Contacts of the helix formed by residues 41 - 55 (chain C) in PDB entry 1JPL
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 GLU 41 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLU* 5.9 3.6 - - + +
39C GLU* 4.5 2.5 + - - +
40C LEU* 1.3 89.6 - - + +
42C GLY* 1.3 64.1 + - - +
44C GLN* 3.3 35.7 + - + +
45C ILE* 3.0 41.6 + - + +
204C GLY* 4.6 4.5 - - - -
205C SER* 3.2 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.1 12.8 - - - +
36C ILE* 3.9 14.1 - - - -
39C GLU* 3.2 25.6 + - - +
41C GLU* 1.3 78.1 - - - +
43C PRO* 1.3 64.6 - - - +
45C ILE* 3.7 1.0 - - - +
46C ALA* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.9 8.3 - - + -
42C GLY* 1.3 82.2 - - - +
44C GLN* 1.3 74.9 + - - +
46C ALA* 4.4 0.2 - - + -
47C VAL* 3.1 30.0 + - - +
79C ARG* 3.0 63.9 - - + +
80C PHE* 4.1 19.7 - - + +
83C GLU* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU 3.9 5.3 + - - +
41C GLU* 3.3 50.5 + - + +
43C PRO* 1.3 82.4 - - - +
45C ILE* 1.3 63.3 + - + +
47C VAL* 3.2 16.2 - - - +
48C ARG* 3.6 15.1 + - - +
79C ARG* 4.8 0.2 + - - -
83C GLU* 3.5 32.5 - - - +
88C ARG* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.5 33.6 - - + +
5C GLU* 4.1 12.8 - - + -
6C GLY* 4.2 5.6 - - - +
9C LEU* 3.5 19.7 - - + -
41C GLU* 3.0 30.3 + - + +
42C GLY 3.7 2.5 - - - +
44C GLN* 1.3 78.5 - - + +
46C ALA* 1.3 65.6 + - - +
48C ARG* 3.3 2.3 + - - +
49C LEU* 3.1 32.9 + - + +
205C SER* 3.8 41.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 5.1 1.8 - - + -
32C PHE* 3.9 16.2 - - + -
36C ILE* 3.5 31.6 - - + -
42C GLY 2.8 21.9 + - - +
43C PRO 3.9 0.4 - - - +
45C ILE* 1.3 76.0 - - - +
47C VAL* 1.3 58.6 + - - +
49C LEU* 3.2 4.4 + - - +
50C LEU* 2.8 36.4 + - + +
80C PHE* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO 3.1 13.5 + - - +
44C GLN* 3.2 21.1 - - - +
46C ALA* 1.3 75.9 - - - +
48C ARG* 1.3 65.5 + - + +
50C LEU* 4.5 4.5 - - - -
51C ALA* 3.0 29.1 + - - +
69C LEU* 5.8 0.2 - - + -
80C PHE* 4.0 13.5 - - + -
83C GLU* 3.7 30.1 - - + +
84C VAL* 3.9 24.9 - - + +
89C PHE* 3.3 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.5 48.3 - - + +
44C GLN 3.6 14.7 + - - +
45C ILE* 3.3 7.4 + - - +
46C ALA 3.2 0.4 - - - -
47C VAL* 1.3 83.4 - - + +
49C LEU* 1.3 62.1 + - - +
51C ALA* 3.4 6.8 + - - +
52C HIS* 3.1 22.7 + - - +
88C ARG* 5.7 10.1 - - + +
203C MSE 5.4 4.8 + - - +
57D PRO* 3.9 26.2 + - + +
105D ARG* 3.4 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.9 24.0 - - + -
6C GLY 4.3 1.8 - - - +
9C LEU* 3.7 19.5 - - + +
10C GLU* 3.3 49.6 - - + +
13C LEU* 3.7 13.2 - - + +
