Contacts of the helix formed by residues 16 - 36 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.1 10.3 + - - +
15A SER* 1.3 76.8 - - - +
17A ALA* 1.3 54.9 + - - +
18A ARG* 3.6 13.5 + - - +
19A MET* 3.1 21.5 + - - +
20A GLN* 2.7 35.1 + - - +
14B GLU* 5.9 7.0 - - - +
15B SER 6.2 0.7 - - - +
16B THR* 4.1 20.0 - - - +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 1.3 70.4 - - - +
18A ARG* 1.3 66.8 + - - +
20A GLN* 3.6 7.7 - - - +
21A GLY* 2.8 23.0 + - - -
137A LYS* 4.6 1.3 + - - -
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Residues in contact with ARG 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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16A THR* 3.6 10.7 + - - +
17A ALA* 1.3 79.3 - - - +
19A MET* 1.3 62.8 + - - +
22A ALA* 2.9 26.9 + - - +
137A LYS* 3.4 18.5 + - - +
141A PHE* 3.0 51.2 + - + -
144A GLU* 3.2 38.8 + - - +
145A SER* 3.0 21.2 + - - +
13B PRO* 3.9 20.0 - - - +
14B GLU* 4.0 25.8 + - - +
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Residues in contact with MET 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.4 50.5 - - + +
15A SER* 4.7 2.2 - - - -
16A THR* 3.1 14.1 + - - +
18A ARG* 1.3 82.1 - - + +
20A GLN* 1.3 66.7 + - - +
22A ALA* 3.4 4.0 + - - +
23A GLY* 3.1 19.9 + - - -
141A PHE* 4.1 17.5 - - + -
154A SER* 3.4 19.1 - - - +
155A ILE* 3.8 9.4 - - - +
156A THR* 3.5 40.1 - - + +
158A PRO* 5.6 0.5 - - - +
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Residues in contact with GLN 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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15A SER* 4.2 16.9 + - - +
16A THR 2.7 21.8 + - - +
17A ALA* 3.6 9.0 - - - +
19A MET* 1.3 73.9 - - - +
21A GLY* 1.3 61.6 + - - +
23A GLY* 3.4 1.2 + - - -
24A LYS* 3.2 56.5 + - - +
158A PRO* 3.0 41.2 - - + +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.8 19.2 + - - -
18A ARG 3.7 1.3 - - - -
20A GLN* 1.3 71.5 - - - +
22A ALA* 1.3 58.9 + - - +
24A LYS* 3.3 6.1 + - - +
25A ALA* 2.9 30.7 + - - +
137A LYS* 3.8 14.5 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 2.9 10.8 + - - +
19A MET 3.4 4.7 + - - +
21A GLY* 1.3 74.3 - - - +
23A GLY* 1.3 62.7 + - - +
25A ALA* 3.3 1.0 + - - -
26A LEU* 3.0 20.8 + - - +
137A LYS* 3.5 8.8 - - - +
138A LEU* 3.4 17.0 - - + +
141A PHE* 3.4 46.0 - - + -
155A ILE* 3.9 11.9 - - + -
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Residues in contact with GLY 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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19A MET 3.1 13.5 + - - -
20A GLN 3.4 2.7 + - - -
22A ALA* 1.3 76.7 - - - +
24A LYS* 1.3 57.6 + - - +
26A LEU* 3.4 3.8 + - - +
27A HIS* 3.0 28.1 + - - +
155A ILE* 3.5 19.0 - - - +
156A THR 4.2 8.3 - - - -
158A PRO* 4.2 13.8 - - - +
1160A MLA 4.1 5.9 - - - +
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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
----------------------------------------------------------
20A GLN* 3.2 39.4 + - - +
21A GLY* 3.8 6.3 - - - +
23A GLY* 1.3 74.1 - - - +
25A ALA* 1.3 64.1 + - - +
27A HIS* 3.4 15.8 + - - +
28A GLU* 3.0 22.9 + - - +
158A PRO* 3.7 21.1 - - + +
159A GLU 5.4 0.8 - - - +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 2.9 16.8 + - - +
22A ALA 3.6 5.2 - - - +
24A LYS* 1.3 74.8 - - - +
26A LEU* 1.3 53.3 + - - +
28A GLU* 3.1 5.0 + - - +
29A LEU* 2.8 30.3 + - - +
134A ALA* 3.3 26.3 - - + +
137A LYS* 3.8 24.5 - - + -
138A LEU* 3.9 13.0 - - + -
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Residues in contact with LEU 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 ALA 3.0 16.9 + - - +
23A GLY* 3.6 5.6 - - - +
24A LYS 3.3 0.2 - - - -
25A ALA* 1.3 73.6 - - - +
27A HIS* 1.3 59.9 + - - +
29A LEU* 3.1 3.7 + - + -
30A LEU* 2.8 55.5 + - + +
59A PHE* 4.5 4.7 - - + -
61A VAL* 3.9 25.4 - - + -
93A VAL* 4.9 0.2 - - + -
95A VAL* 4.0 24.0 - - + -
101A LEU* 5.5 0.4 - - + -
122A ILE* 5.0 1.8 - - + -
138A LEU* 3.7 19.9 - - + +
155A ILE* 4.6 15.9 - - + -
