Contacts of the helix formed by residues 3 - 17 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MSE 3.8 0.2 - - - +
2B ALA* 1.3 81.1 - - - +
4B ALA* 1.3 79.7 + - + +
5B GLU* 3.1 24.6 + - - +
6B GLY* 3.1 10.6 + - - -
7B GLU* 3.1 20.6 + - - +
204B GLY 3.7 3.8 + - - +
205B SER* 2.9 24.3 + - - +
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Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 1.3 89.5 - - + +
5B GLU* 1.3 61.5 + - - +
7B GLU* 3.8 16.1 + - - +
8B SER* 2.9 26.5 + - - -
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Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 3.1 15.8 + - - +
4B ALA* 1.3 79.2 - - - +
6B GLY* 1.3 60.9 + - - +
8B SER* 3.5 6.0 + - - -
9B LEU* 2.9 51.8 + - - +
35B GLN* 4.7 3.3 - - - +
39B GLU* 2.5 55.9 - - + +
41B GLU* 5.4 1.3 - - + -
45B ILE* 3.7 17.7 - - + -
205B SER* 4.0 13.0 - - - +
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Residues in contact with GLY 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 3.6 6.1 - - - +
1B MSE 3.0 39.3 - - - +
3B GLU 3.1 4.2 + - - -
5B GLU* 1.3 78.6 - - - +
7B GLU* 1.3 63.7 + - - +
9B LEU* 3.5 0.9 + - - +
10B GLU* 3.1 25.1 + - - +
45B ILE* 4.3 4.3 - - - -
205B SER 3.2 5.7 + - - -
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.5 31.4 - - + +
20A SER* 5.8 0.7 - - - -
58A GLN* 3.0 29.9 - - - +
60A TRP* 4.0 18.0 - - + +
2B ALA 4.0 11.1 - - - +
3B GLU* 3.1 19.8 + - - +
4B ALA* 3.8 12.1 - - - +
6B GLY* 1.3 75.7 - - - +
8B SER* 1.3 58.6 + - - +
10B GLU 3.4 0.3 + - - -
11B SER* 3.0 29.0 + - - -
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Residues in contact with SER 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER* 6.4 0.7 - - - +
4B ALA 2.9 19.4 + - - -
5B GLU* 3.8 9.2 - - - -
6B GLY 3.2 0.2 - - - -
7B GLU* 1.3 78.0 - - - +
9B LEU* 1.3 62.6 + - - +
11B SER* 3.1 14.7 + - - -
12B TRP* 3.1 33.8 + - - -
35B GLN* 4.2 10.6 + - - -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 2.9 37.2 + - - +
6B GLY 4.0 0.9 - - - +
7B GLU 3.4 0.2 - - - -
8B SER* 1.3 78.7 - - - +
10B GLU* 1.3 57.4 + - - +
12B TRP* 3.3 4.3 + - - +
13B LEU 3.0 22.9 + - - -
32B PHE* 3.3 21.2 - - + -
35B GLN* 3.3 35.4 - - + +
36B ILE* 3.8 28.9 - - + -
42B GLY* 4.1 8.5 - - - +
45B ILE* 3.6 29.8 - - + -
46B ALA* 4.6 0.7 - - + +
49B LEU* 3.9 13.5 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.6 16.2 - - + -
58A GLN* 4.3 6.5 - - + -
61A GLU* 2.6 42.0 - - - +
6B GLY 3.1 17.9 + - - +
7B GLU 3.9 3.1 - - - +
9B LEU* 1.3 73.8 - - - +
11B SER* 1.3 61.1 + - - +
13B LEU* 3.8 12.7 - - - +
14B ASN* 2.8 28.6 + - - +
49B LEU* 3.2 31.7 - - + +
52B HIS* 5.9 1.7 - - - -
53B LYS* 3.2 23.9 + - - -
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Residues in contact with SER 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 2.8 34.9 + - - +
19A PRO* 4.5 0.6 - - - +
20A SER* 3.3 18.6 + - - -
7B GLU 3.0 18.0 + - - -
8B SER* 3.1 10.0 + - - -
10B GLU* 1.3 78.8 - - - +
12B TRP* 1.3 62.1 + - - +
14B ASN* 3.1 17.0 - - - +
15B LYS* 3.3 16.2 + - - +
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Residues in contact with TRP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER* 3.1 35.6 + - - -
9B LEU* 3.6 6.7 - - - +
11B SER* 1.3 73.4 - - - +
13B LEU* 1.3 67.2 + - - +
14B ASN 3.0 1.8 - - - -
15B LYS* 2.9 11.2 + - + +
16B ALA* 2.8 22.7 + - - +
27B GLU 4.3 2.9 - - - -
28B TYR* 3.9 35.5 - + - +
31B GLY* 3.7 29.4 - - - -
32B PHE* 3.9 15.7 - - + -
35B GLN* 3.4 45.3 - - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU 3.0 16.1 + - - +
10B GLU* 3.6 14.8 - - - +
12B TRP* 1.3 75.9 - - - +
14B ASN* 1.3 53.5 + - - +
16B ALA* 3.2 4.2 + - + -
17B THR* 2.6 55.2 + - + +
32B PHE* 4.0 15.0 - - + -
49B LEU* 3.8 43.1 - - + +
50B LEU* 3.7 29.2 - - + +
53B LYS* 4.0 16.2 - - + -
68B VAL* 4.0 14.1 - - + -
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 3.3 53.9 + - - +
17A THR 5.2 0.2 - - - -
18A ASN* 4.2 16.0 - - - +
19A PRO* 4.7 1.4 - - - +
53A LYS* 3.9 3.9 + - - +
61A GLU* 3.9 3.0 + - - +
10B GLU* 2.8 20.4 + - - +
11B SER* 3.1 14.6 - - - +
13B LEU* 1.3 76.3 - - - +
15B LYS* 1.3 57.5 + - + +
17B THR* 3.5 3.3 - - - -
18B ASN* 2.8 33.7 + - - +
53B LYS* 3.1 22.3 + - - +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 5.7 4.3 - - - -
11B SER* 3.7 15.5 - - - +
12B TRP* 2.9 14.5 + - + +
14B ASN* 1.3 78.9 - - + +
16B ALA* 1.3 58.3 + - - +
17B THR 3.3 0.5 + - - -
18B ASN* 3.6 7.7 + - - +
21B ASN* 3.0 23.2 + - - +
28B TYR* 3.6 58.8 + - + +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP 2.8 15.0 + - - +
13B LEU* 3.7 9.9 - - + +
15B LYS* 1.3 76.4 - - - +
17B THR* 1.3 62.4 + - - +
18B ASN 3.7 0.2 - - - -
21B ASN* 4.2 0.8 - - - +
25B ASP* 4.9 5.3 + - - -
28B TYR* 3.8 32.0 - - - +
29B ILE* 4.1 11.2 - - + +
32B PHE* 5.0 2.5 - - + -
64B GLN* 3.2 18.9 - - - +
68B VAL* 4.1 22.7 - - + +
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 5.0 0.4 + - - -
13B LEU* 2.6 39.9 + - + +
14B ASN 3.5 2.0 + - - -
16B ALA* 1.3 82.6 - - - +
18B ASN* 1.3 66.6 + - - +
19B PRO* 3.1 7.8 - - - +
53B LYS* 3.6 23.5 + - + +
61B GLU* 3.6 28.3 + - - +
64B GLN* 3.7 11.4 + - - -
65B ALA* 3.6 34.3 - - + +
68B VAL* 4.1 2.9 - - + -
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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