Contacts of the helix formed by residues 13 - 33 (chain A) in PDB entry 1WJ5
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 ASP 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 5.1 7.8 - - - +
12A LEU* 1.3 88.1 - - - +
14A LEU* 1.3 57.7 + - - +
15A ALA* 3.6 11.2 - - + +
16A GLY* 2.6 33.3 + - - -
17A LEU* 2.5 35.2 + - - +
56A VAL* 2.9 13.2 - - - -
57A THR* 4.1 7.6 - - + +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 1.3 72.0 - - - +
15A ALA* 1.3 50.7 + - - +
17A LEU* 4.3 2.0 - - - +
18A THR* 2.4 54.4 + - - +
56A VAL* 2.8 16.7 - - + +
57A THR* 4.8 1.0 + - - -
58A HIS* 3.6 32.3 + - + +
75A VAL* 5.2 2.7 - - + -
78A ARG* 4.6 15.3 - - + -
79A VAL* 3.2 26.5 - - + +
82A ASN* 4.1 12.6 - - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 2.7 10.8 + - + +
14A LEU* 1.3 78.5 - - - +
16A GLY* 1.3 56.6 + - - +
18A THR* 3.3 6.3 - - - +
19A SER* 2.7 36.6 + - - -
82A ASN* 6.0 1.6 - - - +
86A LEU* 5.6 0.9 - - - +
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Residues in contact with GLY 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.4 12.1 - - - +
13A ASP* 2.6 36.9 + - - -
15A ALA* 1.3 74.2 - - - +
17A LEU* 1.3 60.9 + - - +
19A SER* 3.5 14.8 + - - -
20A LEU* 3.6 6.4 + - - +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.3 23.0 - - + +
13A ASP 2.5 19.2 + - - +
14A LEU 4.3 2.5 - - - +
16A GLY* 1.3 69.8 - - - -
18A THR* 1.3 66.3 + - - +
20A LEU* 3.1 11.2 + - + +
21A LEU 3.1 12.6 + - - -
51A LEU* 3.1 48.2 - - + +
52A ALA 5.3 0.7 - - - -
54A ARG* 3.7 16.6 - - + +
55A PRO 3.7 4.9 - - - +
56A VAL* 3.3 31.6 - - + -
79A VAL* 4.0 21.5 - - + -
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.4 33.9 + - - +
15A ALA* 3.1 7.6 + - - +
17A LEU* 1.3 73.0 - - - +
19A SER* 1.3 58.3 + - - +
20A LEU 2.8 1.3 - - - -
21A LEU* 2.5 25.9 + - - +
22A SER* 2.9 10.0 + - - -
79A VAL* 2.6 35.8 - - - +
82A ASN* 3.2 33.7 - - + +
83A ALA 3.7 0.2 - - - +
86A LEU* 3.3 17.3 - - + -
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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
----------------------------------------------------------
15A ALA 2.7 20.5 + - - -
16A GLY* 3.6 8.7 - - - -
18A THR* 1.3 73.1 - - - +
20A LEU* 1.3 61.9 + - - +
22A SER* 3.2 16.5 + - - -
23A GLU* 3.8 9.0 + - - +
86A LEU* 3.7 27.8 - - - +
90A LYS* 4.5 12.3 + - - -
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Residues in contact with LEU 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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12A LEU* 6.2 4.3 - - + -
16A GLY 3.6 5.3 + - - +
17A LEU* 3.1 15.4 + - + +
18A THR 2.6 4.2 + - - -
19A SER* 1.3 72.5 - - - +
21A LEU* 1.3 66.4 + - - +
22A SER 2.9 1.6 - - - -
23A GLU* 2.7 31.8 + - + +
24A LYS* 3.0 22.5 + - + +
51A LEU* 3.9 24.2 - - + -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.1 9.4 + - - +
18A THR 2.5 13.8 + - - +
20A LEU* 1.3 71.0 - - - +
22A SER* 1.3 54.3 + - - +
24A LYS* 2.7 33.2 + - + +
25A ILE* 2.8 35.4 + - + +
48A LEU* 4.2 18.8 - - + +
51A LEU* 3.1 21.8 - - + +
52A ALA* 3.0 32.5 - - + -
79A VAL* 3.3 35.4 - - + +
80A PHE* 3.6 10.5 - - + +
83A ALA* 3.5 3.4 - - + -
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR 2.9 4.9 + - - -
19A SER 3.2 13.2 - - - -
20A LEU 2.8 0.4 + - - -
21A LEU* 1.3 75.7 - - - +
23A GLU* 1.3 57.9 + - - +
25A ILE* 2.9 19.1 + - - +
26A LYS 2.9 10.9 + - - -
83A ALA* 3.2 34.3 + - - +
86A LEU* 3.7 12.8 - - - -
87A LEU* 2.6 37.6 + - - +
90A LYS* 3.8 11.7 - - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 3.8 11.2 - - - +
20A LEU* 2.7 27.2 + - + +
22A SER* 1.3 73.2 - - - +
24A LYS* 1.3 56.1 + - - +
26A LYS* 3.4 39.8 + - - +
27A GLU* 2.8 39.1 + - + +
90A LYS* 3.8 20.0 + - - +
92A LEU* 4.0 8.5 - - - +