1160A MLA 3.3 22.4 - - + +
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Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.0 11.5 + - - +
24A LYS* 3.4 21.0 + - - +
26A LEU* 1.3 80.4 - - - +
28A GLU* 1.3 63.9 + - - +
30A LEU* 3.4 3.3 + - - +
31A LEU* 3.2 34.6 + - + +
100A ARG* 3.4 30.0 + - - -
104A ILE* 3.7 37.4 - - + +
158A PRO* 6.0 3.2 - - + +
1160A MLA 4.5 3.0 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS 3.0 14.5 + - - +
25A ALA* 3.1 9.9 + - - +
27A HIS* 1.3 78.0 - - - +
29A LEU* 1.3 58.6 + - - +
31A LEU* 3.2 11.3 + - + +
32A SER* 2.9 30.1 + - - -
130A TRP* 3.2 20.1 - - + -
132A ASP* 2.8 32.1 - - - +
133A PRO* 5.1 0.5 - - - +
134A ALA* 4.2 5.9 - - + +
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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
----------------------------------------------------------
25A ALA 2.8 19.1 + - - +
26A LEU* 3.1 5.4 + - + +
28A GLU* 1.3 73.7 - - - +
30A LEU* 1.3 58.6 + - - +
32A SER* 3.6 10.8 - - - +
33A ALA* 2.9 36.3 + - + +
59A PHE* 4.3 6.1 - - + -
122A ILE* 3.3 47.1 - - + -
132A ASP* 3.9 16.2 - - + +
134A ALA* 4.3 1.3 - - + -
135A LEU* 4.2 34.1 - - + +
138A LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 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 LEU* 2.8 42.6 + - + +
27A HIS 3.8 4.3 - - - +
29A LEU* 1.3 77.2 - - - +
31A LEU* 1.3 56.9 + - - +
33A ALA* 4.6 0.4 - - - -
34A GLN* 3.1 29.2 + - - +
39A LEU* 3.6 12.4 - - + +
61A VAL* 4.7 2.7 - - + -
101A LEU* 3.2 33.9 - - + -
104A ILE* 3.8 28.7 - - + -
105A VAL* 4.4 8.1 - - + +
120A ILE* 4.0 20.2 - - + -
122A ILE* 3.8 22.2 - - + -
1160A MLA 5.1 0.4 - - - +
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Residues in contact with LEU 31 (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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27A HIS* 3.2 35.5 + - + +
28A GLU* 3.6 10.5 - - + +
30A LEU* 1.3 75.6 - - - +
32A SER* 1.3 60.2 + - - +
34A GLN* 3.5 14.3 + - - +
35A ARG* 2.9 29.2 + - - +
104A ILE* 3.4 33.4 - - + +
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Residues in contact with SER 32 (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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28A GLU* 2.9 14.8 + - - -
29A LEU* 3.3 8.0 + - - +
31A LEU* 1.3 73.1 - - - +
33A ALA* 1.3 63.3 + - - +
35A ARG* 3.2 14.8 + - - +
36A GLN* 2.9 45.5 + - - +
130A TRP* 3.8 19.1 - - - -
132A ASP* 2.7 29.4 + - - +
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Residues in contact with ALA 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* 2.9 21.2 + - + +
30A LEU 4.0 1.8 - - - +
32A SER* 1.3 74.0 + - - +
34A GLN* 1.3 66.8 + - - +
36A GLN* 3.4 1.5 + - - -
37A GLY 3.1 4.3 + - - -
38A CYS* 2.9 40.6 + - - +
39A LEU* 3.9 11.4 - - + -
122A ILE* 3.9 35.4 - - + -
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Residues in contact with GLN 34 (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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30A LEU 3.1 17.1 + - - +
31A LEU* 3.5 17.2 + - - +
33A ALA* 1.3 76.6 - - - +
35A ARG* 1.3 63.1 + - - +
37A GLY* 3.0 14.9 + - - -
39A LEU* 3.9 19.4 - - + +
104A ILE 3.7 17.2 + - - -
105A VAL* 3.0 4.0 - - + +
106A GLY* 2.5 39.1 + - - +
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Residues in contact with ARG 35 (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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31A LEU 2.9 17.6 + - - +
32A SER* 3.2 16.7 + - - +
34A GLN* 1.3 78.4 - - - +
36A GLN* 1.3 77.6 + - + +
37A GLY 3.2 1.1 + - - -
130A TRP* 3.9 30.5 - - - +
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 2.9 34.9 + - - +
33A ALA* 5.0 0.9 - - - -
35A ARG* 1.3 93.7 + - - +
37A GLY* 1.3 63.2 + - - +
38A CYS* 3.3 16.9 + - - +
125A PRO* 3.9 13.9 - - + +
129A ALA* 3.2 32.7 - - - +
130A TRP* 3.4 31.8 + - - +
132A ASP* 5.6 1.4 - - - +
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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