Contacts of the helix formed by residues 3 - 18 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 92.4 - - - +
4A ALA* 1.3 68.3 + - - +
5A GLU* 3.1 16.4 - - - +
6A GLY 3.1 3.5 + - - -
7A GLU* 3.0 26.3 + - - +
204A GLY 3.5 16.0 - - - +
205A SER* 3.0 14.9 + - - +
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Residues in contact with ALA 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 1.3 76.5 + - - +
5A GLU* 1.3 72.0 - - - +
7A GLU* 3.9 13.3 - - - +
8A SER* 2.9 28.4 + - - -
133C ASP* 5.9 2.2 - - - +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 3.6 14.2 - - - +
4A ALA* 1.3 84.7 + - - +
6A GLY* 1.3 62.8 + - - +
8A SER* 3.8 4.0 - - - -
9A LEU* 3.1 28.6 + - + +
39A GLU* 3.2 33.3 - - + +
41A GLU* 4.3 7.9 - - - +
45A ILE* 3.8 10.8 - - + -
205A SER* 3.4 34.3 + - - +
132C LYS* 5.9 2.3 - - - +
133C ASP* 5.7 1.2 - - - +
136C HIS* 5.1 10.0 + - - -
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Residues in contact with GLY 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.3 36.1 - - - +
3A GLU 3.1 0.6 + - - -
5A GLU* 1.3 73.3 - - - +
7A GLU* 1.3 64.7 + - - +
9A LEU* 3.2 2.1 + - - +
10A GLU* 2.9 25.8 + - - +
45A ILE* 4.0 11.6 - - - +
49A LEU* 4.3 0.2 - - - +
205A SER 3.0 14.2 + - - -
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA 3.8 10.8 - - - +
3A GLU 3.0 22.5 + - - +
4A ALA* 3.9 8.3 - - - +
6A GLY* 1.3 73.5 - - - +
8A SER* 1.3 57.3 + - - +
11A SER* 3.0 27.1 + - - -
19B PRO* 3.2 44.0 - - + +
20B SER* 5.0 1.3 - - - -
58B GLN* 3.5 16.8 + - - +
60B TRP* 3.5 22.6 - - - +
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Residues in contact with SER 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ALA 2.9 19.5 + - - -
5A GLU* 3.8 4.7 - - - -
7A GLU* 1.3 77.0 - - - +
9A LEU* 1.3 58.6 + - - +
11A SER* 3.1 8.7 + - - -
12A TRP* 3.0 47.2 + - - -
35A GLN* 4.7 6.6 + - - +
20B SER* 6.2 0.9 - - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 3.1 16.9 + - - +
6A GLY 3.8 1.1 - - - +
8A SER* 1.3 76.4 + - - +
10A GLU* 1.3 62.1 + - - +
12A TRP* 3.3 3.0 + - - +
13A LEU* 2.9 21.8 + - - +
32A PHE* 3.4 32.9 - - + -
35A GLN* 3.7 31.4 - - + -
36A ILE* 4.1 11.4 - - + +
39A GLU* 4.9 10.5 - - + -
42A GLY* 4.1 22.2 - - - +
45A ILE* 3.6 32.5 - - + -
46A ALA* 4.4 2.9 - - - +
49A LEU* 3.8 14.1 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 2.9 16.5 + - - +
9A LEU* 1.3 74.7 - - - +
11A SER* 1.3 61.0 + - - +
13A LEU* 3.1 12.4 + - - +
14A ASN* 2.9 40.1 + - - +
49A LEU* 3.2 27.4 - - + +
53A LYS* 3.0 17.9 + - - +
19B PRO* 3.3 19.5 - - + -
56B SER* 5.3 0.2 - - - -
58B GLN* 4.1 11.0 - - + -
61B GLU* 2.7 41.4 - - - +
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Residues in contact with SER 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 3.0 15.3 + - - -
8A SER* 3.3 12.6 - - - -
10A GLU* 1.3 79.3 - - - +
12A TRP* 1.3 62.1 + - - +
