Contacts of the helix formed by residues 98 - 105 (chain N) in PDB entry 1JJ2
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 LEU 98 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N LEU* 4.1 25.6 - - + -
14N LEU* 4.3 12.6 - - + -
26N TRP* 4.6 7.4 - - + -
29N VAL* 3.7 28.7 - - + -
33N LEU* 4.6 0.2 - - + -
59N VAL* 4.3 13.5 - - + -
60N VAL 4.5 3.4 - - - +
77N ALA* 3.5 40.6 - - + +
78N ALA 3.2 12.9 + - - +
79N VAL* 4.2 17.9 - - + +
97N SER* 1.3 72.6 - - - +
99N GLU* 1.3 67.7 + - - +
100N GLN 3.3 0.2 - - - -
101N ALA* 3.7 3.8 - - + +
102N ILE* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N ARG* 5.3 10.0 + - - +
10N LEU* 3.9 35.9 - - + +
13N ASP* 5.3 7.0 - - + +
78N ALA 5.0 0.9 - - - +
79N VAL 5.2 4.2 - - - +
97N SER* 2.9 14.9 + - - +
98N LEU* 1.3 90.1 + - - +
100N GLN* 1.3 61.1 + - + +
102N ILE* 3.9 7.1 + - - +
103N GLU* 3.6 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95N ALA 5.2 1.4 + - - -
96N VAL* 3.5 20.7 - - + +
97N SER* 2.8 38.4 + - - +
99N GLU* 1.3 75.2 - - + +
101N ALA* 1.3 67.2 + - - +
103N GLU* 2.9 11.3 + - - +
104N ASN* 2.9 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N TRP* 3.8 22.2 - - + -
57N THR* 5.6 4.9 - - + -
77N ALA* 3.9 20.9 - - + -
96N VAL* 3.9 5.5 - - + +
97N SER 3.0 11.0 + - - +
98N LEU* 3.7 9.9 - - - +
100N GLN* 1.3 77.5 - - - +
102N ILE* 1.3 64.7 + - - +
103N GLU 2.9 0.3 + - - -
104N ASN* 3.7 4.4 - - - +
105N ASN* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N LEU* 4.2 8.7 - - + -
13N ASP* 4.0 11.2 - - + +
14N LEU* 3.2 55.6 - - + +
17N ALA* 3.5 25.6 - - + -
26N TRP* 4.2 17.9 - - + +
98N LEU 3.1 17.2 + - - +
99N GLU* 4.0 7.0 - - - +
100N GLN 3.3 0.2 - - - -
101N ALA* 1.3 78.5 - - - +
103N GLU* 1.3 56.4 + - - +
106N PRO* 3.2 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99N GLU 3.6 9.8 + - - +
100N GLN* 2.9 15.4 + - - +
102N ILE* 1.3 78.0 - - - +
104N ASN* 1.3 70.4 + - - +
105N ASN 3.1 5.4 + - - -
106N PRO* 3.5 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N VAL* 5.3 5.3 - - - +
100N GLN* 2.9 37.7 + - - +
101N ALA* 4.3 3.7 - - - +
103N GLU* 1.3 84.4 - - - +
105N ASN* 1.3 63.1 + - + +
106N PRO* 4.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N TRP* 3.1 18.9 + - + -
57N THR* 5.7 5.5 + - - -
101N ALA* 2.9 13.5 + - + +
103N GLU 3.1 0.4 - - - -
104N ASN* 1.3 84.1 - - + +
106N PRO* 1.3 61.7 - - - +
107N GLU* 3.4 7.9 + - - +
108N GLY* 2.8 27.0 + - - -
109N SER* 3.0 44.9 + - - +
111N VAL* 5.2 3.4 - - - +
----------------------------------------------------------
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