Contacts of the helix formed by residues 16 - 33 (chain B) in PDB entry 2WAL
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 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A THR* 6.1 4.5 - - + -
14A GLU* 5.6 6.8 - - - +
16A THR* 4.1 21.0 - - - +
14B GLU 3.1 8.3 + - - -
15B SER* 1.3 75.0 - - - +
17B ALA* 1.3 66.4 + - + +
18B ARG* 3.2 24.5 - - + +
19B MET* 3.2 16.4 + - - +
20B GLN* 3.0 33.6 + - - +
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Residues in contact with ALA 17 (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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16B THR* 1.3 76.1 - - + +
18B ARG* 1.3 63.0 + - - +
20B GLN* 3.3 14.4 + - - +
21B GLY* 3.0 20.8 + - - -
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Residues in contact with ARG 18 (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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11A THR 6.1 0.2 - - - -
13A PRO* 3.8 18.0 - - - +
14A GLU* 3.9 27.0 - - - +
16B THR* 3.2 15.6 - - + +
17B ALA* 1.3 79.3 - - - +
19B MET* 1.3 64.9 + - - +
21B GLY* 3.4 2.2 + - - -
22B ALA* 3.0 26.2 + - - +
141B PHE* 3.2 42.3 + - + -
144B GLU* 2.8 31.2 + - - +
145B SER* 3.0 36.6 + - - +
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Residues in contact with MET 19 (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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14A GLU* 6.2 2.2 - - - -
14B GLU* 3.3 51.8 - - + +
15B SER* 4.9 0.7 - - - -
16B THR* 3.2 20.3 + - - +
18B ARG* 1.3 84.0 - - - +
20B GLN* 1.3 61.9 + - + +
22B ALA* 3.1 6.9 + - - +
23B GLY* 3.0 24.4 + - - -
141B PHE* 3.8 26.7 - - + -
154B SER* 3.7 17.3 - - - +
155B ILE* 5.0 2.8 - - - +
156B THR* 4.1 32.9 + - - +
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Residues in contact with GLN 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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15B SER* 4.2 15.8 + - - -
16B THR 3.0 26.1 + - - +
17B ALA* 3.5 11.6 - - - +
19B MET* 1.3 77.0 - - + +
21B GLY* 1.3 61.3 + - - +
23B GLY* 3.2 2.6 + - - -
24B LYS* 3.1 44.6 + - - +
156B THR 5.6 1.1 - - - -
158B PRO* 5.8 0.7 - - - +
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Residues in contact with GLY 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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17B ALA 3.0 14.4 + - - -
18B ARG* 3.8 3.4 - - - -
20B GLN* 1.3 74.3 - - - +
22B ALA* 1.3 63.4 + - - +
24B LYS* 4.0 6.7 - - - +
25B ALA* 3.1 25.3 + - - +
137B LYS* 4.0 17.9 - - - +
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Residues in contact with ALA 22 (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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18B ARG 3.0 5.4 + - - +
19B MET* 3.1 10.1 + - - +
21B GLY* 1.3 75.1 - - - +
23B GLY* 1.3 65.9 + - - +
25B ALA* 3.1 6.9 + - - +
26B LEU* 2.9 24.6 + - - +
137B LYS* 5.7 1.8 - - - -
138B LEU* 3.7 6.1 - - - +
141B PHE* 3.4 42.4 - - + -
155B ILE* 3.9 18.8 - - + -
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Residues in contact with GLY 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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19B MET 3.0 11.3 + - - -
20B GLN 3.2 3.5 + - - -
22B ALA* 1.3 74.2 - - - +
24B LYS* 1.3 62.1 + - - +
26B LEU* 3.2 4.9 + - - +
27B HIS* 3.0 21.8 + - - +
155B ILE* 3.7 9.8 - - - +
156B THR 3.5 24.7 - - - -
157B LEU* 4.3 1.5 - - - +
158B PRO* 3.8 15.0 - - - +
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Residues in contact with LYS 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 GLN* 3.1 33.2 + - - +
21B GLY* 4.0 7.2 - - - +
23B GLY* 1.3 73.7 - - - +
25B ALA* 1.3 57.0 + - - +
27B HIS* 3.1 8.4 - - - +
28B GLU* 2.5 44.5 + - - +
158B PRO* 4.2 22.9 - - + +
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Residues in contact with ALA 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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21B GLY 3.1 20.7 + - - +
