Contacts of the helix formed by residues 2 - 19 (chain D) in PDB entry 4PCW
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 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.4 1.6 - - - -
39C GLU* 3.6 18.8 - - - +
1D SER* 1.3 76.0 - - - +
3D LEU* 1.3 66.1 + - - +
4D LEU* 3.9 6.4 + - - +
5D GLU* 2.9 38.0 + - - +
6D ASN* 3.2 26.8 + - - -
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Residues in contact with LEU 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.2 21.8 - - + -
13C LEU* 3.6 16.6 - - + +
35C LEU* 4.6 4.0 - - + -
39C GLU* 2.8 27.4 + - + +
40C PHE* 3.6 30.7 - - + -
73C PHE* 4.1 26.2 - - + -
77C VAL* 4.2 23.3 - - + -
80C LEU* 5.5 0.2 - - + -
2D THR* 1.3 70.3 - - - +
4D LEU* 1.3 66.9 + - - +
6D ASN* 3.3 5.3 + - - +
7D ILE* 3.1 39.7 + - + +
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLU* 3.8 23.3 + - - +
40C PHE* 4.7 3.6 - - + -
42C GLN* 4.9 13.5 - - + +
43C ILE* 3.8 32.8 - - + -
80C LEU* 4.5 10.8 - - + -
84C TYR* 3.8 34.1 - - + +
2D THR* 3.4 7.0 + - - +
3D LEU* 1.3 78.4 - - - +
5D GLU* 1.3 63.8 + - + +
7D ILE* 3.2 6.7 + - + +
8D PHE* 3.0 39.6 + - + -
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Residues in contact with GLU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D SER* 3.4 16.4 + - - +
2D THR* 2.9 41.9 + - - +
3D LEU 3.3 0.4 - - - -
4D LEU* 1.3 77.0 - - + +
6D ASN* 1.3 59.3 + - - +
8D PHE* 3.9 4.1 - - - +
9D ALA* 2.9 29.9 + - - +
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Residues in contact with ASN 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASN* 3.7 18.6 + - + +
9C ALA* 3.3 39.8 + - - +
10C ILE* 3.8 21.6 - - + +
13C LEU* 5.2 2.4 - - - +
1D SER* 3.5 20.6 + - - -
2D THR 3.2 18.5 + - - -
3D LEU* 3.3 9.5 + - - +
4D LEU 3.2 0.4 - - - -
5D GLU* 1.3 77.6 - - - +
7D ILE* 1.3 61.5 + - - +
9D ALA* 3.4 6.6 + - - +
10D ILE* 3.1 30.2 + - - +
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Residues in contact with ILE 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 5.4 1.6 - - + -
77C VAL* 3.9 34.5 - - + +
80C LEU* 3.8 31.0 - - + +
81C ALA* 3.7 31.9 - - + +
84C TYR* 4.8 7.6 - - + -
3D LEU* 3.1 32.1 + - + +
4D LEU* 3.6 12.1 - - + +
6D ASN* 1.3 77.4 - - + +
8D PHE* 1.3 60.2 + - + +
10D ILE* 3.2 11.9 + - + +
11D ILE* 3.0 33.5 + - + +
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Residues in contact with PHE 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TYR* 3.3 57.7 - + + -
88C THR* 5.0 13.9 - - + -
4D LEU* 3.0 34.0 + - + +
5D GLU* 4.1 4.0 - - - +
7D ILE* 1.3 78.0 - - + +
9D ALA* 1.3 57.0 + - - +
11D ILE* 3.4 17.2 - - + +
12D ASN* 2.7 53.0 + - - +
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C SER* 5.4 4.3 - - - -
6C ASN* 3.4 33.7 - - - +
5D GLU 2.9 19.0 + - - +
6D ASN 3.5 2.7 - - - +
8D PHE* 1.3 76.7 - - - +
10D ILE* 1.3 55.9 + - - +
12D ASN* 3.9 4.9 - - - +
13D LEU* 3.0 29.5 + - - +
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.0 15.7 - - + -
6C ASN* 4.0 19.5 - - + +
7C ILE* 5.3 1.3 - - + -
10C ILE* 3.9 24.7 - - + -
77C VAL* 6.2 0.9 - - + -
78C PHE* 5.1 5.2 - - + -
81C ALA* 6.1 2.0 - - + -
6D ASN 3.1 17.5 + - - +
7D ILE* 3.5 9.9 - - + +
9D ALA* 1.3 74.0 - - - +
11D ILE* 1.3 67.2 + - - +
13D LEU* 3.6 6.5 + - - +
14D PHE* 3.3 19.8 + - - +
70D PHE* 4.2 2.6 - - + -
73D PHE* 3.8 23.0 - - + -
74D LEU* 4.3 17.9 - - + -
77D VAL* 4.2 19.5 - - + -
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Residues in contact with ILE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA* 3.6 20.2 - - + +
