU* 2.9 12.1 - - - +
125G MET 2.9 0.4 + - - -
126G ASP* 1.3 82.8 - - - +
128G ALA* 1.3 68.3 + - - +
129G GLU 2.8 0.2 + - - -
130G GLY* 2.8 8.3 + - - -
131G LYS 3.7 6.3 + - - -
134G ALA* 4.4 4.9 - - + -
135G VAL* 4.1 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G VAL* 3.6 29.2 - - + +
64G GLN* 3.6 36.9 + - + +
65G ALA* 3.6 7.7 - - - +
68G ASN* 3.8 7.3 + - - +
124G LEU 2.6 16.8 + - - +
125G MET* 3.9 2.5 - - - +
127G ALA* 1.3 72.2 - - - +
129G GLU* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN* 4.5 1.4 + - - -
125G MET 2.7 23.9 + - - +
126G ASP* 3.6 7.2 - - - +
127G ALA 2.8 0.4 + - - -
128G ALA* 1.3 77.3 - - - +
130G GLY* 1.3 67.5 + - - +
131G LYS* 4.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN* 4.3 7.6 - - - -
126G ASP 2.8 11.5 + - - -
127G ALA 2.8 7.9 + - - -
129G GLU* 1.3 84.0 + - - +
131G LYS* 1.3 57.8 + - - +
135G VAL* 3.5 15.1 - - - +
139G GLU* 5.1 4.3 - - - +
----------------------------------------------------------
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