22B ALA* 3.5 4.3 - - - +
24B LYS* 1.3 76.4 - - - +
26B LEU* 1.3 57.0 + - - +
28B GLU* 3.4 2.4 + - - -
29B LEU* 2.8 26.3 + - - +
134B ALA* 3.2 41.1 - - - +
137B LYS* 4.2 16.6 - - + -
138B LEU* 3.9 9.2 - - + -
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Residues in contact with LEU 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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22B ALA 2.9 12.4 + - - +
23B GLY 3.7 7.2 - - - +
25B ALA* 1.3 73.2 - - - +
27B HIS* 1.3 61.9 + - - +
29B LEU* 4.6 4.9 - - + -
30B LEU* 2.8 54.1 + - + +
59B PHE* 3.8 19.7 - - + -
61B VAL* 3.9 20.0 - - + -
93B VAL* 4.3 2.9 - - + -
95B VAL* 4.0 26.9 - - + -
122B ILE* 6.4 0.4 - - + -
138B LEU* 3.7 24.2 - - + +
155B ILE* 4.2 17.5 - - + -
157B LEU* 4.2 11.2 - - + -
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Residues in contact with HIS 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 GLY 3.0 12.4 + - - +
24B LYS* 3.1 14.6 - - - +
26B LEU* 1.3 75.8 - - - +
28B GLU* 1.3 69.4 + - - +
30B LEU* 3.7 9.9 - - - +
31B LEU* 3.0 44.2 + - + +
104B ILE* 4.3 30.2 - - + +
157B LEU* 4.5 1.4 - - + +
158B PRO* 3.9 20.9 - - + +
159B GLU 3.7 23.1 + - - -
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Residues in contact with GLU 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 LYS* 2.5 44.9 + - - +
25B ALA* 3.6 7.9 - - - +
27B HIS* 1.3 81.2 - - - +
29B LEU* 1.3 58.7 + - - +
31B LEU* 3.3 9.5 + - + +
32B SER* 2.9 28.6 + - - -
132B ASP* 4.9 1.5 - - - +
134B ALA* 3.6 15.3 - - + -
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Residues in contact with LEU 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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25B ALA 2.8 20.2 + - - +
26B LEU* 3.2 7.6 + - + +
28B GLU* 1.3 70.6 - - - +
30B LEU* 1.3 67.0 + - - +
32B SER* 2.6 22.3 + - - +
33B ALA* 3.2 6.9 + - - +
59B PHE* 4.2 21.8 - - + -
122B ILE* 4.6 15.5 - - + -
130B TRP* 3.4 37.0 - - + -
132B ASP* 4.3 3.6 - - - +
134B ALA* 4.3 4.3 - - + -
135B LEU* 3.8 32.3 - - + +
138B LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 30 (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 LEU* 2.8 48.6 + - + +
27B HIS* 3.7 3.1 - - - +
29B LEU* 1.3 75.4 - - - +
31B LEU* 1.3 53.5 + - - +
33B ALA* 2.3 31.8 + - - +
34B GLN* 4.0 2.3 - - - +
39B LEU* 3.5 16.8 - - + +
61B VAL* 5.0 7.6 - - + -
101B LEU* 4.1 21.3 - - + -
104B ILE* 4.0 29.4 - - + -
105B VAL* 5.3 4.7 - - + -
120B ILE* 3.8 37.7 - - + -
122B ILE* 5.0 6.7 - - + -
157B LEU* 4.6 4.0 - - + -
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Residues in contact with LEU 31 (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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27B HIS* 3.0 35.5 + - + +
28B GLU* 3.6 8.5 - - + +
30B LEU* 1.3 73.1 - - - +
32B SER* 1.3 57.7 + - - +
33B ALA 2.7 17.9 - - - +
34B GLN* 4.2 5.1 - - + +
35B ARG* 3.2 60.7 + - - +
104B ILE* 3.4 39.5 - - + +
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Residues in contact with SER 32 (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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28B GLU 2.9 16.6 + - - -
29B LEU* 2.6 22.4 + - - +
31B LEU* 1.3 70.8 - - - +
33B ALA* 1.3 58.1 + - - +
35B ARG* 2.7 40.3 + - - +
36B GLN* 4.2 1.1 - - - +
130B TRP* 3.3 24.9 - - - -
132B ASP* 3.5 15.3 + - - -
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Residues in contact with ALA 33 (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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29B LEU 3.2 6.3 + - - +
30B LEU* 2.3 26.0 - - - +
31B LEU 2.7 8.5 - - - +
32B SER* 1.3 76.6 + - - +
34B GLN* 1.3 62.7 + - - +
35B ARG 2.9 4.9 - - - -
36B GLN 4.3 0.2 - - - +
38B CYS* 3.6 35.0 - - + -
39B LEU* 3.5 20.0 - - + -
122B ILE* 4.6 9.0 - - + -
130B TRP* 4.3 8.2 - - + -
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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