Contacts of the helix formed by residues 137 - 149 (chain C) in PDB entry 3J8B
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 137 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C THR* 3.6 7.5 + - - +
136C ASP* 1.3 70.2 - - - +
138C ALA* 1.3 60.1 + - - +
140C GLN* 3.7 8.4 - - - +
141C ILE* 2.9 31.5 + - - +
171C SER 5.5 1.5 - - - +
175C TYR* 3.5 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP* 5.1 2.7 - - + -
137C ARG* 1.3 79.6 - - - +
139C ALA* 1.3 56.6 + - - +
141C ILE* 3.4 5.6 + - - +
142C GLU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP* 3.2 20.7 + - + +
138C ALA* 1.3 77.0 - - - +
140C GLN* 1.3 59.8 + - - +
142C GLU* 4.0 6.0 - - - +
143C LEU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 6.3 2.9 - - + -
135C THR* 5.8 5.2 - - - -
136C ASP 3.0 16.4 + - - +
137C ARG* 3.2 10.3 + - - +
139C ALA* 1.3 74.8 - - - +
141C ILE* 1.3 64.9 + - - +
143C LEU* 3.8 5.3 - - - +
144C LEU* 3.2 22.5 + - - +
171C SER* 6.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG 2.9 16.7 + - - +
138C ALA* 3.7 5.4 - - - +
140C GLN* 1.3 75.3 - - - +
142C GLU* 1.3 65.3 + - - +
144C LEU* 3.2 8.3 + - - +
145C GLN* 3.0 23.1 + - - +
171C SER* 5.8 8.9 - - - +
172C LEU* 5.8 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ALA 3.0 17.5 + - - +
139C ALA* 4.0 7.9 - - - +
141C ILE* 1.3 76.8 - - - +
143C LEU* 1.3 57.5 + - - +
145C GLN* 3.4 7.6 + - - +
146C LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 6.4 1.8 - - + -
139C ALA 2.9 19.7 + - - +
140C GLN* 3.8 6.3 - - - +
142C GLU* 1.3 74.7 - - - +
144C LEU* 1.3 55.9 + - - +
146C LEU* 3.3 5.5 + - - +
147C LEU* 2.7 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLN 3.2 11.8 + - - +
141C ILE* 3.2 10.9 + - - +
143C LEU* 1.3 77.3 - - - +
145C GLN* 1.3 53.1 + - - +
147C LEU* 3.1 7.2 + - - +
148C VAL* 2.4 40.8 + - + +
164C ILE* 5.7 1.5 - - - +
168C ILE* 4.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE 3.0 13.0 + - - +
142C GLU* 3.6 11.4 - - - +
144C LEU* 1.3 74.8 - - - +
146C LEU* 1.3 66.2 + - - +
148C VAL* 3.1 16.7 + - - +
149C GLN* 3.4 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLU 2.9 18.4 + - - +
143C LEU* 3.7 5.4 - - - +
145C GLN* 1.3 78.0 - - - +
147C LEU* 1.3 61.5 + - - +
149C GLN* 3.8 12.1 + - - +
150C ILE 4.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS* 5.7 9.2 - - + -
143C LEU 2.7 23.1 + - - +
144C LEU* 3.3 8.5 - - - +
146C LEU* 1.3 74.3 - - - +
148C VAL* 1.3 62.0 + - - +
149C GLN 3.3 0.7 + - - -
150C ILE* 3.4 14.9 + - - +
155C ASN* 5.2 1.0 - - - +
164C ILE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 2.4 26.3 + - + +
145C GLN* 3.1 12.9 + - - +
147C LEU* 1.3 75.0 - - - +
149C GLN* 1.3 63.0 + - - +
150C ILE* 3.3 5.4 + - - +
160C VAL 6.0 0.5 - - - -
161C ILE* 5.3 7.8 - - - +
164C ILE* 4.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLN 3.4 8.1 + - - +
146C LEU* 4.2 9.0 - - - +
147C LEU 3.3 0.8 - - - -
148C VAL* 1.3 79.2 - - - +
150C ILE* 1.3 69.8 + - - +
151C ALA* 3.2 10.8 + - + +
156C 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