84C TYR* 3.7 22.4 - - + -
85C TYR* 3.8 25.6 - - + +
88C THR* 4.8 2.9 - - - +
7D ILE* 3.0 27.8 + - + +
8D PHE* 3.2 23.1 + - + +
10D ILE* 1.3 77.1 - - - +
12D ASN* 1.3 66.9 + - - +
14D PHE* 3.2 7.8 + - - +
15D LYS* 3.0 35.9 + - - +
70D PHE* 3.7 23.7 - - + -
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Residues in contact with ASN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PHE* 2.7 37.0 + - - +
9D ALA* 4.1 4.6 - - - +
11D ILE* 1.3 79.6 - - - +
13D LEU* 1.3 66.1 + - - +
15D LYS* 3.6 17.2 - - - +
16D GLN* 3.1 25.4 + - - +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER 5.7 3.8 - - - +
3C LEU* 3.6 48.9 - - + +
6C ASN* 5.5 1.3 - - - +
9D ALA 3.0 19.1 + - - +
10D ILE* 3.7 4.7 - - - +
12D ASN* 1.3 75.1 - - - +
14D PHE* 1.3 66.0 + - - +
16D GLN* 3.2 21.0 + - - +
17D TYR* 3.2 48.5 - - + -
35D LEU* 4.8 3.8 - - + -
38D LYS* 5.8 1.1 - - - +
39D GLU* 3.1 29.8 - - + +
73D PHE* 4.4 9.0 - - + -
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Residues in contact with PHE 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.3 33.4 - + - -
10D ILE 3.3 9.2 + - - +
11D ILE 3.2 8.6 + - - +
13D LEU* 1.3 80.9 - - - +
15D LYS* 1.3 59.3 + - - +
17D TYR* 3.4 3.9 + - - -
18D SER* 2.9 42.1 + - - -
25D ASP 3.5 18.2 - - - -
26D THR* 4.1 4.7 - - - -
27D LEU* 3.5 22.7 - - + +
35D LEU* 5.1 2.7 - - - -
68D ILE 3.5 22.9 - - - -
69D ASP 3.8 10.1 - - - -
70D PHE* 3.6 30.5 - + + -
73D PHE* 3.7 29.6 - + + -
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C TYR* 4.2 24.5 + - + +
88C THR* 3.5 39.3 + - - -
89C ARG* 4.4 6.9 - - - +
11D ILE* 3.0 23.8 + - + +
12D ASN* 3.6 25.4 - - - +
13D LEU 3.1 0.4 - - - -
14D PHE* 1.3 76.1 - - - +
16D GLN* 1.3 64.3 + - - +
18D SER* 3.4 6.7 - - - +
19D LYS* 3.1 61.2 + - + +
24D THR 5.9 0.4 - - - +
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Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN 3.1 15.0 + - - +
13D LEU* 3.2 20.3 + - - +
15D LYS* 1.3 77.9 - - - +
17D TYR* 1.3 84.2 + - + +
19D LYS* 4.3 5.3 + - - +
20D LYS* 3.6 21.9 + - - +
38D LYS* 4.4 16.0 + - - +
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Residues in contact with TYR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.2 42.6 - - + -
14D PHE 3.4 2.8 + - - +
15D LYS 3.2 0.4 - - - -
16D GLN* 1.3 94.6 - - + +
18D SER* 1.3 60.9 + - - +
19D LYS 3.2 1.8 - - - -
20D LYS* 3.1 29.0 - - - +
27D LEU* 3.5 19.7 - - + -
31D GLU* 3.0 42.3 - - - +
34D GLU* 3.8 10.8 - - + -
35D LEU* 3.5 40.1 + - + -
38D LYS* 3.3 42.6 + - + +
39D GLU* 4.2 3.3 + - - -
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 5.0 0.2 + - - -
14D PHE* 2.9 31.3 + - - -
15D LYS* 3.3 12.8 + - - +
17D TYR* 1.3 78.2 - - - +
19D LYS* 1.3 59.0 + - - +
20D LYS 3.2 1.1 + - - -
21D ASP 3.6 0.9 + - - -
23D ASN 3.1 9.4 - - - +
24D THR 2.8 21.2 + - - -
26D THR 3.2 28.3 - - - -
27D LEU* 3.4 6.9 - - - +
31D GLU* 3.1 3.6 - - - +
101D CA 2.6 22.2 - - - -
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LYS* 3.1 51.9 + - + +
16D GLN* 4.7 4.3 - - - +
17D TYR 3.2 0.4 - - - -
18D SER* 1.3 75.4 + - - +
20D LYS* 1.3 62.6 + - - +
21D ASP 3.3 8.0 - - - +
24D THR* 4.1 36.7 - - + +
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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
------------------------------------------------------------
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