Contacts of the helix formed by residues 3 - 17 (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 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ALA* 1.3 90.7 - - - +
4C ALA* 1.3 69.2 + - - +
5C GLU* 3.3 10.8 - - - +
6C GLY 3.5 0.7 + - - -
7C GLU* 3.2 27.4 + - - +
204C GLY 3.6 17.2 - - - +
205C SER* 3.0 19.5 + - - +
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Residues in contact with ALA 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLU* 1.3 75.5 + - - +
5C GLU* 1.3 66.2 + - - +
7C GLU* 3.2 11.4 + - - +
8C SER* 2.8 37.5 + - - -
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Residues in contact with GLU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLU* 4.1 8.5 - - - +
4C ALA* 1.3 86.4 + - - +
6C GLY* 1.3 63.5 + - - +
8C SER* 3.5 4.8 - - - -
9C LEU* 2.9 31.2 + - + +
39C GLU* 3.4 43.7 - - + +
41C GLU* 5.9 4.0 - - + +
45C ILE* 4.1 8.5 - - + -
205C SER* 3.7 30.9 + - - +
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Residues in contact with GLY 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 3.5 22.4 - - - -
4C ALA 3.3 0.2 - - - -
5C GLU* 1.3 80.2 - - - +
7C GLU* 1.3 62.6 + - - +
9C LEU* 3.5 1.2 + - - +
10C GLU* 3.1 25.8 + - - +
45C ILE* 4.2 15.9 - - - +
49C LEU* 4.3 1.6 - - - +
205C SER 3.0 10.3 + - - -
58D GLN* 3.7 9.2 - - - +
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Residues in contact with GLU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ALA 3.9 11.1 - - - +
3C GLU 3.2 22.8 + - - +
4C ALA* 3.5 12.1 - - - +
6C GLY* 1.3 76.5 - - - +
8C SER* 1.3 57.1 + - - +
10C GLU 3.5 0.2 + - - -
11C SER* 2.8 32.6 + - - -
19D PRO* 3.4 34.4 - - - +
20D SER* 5.8 0.7 - - - -
58D GLN* 3.6 22.5 - - - +
60D TRP* 4.3 15.0 - - + +
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Residues in contact with SER 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ALA 2.8 21.3 + - - -
5C GLU* 3.5 5.2 - - - -
7C GLU* 1.3 72.3 - - - +
9C LEU* 1.3 63.9 + - - +
11C SER* 3.0 17.5 + - - -
12C TRP* 3.1 21.2 + - - -
35C GLN* 3.4 23.4 + - - -
39C GLU* 5.8 2.7 - - - -
20D SER* 5.7 0.2 - - - -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU* 2.9 19.2 + - + +
6C GLY 4.0 1.3 - - - +
8C SER* 1.3 77.2 - - - +
10C GLU* 1.3 57.7 + - - +
12C TRP* 3.4 2.3 + - - -
13C LEU* 2.9 22.0 + - - +
32C PHE* 3.1 30.7 - - + -
35C GLN* 3.5 33.9 - - + +
36C ILE* 4.3 11.4 - - + +
39C GLU* 5.0 10.1 - - + -
42C GLY* 4.1 22.0 - - - +
45C ILE* 3.5 33.9 - - + -
46C ALA* 4.6 2.9 - - - +
49C LEU* 3.7 13.9 - - + -
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLY 3.1 17.7 + - - +
9C LEU* 1.3 73.6 - - - +
11C SER* 1.3 57.3 + - - +
13C LEU* 3.8 13.1 - - - +
14C ASN* 2.7 42.0 + - - +
49C LEU* 3.3 32.9 - - + +
52C HIS* 6.2 0.2 - - - -
53C LYS* 2.8 26.9 + - - -
19D PRO* 3.4 18.6 - - + -
58D GLN* 4.4 4.3 - - + -
61D GLU* 2.8 38.1 - - - +
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Residues in contact with SER 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU 2.8 21.7 + - - -
8C SER* 3.0 11.2 + - - -
10C GLU* 1.3 77.6 - - - +
12C TRP* 1.3 64.7 + - - +
14C ASN* 3.1 14.4 + - - +
15C LYS* 3.1 24.7 + - - +
18D ASN* 4.1 12.8 - - - +
19D PRO* 4.0 0.8 - - - +
20D SER* 2.7 36.9 + - - -
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Residues in contact with TRP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C SER* 3.1 26.2 + - - -
9C LEU* 3.6 7.9 - - - +
11C SER* 1.3 81.0 - - - +
13C LEU* 1.3 51.6 + - - +
15C LYS* 3.0 11.2 + - + +
16C ALA* 2.7 37.1 + - - +
27C GLU* 4.4 3.4 - - + -
28C TYR* 3.8 47.2 - + - +
31C GLY* 3.5 24.5 - - - -
32C PHE* 3.9 15.3 - - + -
35C GLN* 2.7 50.5 - - + +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU 2.9 17.8 + - - +
10C GLU* 3.2 13.0 + - - +
12C TRP* 1.3 76.2 - - - +
14C ASN* 1.3 57.3 + - - +
16C ALA* 4.2 3.1 - - + -
17C THR* 2.8 42.8 + - + +
32C PHE* 3.6 31.2 - - + -
49C LEU* 3.7 35.9 - - + +
50C LEU* 4.0 9.4 - - + +
53C LYS* 3.7 27.6 - - + -
68C VAL* 3.9 19.1 - - + -
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Residues in contact with ASN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 2.7 44.8 + - - +
11C SER* 3.1 11.9 + - - +
13C LEU* 1.3 73.0 - - - +
15C LYS* 1.3 59.7 + - + +
17C THR* 3.5 3.6 - - - -
18C ASN* 2.8 33.5 + - - +
53C LYS* 3.0 6.5 + - - +
14D ASN* 3.4 53.2 + - + +
18D ASN* 4.3 13.0 - - - +
19D PRO* 4.6 2.2 - - - -
53D LYS* 4.1 3.8 - - - +
61D GLU* 3.7 6.7 + - - +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 3.1 18.0 + - - +
12C TRP* 3.0 12.4 + - + +
14C ASN* 1.3 78.8 - - + +
16C ALA* 1.3 61.4 + - - +
17C THR 3.4 0.7 + - - -
18C ASN* 3.8 8.9 + - - +
21C ASN* 3.5 15.8 + - - +
25C ASP* 4.9 0.5 - - - +
28C TYR* 3.7 59.1 + - + +
18D ASN* 5.4 7.9 - - - -
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C TRP 2.7 19.8 + - - +
13C LEU* 3.8 10.5 - - + +
14C ASN 3.3 0.2 - - - -
15C LYS* 1.3 74.0 - - - +
17C THR* 1.3 62.1 + - + +
18C ASN 3.7 0.2 - - - -
21C ASN* 4.4 0.4 - - - -
25C ASP* 5.1 3.2 + - - -
28C TYR* 3.8 28.9 - - - +
29C ILE* 4.0 13.1 - - - +
32C PHE* 5.0 2.5 - - + -
64C GLN* 3.6 17.0 + - - +
68C VAL* 4.1 22.0 - - + +
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 2.8 30.2 + - + +
14C ASN 3.5 1.8 + - - -
16C ALA* 1.3 83.0 - - - +
18C ASN* 1.3 67.7 + - - +
19C PRO* 3.1 9.9 - - - +
53C LYS* 2.9 24.6 - - - -
61C GLU* 3.5 23.6 - - - +
64C GLN* 3.6 16.0 - - - +
65C ALA* 3.6 33.2 - - + +
68C VAL* 4.0 8.7 - - + -
14D ASN* 5.0 0.8 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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