Contacts of the helix formed by residues 13 - 26 (chain A) in PDB entry 2WJP
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 LEU 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 1.3 73.8 - - - +
14A GLY* 1.3 71.1 + - - +
16A THR* 5.0 0.3 - - - -
17A GLY* 3.0 24.3 + - - +
18A LEU* 3.9 31.6 - - + +
21A VAL* 4.6 2.0 - - + -
33A VAL* 4.1 22.4 - - + -
35A ASP* 2.9 17.6 + - + +
37A ARG* 4.0 6.0 + - - +
40A PRO* 4.2 10.3 - - + -
41A PRO 3.6 5.8 - - - +
42A GLY 3.6 4.3 - - - +
43A LEU* 3.6 46.7 - - + +
46A LEU* 4.2 17.0 - - + -
71A SER* 5.5 1.4 + - - -
1441A D17 5.7 3.6 - - - -
1451A SO4 3.9 3.5 + - - -
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Residues in contact with GLY 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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13A LEU* 1.3 79.3 - - - +
15A LEU* 1.3 61.3 + - - -
16A THR 3.2 0.2 - - - -
18A LEU* 2.9 36.9 + - - +
37A ARG* 4.6 1.5 - - - +
41A PRO* 2.9 35.7 + - - +
42A GLY* 5.3 0.2 - - - -
1451A SO4 3.7 8.1 - - - -
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Residues in contact with LEU 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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14A GLY* 1.3 72.1 - - - -
16A THR* 1.3 58.3 + - - +
18A LEU* 3.3 14.0 + - + +
19A SER* 2.9 27.0 + - - -
45A LYS* 6.5 1.1 - - + -
140A GLY 5.1 4.3 - - - +
141A LEU* 5.3 5.4 - - + -
142A PRO* 3.6 27.8 - - + +
145A MET* 4.4 16.6 - - + +
1451A SO4 2.9 21.6 + - - +
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Residues in contact with THR 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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13A LEU 5.0 0.2 - - - -
15A LEU* 1.3 69.7 - - - +
17A GLY* 1.3 64.4 + - - +
19A SER* 2.7 24.2 + - - +
20A CYS* 3.0 11.3 + - - -
71A SER* 6.2 1.6 - - - -
72A PRO* 5.2 13.0 - - + -
94A ASP* 3.3 37.0 - - + +
137A GLY 5.3 1.9 + - - -
142A PRO* 3.7 15.0 - - + +
162A GLN* 6.0 1.6 - - - +
1451A SO4 2.6 35.1 + - - -
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Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.2 7.3 - - - +
12A GLY 3.3 17.3 - - - -
13A LEU* 3.0 29.7 + - - -
16A THR* 1.3 77.4 - - - +
18A LEU* 1.3 61.2 + - - +
20A CYS* 3.1 9.1 + - - +
21A VAL* 3.0 24.4 + - - +
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Residues in contact with LEU 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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13A LEU* 3.9 19.3 - - + +
14A GLY 2.9 24.2 + - - +
15A LEU* 3.6 15.5 - - + +
17A GLY* 1.3 75.8 - - - +
19A SER* 1.3 61.6 + - - +
21A VAL* 3.3 5.7 + - + +
22A ASP* 3.0 34.9 + - - +
42A GLY* 3.9 33.9 - - - +
45A LYS* 4.1 22.0 - - + +
46A LEU* 4.0 25.6 - - + +
47A PRO* 5.1 2.2 - - + -
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Residues in contact with SER 19 (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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15A LEU 2.9 13.9 + - - -
16A THR* 2.7 24.2 + - - +
18A LEU* 1.3 76.7 - - - +
20A CYS* 1.3 57.1 + - - +
22A ASP* 3.5 7.1 + - - +
23A PHE* 3.0 28.1 + - - +
94A ASP* 4.9 0.7 + - - -
142A PRO* 3.8 11.0 - - - +
144A LEU* 4.0 22.1 - - - +
