Contacts of the helix formed by residues 60 - 74 (chain C) in PDB entry 1JLH
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 THR 60 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 4.0 8.5 - - + -
22C GLU* 5.8 3.1 - - - +
23C LEU* 3.9 21.5 - - + -
28C LEU* 4.3 18.4 - - + -
35C ARG* 4.7 1.8 - - - +
39C PHE* 3.8 8.7 - - - -
59C VAL* 1.3 84.1 - - - +
61C GLU* 1.3 67.3 + - - +
62C ASP* 3.4 11.4 + - - +
63C VAL* 3.0 21.9 + - - +
64C MET* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASN* 4.5 3.8 + - - -
38C HIS* 3.5 30.8 + - - +
39C PHE* 3.6 28.3 - - + -
60C THR* 1.3 74.7 - - - +
62C ASP* 1.3 61.8 + - - +
64C MET* 3.5 4.3 + - - +
65C ARG* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 4.5 13.9 + - + +
60C THR* 3.1 8.4 + - - +
61C GLU* 1.3 78.6 - - - +
63C VAL* 1.3 59.6 + - - +
65C ARG* 2.8 36.0 + - - +
66C MET* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.5 1.1 - - + -
15C TRP* 3.5 37.5 - - + -
23C LEU* 5.0 0.2 - - + -
59C VAL* 3.2 25.6 - - + -
60C THR* 3.0 21.4 + - - +
62C ASP* 1.3 74.0 - - - +
64C MET* 1.3 60.7 + - - +
66C MET* 3.2 10.5 + - + +
67C LEU* 2.8 37.8 + - + +
325C TRP* 3.8 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 3.6 25.6 - - + -
54C TYR* 4.2 19.5 - - + +
59C VAL* 3.2 34.3 - - + -
60C THR 3.0 6.0 + - - +
61C GLU* 3.8 7.9 - - - +
63C VAL* 1.3 76.4 - - - +
65C ARG* 1.3 57.3 + - - +
67C LEU* 3.1 16.7 + - + +
68C VAL* 2.9 36.1 + - + +
318C LEU* 4.0 28.5 - - + +
321C LEU* 5.4 2.0 - - + -
322C LEU* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 3.4 27.9 - - - +
61C GLU 3.0 14.3 + - - +
62C ASP* 2.8 44.9 + - - +
64C MET* 1.3 75.6 - - - +
66C MET* 1.3 69.1 + - - +
68C VAL* 3.2 8.3 + - - +
69C ASP* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 4.9 5.1 - - - +
11C LYS* 3.8 48.2 - - + +
12C LEU* 3.6 26.2 - - + +
15C TRP* 3.4 48.9 - - + +
62C ASP* 2.9 28.3 + - + +
63C VAL* 3.6 14.1 - - + +
65C ARG* 1.3 83.1 - - - +
67C LEU* 1.3 62.7 + - - +
69C ASP* 3.2 10.8 + - - +
70C LEU* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.4 27.6 - - + -
59C VAL* 4.9 0.4 - - + -
63C VAL* 2.8 35.6 + - + +
64C MET* 3.4 24.0 - - + +
66C MET* 1.3 77.0 - - - +
68C VAL* 1.3 62.7 + - - +
70C LEU* 3.0 24.7 + - + +
71C ALA 3.2 4.9 + - - -
321C LEU* 3.8 55.3 - - + +
322C LEU* 4.5 4.7 - - + +
324C ILE* 5.0 2.2 - - + -
325C TRP* 4.2 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET* 2.9 20.7 + - + +
65C ARG* 3.7 9.2 - - - +
67C LEU* 1.3 75.2 - - - +
69C ASP* 1.3 63.8 + - - +
71C ALA* 3.1 6.2 + - - +
72C LYS* 3.1 35.5 + - + +
311C LEU* 3.9 27.6 - - + -
312C GLU* 4.1 34.8 - - + +
318C LEU* 4.7 5.6 - - + -
321C LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 3.7 25.9 - - - +
11C LYS* 4.8 3.5 + - - -
65C ARG* 3.0 41.5 + - - +
66C MET* 3.5 11.2 - - - +
68C VAL* 1.3 78.2 - - - +
70C LEU* 1.3 56.8 + - - +
72C LYS* 3.4 17.9 + - - +
73C SER* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.0 11.4 - - + -
6C ASP* 4.0 13.0 - - - +
8C GLN* 4.0 7.2 - - + +
9C PHE* 4.3 22.0 - - + +
12C LEU* 3.7 24.7 - - + -
66C MET 3.1 11.5 + - - +
67C LEU* 3.0 15.5 + - + +
69C ASP* 1.3 75.3 - - - +
71C ALA* 1.3 56.0 + - - +
73C SER* 3.2 0.9 + - - -
74C ARG* 2.7 56.0 + - + +
321C LEU* 6.1 0.7 - - + -
324C ILE* 4.2 22.0 - - + -
503C ILE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU 3.2 6.5 + - - +
68C VAL* 3.1 11.6 + - - +
70C LEU* 1.3 79.7 - - - +
72C LYS* 1.3 61.1 + - - +
74C ARG* 3.5 2.1 + - - -
75C GLY 3.2 3.5 + - - -
76C VAL* 3.0 51.9 + - + +
77C GLU* 5.9 0.2 - - - +
311C LEU* 4.2 14.1 - - + -
317C VAL* 4.6 7.6 - - + -
321C LEU* 4.4 17.9 - - + -
503C ILE* 4.7 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 3.1 24.9 + - + +
69C ASP* 3.6 19.1 + - - +
71C ALA* 1.3 74.3 - - - +
73C SER* 1.3 65.0 + - - +
75C GLY* 2.9 15.6 + - - -
76C VAL 5.0 0.9 - - - +
77C GLU* 4.3 12.1 - - - +
311C LEU* 3.3 30.1 - - + -
312C GLU* 4.9 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ASP* 2.6 30.6 + - - +
7C PRO* 4.5 4.9 - - - +
8C GLN* 3.6 18.0 - - - +
69C ASP 2.8 18.8 + - - -
70C LEU 3.6 3.4 - - - -
72C LYS* 1.3 76.7 - - - +
74C ARG* 1.3 62.2 + - - +
75C GLY 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 3.8 21.5 + - - +
3C LEU* 4.1 10.0 - - - +
6C ASP* 3.7 18.9 + - - -
70C LEU* 2.7 44.4 + - + +
71C ALA 4.0 3.6 - - - +
72C LYS 3.1 0.2 - - - -
73C SER* 1.3 74.5 + - - +
75C GLY* 1.3 62.9 + - - +
76C VAL* 3.5 2.2 + - + +
502C ILE* 3.1 31.1 + - - +
503C ILE* 3.1 36.7 + - + -
505C ASP* 3.2 35.0 + - - +
----------------------------------------------------------
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