32C PHE* 4.7 3.6 - - + -
45C ILE* 3.1 27.1 + - + +
46C ALA* 3.2 9.6 + - - +
48C ARG* 1.3 74.8 - - - +
50C LEU* 1.3 59.3 + - - +
52C HIS* 3.3 7.6 + - - +
53C LYS* 3.0 29.8 + - - +
56D SER* 5.2 0.4 - - - +
57D PRO* 4.8 9.4 - - + -
58D GLN* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.0 14.1 - - + -
32C PHE* 4.1 16.2 - - + -
46C ALA 2.8 25.4 + - - +
47C VAL* 4.1 4.3 - - - +
49C LEU* 1.3 70.6 - - - +
51C ALA* 1.3 60.1 + - - +
53C LYS* 3.1 2.4 + - - +
54C ILE* 2.8 45.4 + - + +
65C ALA* 3.6 27.6 - - - +
68C VAL* 3.6 22.4 - - + -
69C LEU* 3.9 20.9 - - + +
72C CYS* 4.3 1.6 - - - -
80C PHE* 3.8 28.3 - - + -
89C PHE* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL 3.0 20.6 + - - +
48C ARG* 3.5 8.1 - - - +
50C LEU* 1.3 75.9 - - - +
52C HIS* 1.3 61.8 + - - +
54C ILE* 3.4 7.0 + - - +
55C GLN* 2.9 32.8 + - - +
89C PHE* 4.0 16.3 - - + -
92C GLU* 3.9 31.2 - - + +
93C LEU* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 6.2 0.2 - - - -
48C ARG 3.1 9.9 + - - +
49C LEU* 3.5 9.0 - - - +
50C LEU 3.1 0.4 - - - -
51C ALA* 1.3 79.1 - - - +
53C LYS* 1.3 64.9 + - + +
55C GLN* 3.1 17.8 + - - -
52D HIS* 2.7 88.1 + + - -
53D LYS* 5.6 0.7 - - - -
55D GLN* 3.5 28.0 + - + -
56D SER* 3.7 16.0 + - - -
57D PRO* 3.9 16.7 - - + +
61D GLU* 5.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 2.8 30.7 + - - -
13C LEU* 3.7 27.8 - - + -
14C ASN* 3.0 19.5 + - - +
17C THR* 2.9 27.1 - - - +
49C LEU 3.0 10.1 + - - +
50C LEU* 3.1 6.3 + - - +
52C HIS* 1.3 78.1 - - + +
54C ILE* 1.3 58.4 + - - +
56C SER* 3.0 26.9 + - - -
61C GLU* 3.4 31.9 + - + +
62C ALA* 3.6 10.2 + - - -
65C ALA* 3.4 20.4 - - + -
14D ASN* 5.1 0.4 - - - -
52D HIS* 4.9 0.9 - - - -
53D LYS* 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 2.8 32.5 + - + +
51C ALA* 3.7 7.6 - - - +
53C LYS* 1.3 76.3 - - - +
55C GLN* 1.3 58.1 + - + +
56C SER 3.2 3.8 + - - +
62C ALA* 3.7 15.1 - - - +
65C ALA* 3.7 17.7 - - + +
66C LEU* 3.8 38.8 - - + -
69C LEU* 3.8 24.2 - - + -
89C PHE* 4.9 1.6 - - + -
93C LEU* 4.2 22.7 - - + -
96C VAL* 4.3 15.5 - - + +
106C VAL* 5.8 2.1 - - - +
110C VAL* 4.4 7.4 - - + +
114C VAL* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA 2.9 18.6 - - - +
52C HIS* 3.1 22.4 + - - +
54C ILE* 1.3 76.0 - - + +
56C SER* 1.3 65.1 + - - +
57C PRO* 3.6 3.5 - - - +
92C GLU* 2.9 52.4 + - - +
95C LYS* 4.2 14.1 + - - +
96C VAL* 3.6 18.8 - - + -
102C LEU* 3.8 23.3 - - + +
106C VAL* 5.9 3.8 - - - +
52D HIS* 3.2 17.8 + - + -
----------------------------------------------------------
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