145A MET* 3.8 29.4 - - - -
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Residues in contact with CYS 20 (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 ILE* 3.7 23.3 - - + -
16A THR* 3.0 20.3 + - - -
17A GLY* 3.1 9.4 + - - +
19A SER* 1.3 75.5 + - - +
21A VAL* 1.3 65.6 + - - +
23A PHE* 3.2 2.2 + - - +
24A PHE* 3.1 33.0 + - + -
69A VAL* 3.9 20.9 - - + -
94A ASP* 3.7 28.3 - - - -
97A LEU* 4.4 1.6 - - - -
144A LEU* 4.0 13.2 - - + -
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Residues in contact with VAL 21 (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 ILE* 3.5 13.6 - - + +
13A LEU* 4.6 1.3 - - + -
17A GLY 3.0 20.1 + - - +
18A LEU* 3.5 10.3 - - + +
20A CYS* 1.3 75.1 - - - +
22A ASP* 1.3 63.1 + - - +
24A PHE* 3.3 2.3 + - - +
25A LEU* 3.0 49.3 + - + +
31A PRO* 4.2 6.4 - - + +
33A VAL* 3.6 30.1 - - + -
46A LEU* 3.7 16.6 - - + -
47A PRO* 4.5 4.0 - - + -
50A VAL* 4.0 17.0 - - + -
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Residues in contact with ASP 22 (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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18A LEU* 3.0 27.4 + - - +
19A SER* 3.9 7.2 - - - +
21A VAL* 1.3 83.8 - - - +
23A PHE* 1.3 63.9 + - - +
25A LEU* 3.9 11.7 - - - +
26A ALA* 3.0 27.5 + - - +
47A PRO* 4.9 8.1 - - - +
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Residues in contact with PHE 23 (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 TYR* 3.9 24.2 - + - -
19A SER 3.0 17.9 + - - +
20A CYS 3.2 5.1 + - - +
22A ASP* 1.3 78.6 - - - +
24A PHE* 1.3 85.3 + + - +
26A ALA* 3.6 4.2 + - - +
27A ARG* 3.4 56.2 + - - +
97A LEU* 4.3 18.6 - - + -
101A GLU* 3.9 25.1 - - + -
144A LEU* 3.9 31.4 - - + -
147A LEU* 4.5 8.5 - - + -
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Residues in contact with PHE 24 (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 TYR* 3.7 34.5 - + + -
8A VAL* 3.8 32.3 - - + -
10A ILE* 4.2 9.2 - - + -
20A CYS* 3.1 24.8 + - + -
21A VAL 3.9 4.3 - - - +
23A PHE* 1.3 83.0 - + - +
25A LEU* 1.3 66.4 + - - +
27A ARG* 3.0 12.6 + - - +
28A GLY 3.3 0.2 + - - -
29A VAL* 3.0 51.6 + - + +
31A PRO* 4.2 8.5 - - + -
67A LEU* 4.0 7.4 - - + -
69A VAL* 3.9 7.9 - - + -
97A LEU* 3.8 38.6 - - + -
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Residues in contact with LEU 25 (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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21A VAL* 3.0 40.7 + - + +
22A ASP* 3.4 10.5 + - - +
24A PHE* 1.3 75.4 - - - +
26A ALA* 1.3 58.6 + - - +
27A ARG 3.0 0.2 - - - -
28A GLY* 2.9 19.8 + - - -
29A VAL 3.4 13.2 - - - +
30A THR* 4.0 25.8 - - + +
31A PRO* 4.1 4.7 - - + -
47A PRO* 4.1 16.8 - - + -
49A ALA* 6.4 2.0 - - + -
50A VAL* 4.1 12.6 - - + -
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Residues in contact with ALA 26 (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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22A ASP 3.0 18.8 + - - +
23A PHE* 4.0 6.1 - - - +
24A PHE 3.2 0.2 - - - -
25A LEU* 1.3 76.8 - - - +
27A ARG* 1.3 61.4 + - + +
28A GLY 3.4 1.1 + - - -
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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