14A ASN* 3.4 4.7 + - - +
15A LYS* 3.4 31.1 + - - +
18B ASN* 3.3 30.7 + - - +
19B PRO* 4.3 0.6 - - - +
20B SER* 3.4 18.8 + - - -
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Residues in contact with TRP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 3.0 37.9 + - - -
9A LEU* 3.5 8.7 - - - +
11A SER* 1.3 75.9 - - - +
13A LEU* 1.3 65.1 + - - +
15A LYS* 3.4 8.1 + - + +
16A ALA* 3.1 23.2 + - - +
27A GLU* 4.6 4.7 - - - -
28A TYR* 4.0 36.8 - + - +
31A GLY* 4.1 27.1 - - - -
32A PHE* 3.8 16.6 - - + -
35A GLN* 3.3 44.0 - - + +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU 2.9 12.0 + - - +
10A GLU* 3.1 19.3 + - - +
12A TRP* 1.3 74.9 - - - +
14A ASN* 1.3 54.0 + - - +
16A ALA* 3.1 3.2 + - + +
17A THR* 2.7 68.9 + - + +
32A PHE* 3.8 18.4 - - + -
49A LEU* 3.7 26.5 - - + +
50A LEU* 4.0 23.3 - - + +
53A LYS* 3.3 29.4 - - + -
68A VAL* 4.2 14.6 - - + -
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Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 2.9 28.1 + - - +
11A SER* 3.5 10.3 - - - +
12A TRP 3.4 0.2 - - - -
13A LEU* 1.3 73.8 - - - +
15A LYS* 1.3 54.5 + - + +
17A THR* 3.3 5.1 - - - -
18A ASN* 2.6 39.0 + - - +
53A LYS* 2.7 24.5 + - - +
14B ASN* 3.3 51.4 + - - +
17B THR 5.0 0.2 - - - -
18B ASN* 4.2 17.7 - - - +
19B PRO* 4.3 1.1 - - - +
53B LYS* 4.7 0.6 - - - +
61B GLU* 3.6 8.7 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 3.4 19.4 + - - +
12A TRP* 3.5 11.6 - - + +
14A ASN* 1.3 81.8 - - + +
16A ALA* 1.3 61.7 + - - +
17A THR 3.3 1.0 + - - -
18A ASN* 3.5 7.3 + - - +
21A ASN* 3.3 18.2 + - - +
25A ASP* 5.3 0.2 - - - +
28A TYR* 3.5 59.1 + - + +
18B ASN* 5.9 2.2 - - - -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP 3.1 12.7 + - - +
13A LEU* 3.1 8.1 + - + +
15A LYS* 1.3 78.9 - - - +
17A THR* 1.3 61.5 + - + +
18A ASN 3.7 0.2 - - - -
21A ASN* 3.7 2.9 + - - +
25A ASP* 5.0 2.7 + - - -
28A TYR* 3.7 30.7 - - - +
29A ILE* 3.9 9.6 - - + +
32A PHE* 5.1 2.9 - - + -
64A GLN* 3.2 19.4 + - - +
68A VAL* 3.9 24.6 - - + +
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.7 45.3 + - + +
14A ASN 3.3 1.8 + - - -
16A ALA* 1.3 82.1 - - - +
18A ASN* 1.3 67.4 + - - +
19A PRO* 3.1 12.5 - - - +
53A LYS* 3.5 23.0 + - + +
61A GLU* 3.8 24.9 + - - +
64A GLN* 3.8 13.3 - - - +
65A ALA* 3.9 26.0 - - + +
68A VAL* 4.3 2.5 - - + -
14B ASN* 5.2 0.2 - - - -
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Residues in contact with ASN 18 (chain A).
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 2.6 20.8 + - - +
15A LYS* 3.7 6.7 - - - +
17A THR* 1.3 70.6 - - - +
19A PRO* 1.3 73.5 - - - +
20A SER* 2.5 25.1 + - - +
21A ASN* 2.9 35.6 + - - +
64A GLN* 3.1 11.8 - - - +
11B SER* 2.8 29.7 + - - +
14B ASN* 4.2 8.1 - - - +
15B LYS* 5.7 4.3 - - - -
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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