Contacts of the helix formed by residues 17 - 29 (chain B) in PDB entry 1WKJ
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ILE* 5.0 0.2 - - - -
12B GLY* 3.1 20.1 + - - +
15B ARG* 3.9 40.8 - - + +
16B GLY* 1.3 76.7 - - - +
18B VAL* 1.3 65.1 + - - +
19B GLY 3.5 2.0 - - - -
20B GLU* 3.4 24.5 + - - +
21B ILE* 3.1 38.5 + - + +
105B PHE* 3.7 41.1 - - + -
113B VAL* 4.0 17.9 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.5 23.3 - - + -
26A GLU* 3.1 18.1 + - - +
32A ILE* 4.4 10.3 - - + -
35A LEU* 4.7 1.1 - - + -
8B ILE* 3.8 21.4 - - + +
13B VAL* 4.1 24.5 - - + -
17B LEU* 1.3 79.3 - - - +
19B GLY* 1.3 58.4 + - - +
21B ILE* 3.4 1.9 + - - +
22B LEU* 3.0 35.5 + - + +
71B VAL* 3.8 33.9 - - + -
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 3.1 34.4 - - - -
22A LEU* 3.9 6.9 - - - +
23A ALA* 3.8 6.5 - - - -
26A GLU* 2.7 21.7 + - - -
18B VAL* 1.3 73.7 - - - +
20B GLU* 1.3 57.0 + - - +
22B LEU* 3.3 0.6 + - - -
23B ALA* 2.8 27.0 + - - +
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Residues in contact with GLU 20 (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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23A ALA* 4.1 15.7 - - + +
26A GLU* 4.6 0.4 + - - -
27A ARG* 4.9 14.2 + - - +
16B GLY 3.8 10.4 - - - +
17B LEU* 3.4 30.4 + - - +
18B VAL 3.4 0.4 - - - -
19B GLY* 1.3 74.9 - - - +
21B ILE* 1.3 62.5 + - - +
23B ALA* 3.4 7.1 + - - +
24B ARG* 3.3 27.0 + - - +
105B PHE* 3.7 28.2 - - + -
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Residues in contact with ILE 21 (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 ILE* 4.0 28.3 - - + -
17B LEU* 3.1 28.5 + - + +
18B VAL 3.8 2.7 - - - +
20B GLU* 1.3 74.7 - - + +
22B LEU* 1.3 66.8 + - - +
24B ARG* 3.0 20.4 + - - +
25B PHE* 3.4 33.8 + - + -
73B MET* 5.2 0.9 - - + -
101B ILE* 4.2 21.8 - - + -
105B PHE* 4.8 9.0 - - + -
113B VAL* 3.7 30.5 - - + -
114B ILE* 4.2 11.9 - - + -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.0 20.2 - - + -
19A GLY* 3.9 8.1 - - - +
22A LEU* 4.0 26.2 - - + -
35A LEU* 5.5 0.2 - - + -
18B VAL* 3.0 22.5 + - + +
19B GLY 3.8 3.8 - - - +
21B ILE* 1.3 75.7 - - - +
23B ALA* 1.3 62.9 + - - +
25B PHE* 3.0 11.2 + - + +
26B GLU* 2.9 27.4 + - - +
32B ILE* 4.0 22.9 - - + -
35B LEU* 4.2 19.5 - - + -
73B MET* 3.7 35.9 - - + -
75B LEU* 5.4 0.9 - - + -
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Residues in contact with ALA 23 (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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16A GLY 5.8 0.2 - - - -
19A GLY* 3.8 0.6 - - - -
20A GLU* 4.1 27.1 - - + +
23A ALA* 6.3 0.2 - - + -
19B GLY 2.8 19.2 + - - +
20B GLU* 3.5 9.4 - - - +
22B LEU* 1.3 77.8 - - - +
24B ARG* 1.3 57.1 + - + +
26B GLU* 3.8 12.4 - - - +
27B ARG* 2.9 33.5 + - - +
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Residues in contact with ARG 24 (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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20B GLU 3.3 13.8 + - - +
21B ILE* 3.0 11.0 + - - +
23B ALA* 1.3 77.9 - - - +
25B PHE* 1.3 64.2 + - + +
27B ARG* 3.3 36.4 + - - +
28B LYS* 3.2 22.3 + - - +
87B MET* 3.7 18.0 + - + +
99B GLY 3.2 18.6 + - - -
100B THR 3.7 13.7 - - - -
101B ILE* 3.7 20.5 - - + +
104B ASP* 2.9 31.3 + - - +
105B PHE* 3.6 32.5 - - - -
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Residues in contact with PHE 25 (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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6B VAL* 4.4 8.7 - - + -
21B ILE* 3.4 37.0 + - + -
22B LEU* 3.0 11.8 + - + +
24B ARG* 1.3 78.1 - - + +
26B GLU* 1.3 61.7 + - + +
28B LYS* 3.4 5.8 + - - +
29B GLY 3.3 4.0 + - - -
30B PHE* 3.2 32.7 + + + +
32B ILE* 6.1 0.9 - - + -
73B MET* 4.3 7.9 - - - -
75B LEU* 3.5 41.3 - - + -
84B VAL* 4.1 18.6 - - + -
87B MET* 3.9 32.1 - - + -
88B MET* 5.1 0.4 - - + -
101B ILE* 3.6 23.3 - - + -
114B ILE* 4.1 13.5 - - + -
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Residues in contact with GLU 26 (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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13A VAL 4.6 1.4 - - - +
16A GLY* 3.3 37.9 - - - +
18A VAL* 3.1 33.8 + - - +
19A GLY* 2.7 31.0 + - - -
20A GLU 4.5 0.3 + - - -
22B LEU* 2.9 16.7 + - - +
23B ALA* 3.8 6.7 - - - +
25B PHE* 1.3 74.8 - - + +
27B ARG* 1.3 64.8 + - - +
29B GLY* 3.0 14.9 + - - -
30B PHE 4.4 8.6 - - - +
32B ILE* 4.1 22.2 - - + +
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Residues in contact with ARG 27 (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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23B ALA 2.9 16.6 + - - +
24B ARG* 3.3 49.3 + - - +
26B GLU* 1.3 75.8 - - - +
28B LYS* 1.3 61.2 + - - +
29B GLY* 3.4 0.7 + - - -
87B MET* 6.2 0.2 - - - +
99B GLY 5.8 0.6 + - - -
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Residues in contact with LYS 28 (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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24B ARG 3.2 19.6 + - - +
25B PHE 3.5 7.2 - - - +
26B GLU 3.1 0.2 - - - -
27B ARG* 1.3 78.6 - - + +
29B GLY* 1.3 58.0 + - - +
30B PHE* 3.5 27.0 - - + -
83B GLU* 2.7 44.7 + - - -
86B LYS* 4.6 2.4 - - - +
87B MET* 4.0 17.9 - - + +
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Residues in contact with GLY 29 (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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26B GLU 3.0 14.2 + - - -
27B ARG 3.2 1.3 - - - -
28B LYS* 1.3 79.4 - - - +
30B PHE* 1.3 68.0 + - - +
31B ARG* 3.8 1.2 + - - +
76B GLU 4.8 0.5 - - - +
77B GLY* 5.8 0.5 - - - -
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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