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Residues in contact with LYS 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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20A LEU* 3.0 23.3 + - + +
21A LEU* 2.7 21.3 + - + +
23A GLU* 1.3 74.6 - - - +
25A ILE* 1.3 56.2 + - - +
27A GLU* 3.8 11.0 - - + +
28A PHE* 3.2 19.1 + - - +
47A SER 4.9 7.6 - - - +
48A LEU* 3.2 33.3 - - + +
51A LEU* 3.5 31.4 - - + +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 2.8 39.1 + - + +
22A SER* 3.3 4.0 - - - +
24A LYS* 1.3 76.0 - - - +
26A LYS* 1.3 67.4 + - - +
27A GLU 3.0 1.1 - - - -
28A PHE* 2.8 18.6 + - - +
29A LEU* 3.0 15.5 + - + +
37A PHE* 3.6 13.9 - - + -
42A LEU* 3.1 34.1 - - + -
48A LEU* 3.8 12.3 - - + -
80A PHE* 4.2 7.4 - - + -
83A ALA* 3.1 30.3 - - + -
84A LEU* 3.9 13.5 - - + -
87A LEU* 3.5 17.0 - - + -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 2.9 5.7 + - - -
23A GLU* 3.4 47.0 + - - +
25A ILE* 1.3 77.5 - - - +
27A GLU* 1.3 78.6 + - - +
29A LEU* 3.4 20.4 + - - +
30A GLN* 3.3 30.1 + - - +
87A LEU* 3.6 19.1 - - + -
92A LEU* 3.3 43.9 - - + +
106A VAL* 5.4 1.8 - - + +
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Residues in contact with GLU 27 (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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23A GLU* 2.8 27.6 + - + +
24A LYS* 3.8 12.7 - - + +
26A LYS* 1.3 94.5 + - - +
28A PHE* 1.3 67.1 + - - +
30A GLN* 3.0 18.8 + - - +
31A GLU* 2.9 20.8 + - - +
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Residues in contact with PHE 28 (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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24A LYS 3.2 12.7 + - - +
25A ILE* 2.8 15.9 + - - +
27A GLU* 1.3 79.5 - - - +
29A LEU* 1.3 57.6 + - + +
31A GLU* 2.9 11.0 + - + +
32A LYS* 2.7 83.3 + - + +
34A MET* 3.6 7.9 - - + -
41A GLU 4.9 1.1 - - - -
42A LEU* 3.4 28.3 - - + -
45A VAL* 2.9 50.9 - - + -
48A LEU* 4.0 8.3 - - + -
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Residues in contact with LEU 29 (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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25A ILE* 3.0 22.7 + - + +
26A LYS* 3.5 18.2 - - - +
27A GLU 3.1 0.2 - - - -
28A PHE* 1.3 83.7 - - + +
30A GLN* 1.3 55.1 + - + +
33A LYS* 2.6 36.9 + - - -
34A MET* 3.3 29.5 + - + +
37A PHE* 3.1 53.2 - - + -
42A LEU* 4.4 0.7 - - + -
93A VAL* 4.4 4.9 - - + -
106A VAL* 3.8 33.4 - - + -
108A THR* 5.4 2.2 + - - -
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Residues in contact with GLN 30 (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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26A LYS* 3.3 33.5 + - - +
27A GLU* 3.0 15.8 + - - +
29A LEU* 1.3 76.3 - - + +
31A GLU* 1.3 57.3 + - - +
33A LYS* 3.1 42.3 + - - +
92A LEU* 5.0 6.5 - - - +
106A VAL* 6.1 1.6 - - + -
107A THR* 6.1 2.8 - - - +
108A THR* 5.7 13.4 - - - +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 2.9 11.2 + - - +
28A PHE* 2.9 18.3 + - + +
30A GLN* 1.3 78.8 - - - +
32A LYS* 1.3 81.5 + - + +
33A LYS* 3.2 7.4 + - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 2.7 67.1 + - + +
31A GLU* 1.3 88.6 - - + +
33A LYS* 1.3 72.3 + - - +
34A MET* 3.2 28.5 - - + +
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Residues in contact with LYS 33 (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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29A LEU 2.6 15.7 + - - -
30A GLN* 3.1 34.2 + - - +
31A GLU 4.0 5.8 - - - +
32A LYS* 1.3 80.2 - - - +
34A MET* 1.3 57.0 + - - +
35A GLN* 5.7 0.8 - - - +
108A THR* 5.3 6.3 - - - +
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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
------------------------------------------------------------
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