Contacts of the helix formed by residues 137 - 146 (chain C) in PDB entry 3J82
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 GLN 137 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 3.8 6.5 + - - -
12C ASN 3.8 20.9 + - - +
13C GLY* 4.8 0.6 - - - -
18C LYS* 4.5 10.5 - - - +
74C GLY* 5.7 2.4 - - - -
106C THR* 3.4 31.5 + - - -
107C GLU* 3.1 28.8 + - - +
108C ALA* 3.8 12.0 + - - +
109C PRO* 4.7 5.7 - - + +
136C ILE* 1.3 74.7 - - - +
138C ALA* 1.3 63.2 + - - +
140C LEU* 3.0 10.7 + - - +
141C SER* 2.9 18.2 + - - -
339C VAL* 3.5 26.4 - - + +
401C ADP 5.6 3.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
109C PRO* 5.9 8.0 - - + +
136C ILE* 3.0 5.6 + - + +
137C GLN* 1.3 79.4 - - - +
139C VAL* 1.3 58.5 + - - +
141C SER* 2.8 13.3 + - - +
142C LEU* 2.7 27.8 + - - +
154C ASP* 4.9 10.5 - - + +
161C HIS* 6.3 0.9 - - - +
163C VAL* 6.2 6.7 - - + -
339C VAL* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 5.2 0.2 - - + -
136C ILE* 2.7 44.9 + - + +
138C ALA* 1.3 79.0 - - - +
140C LEU* 1.3 65.6 + - + +
142C LEU* 3.0 14.1 + - + +
143C TYR* 2.6 38.8 + - + +
346C LEU* 5.9 4.5 - - + -
375C PHE* 5.8 2.2 - - + -
44D MET* 6.4 1.6 - - - -
45D VAL* 5.8 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.8 0.9 - - + -
104C LEU* 5.7 1.8 - - + -
106C THR* 3.5 16.6 - - + -
135C ALA* 3.0 37.9 - - + -
136C ILE 2.7 30.5 - - - +
137C GLN* 3.0 7.1 + - - +
139C VAL* 1.3 91.3 - - + +
141C SER* 1.3 62.4 + - - +
143C TYR* 3.1 4.7 + - - +
144C ALA 2.9 9.5 + - - -
338C SER 4.3 0.2 - - - -
339C VAL* 3.4 9.2 - - + +
342C GLY* 2.7 37.4 - - - +
343C GLY* 2.9 30.5 - - - +
346C LEU* 5.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLN 2.9 6.6 + - - -
138C ALA* 2.8 13.0 + - - +
140C LEU* 1.3 76.8 - - - +
142C LEU* 1.3 66.9 + - - +
144C ALA* 3.0 14.0 + - - +
145C SER* 3.2 10.9 + - - -
154C ASP* 4.3 9.9 + - - -
300C SER* 4.1 15.7 + - - -
335C ARG* 5.7 0.2 + - - -
338C SER* 3.4 29.9 + - - -
339C VAL* 3.9 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ALA 2.7 16.2 + - - +
139C VAL* 3.5 17.0 - - + +
141C SER* 1.3 73.7 + - - +
143C TYR* 1.3 68.0 + - - +
145C SER* 3.1 15.7 + - - -
146C GLY* 3.4 8.3 + - - -
147C ARG* 4.0 25.5 + - + +
152C VAL* 4.9 18.6 - - + -
163C VAL* 5.0 2.7 - - + -
165C ILE* 3.8 41.7 - - + -
168C GLY* 4.7 11.4 - - - +
170C ALA* 6.1 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 2.6 20.0 + - + +
140C LEU* 3.3 13.5 - - - +
142C LEU* 1.3 74.7 - - - +
144C ALA* 1.3 65.2 + - - +
145C SER 3.1 0.7 + - - -
146C GLY* 3.2 12.1 + - - -
342C GLY* 4.4 4.0 - - - +
345C ILE* 3.1 36.7 - - + +
346C LEU* 3.4 22.0 - - + -
349C LEU* 3.2 27.3 - - + +
45D VAL* 3.0 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU 2.9 7.4 + - - +
141C SER 3.0 10.7 + - - +
143C TYR* 1.3 80.8 - - - +
145C SER* 1.3 64.2 + - - +
146C GLY* 3.4 0.5 + - - -
338C SER* 3.5 27.8 - - - +
341C ILE* 3.9 14.1 - - + -
342C GLY* 3.8 10.8 - - - +
345C ILE* 5.0 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER 3.2 6.7 + - - -
142C LEU* 3.1 14.7 + - - -
143C TYR 3.1 0.8 - - - -
144C ALA* 1.3 82.7 - - - +
146C GLY* 1.3 61.9 + - - +
147C ARG* 3.1 53.8 + - - +
298C VAL* 4.9 2.9 - - - +
332C PRO* 4.6 0.7 - - - +
335C ARG* 3.8 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU 3.4 2.6 + - - -
143C TYR 3.2 14.2 + - - -
144C ALA 4.4 0.7 - - - -
145C SER* 1.3 77.8 - - - +
147C ARG* 1.3 67.4 + - - +
148C THR* 3.8 4.5 + - - -
----------------------------------------------------------
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