Contacts of the helix formed by residues 20 - 36 (chain B) in PDB entry 5M4G
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B PRO* 3.0 32.6 + - + +
8B SER* 3.7 3.8 - - - +
9B PHE* 3.6 26.9 - - + +
18B VAL 4.0 1.1 - - - +
19B PRO* 1.3 71.0 - - - +
21B ALA* 1.3 61.6 + - - +
22B LEU 3.0 1.3 - - - -
23B PHE* 3.0 32.6 + - + +
24B ALA* 3.3 9.5 + - - +
27B ARG* 5.3 0.5 + - - -
75B PHE 4.4 3.6 - - - +
120B LYS* 3.4 22.7 - - + +
121B TYR* 3.8 40.4 - - + +
122B ALA* 4.5 5.3 - - + +
282B TYR* 3.7 20.4 - - - +
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Residues in contact with ALA 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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7B PRO* 4.7 1.2 + - - +
19B PRO* 4.0 13.0 - - + +
20B LEU* 1.3 75.7 - - - +
22B LEU* 1.3 64.1 + - - +
24B ALA* 3.7 11.2 - - + +
25B LEU* 2.9 24.9 + - - +
122B ALA* 5.8 0.8 - - - +
190B MET* 3.5 13.1 - - + +
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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
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18B VAL* 3.8 22.4 - - + -
19B PRO* 2.9 17.6 + - + +
21B ALA* 1.3 79.3 - - - +
23B PHE* 1.3 82.8 + - + +
25B LEU* 3.3 4.5 + - - +
26B ASN* 3.1 39.0 + - - +
188B THR* 4.9 1.6 + - - +
190B MET* 3.7 53.3 - - + +
191B GLU* 3.9 17.7 - - + +
194B VAL* 3.9 8.3 - - + -
284B PHE* 4.2 8.1 - - + -
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Residues in contact with PHE 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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18B VAL* 4.6 2.5 - - + -
19B PRO 4.3 8.1 - - - -
20B LEU* 3.0 30.7 + - + +
22B LEU* 1.3 93.8 - - + +
24B ALA* 1.3 67.3 + - - +
26B ASN* 3.1 3.3 + - - +
27B ARG* 3.0 35.0 + - - +
72B HIS* 3.1 44.9 - + - -
73B TRP* 3.4 12.8 - - - -
74B ALA 3.5 12.9 - - - +
75B PHE 4.0 4.3 - - - +
76B GLY* 3.5 12.8 - - - -
121B TYR 6.1 0.2 - - - +
282B TYR* 3.6 40.8 - + - -
284B PHE* 4.4 6.1 - + - -
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Residues in contact with ALA 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 LEU 3.3 5.1 + - - +
21B ALA* 3.7 17.3 - - + +
23B PHE* 1.3 78.9 - - - +
25B LEU* 1.3 56.8 + - - +
27B ARG* 3.3 29.7 + - - +
28B GLN* 2.9 28.3 + - - +
122B ALA* 5.2 5.2 - - + +
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Residues in contact with LEU 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 ALA 2.9 16.7 + - - +
22B LEU 3.5 5.4 - - - +
23B PHE 3.2 0.2 - - - -
24B ALA* 1.3 75.4 - - - +
26B ASN* 1.3 59.6 + - - +
28B GLN* 3.2 24.4 + - - +
29B ARG* 2.8 52.0 + - + +
188B THR* 3.7 27.6 - - + +
189B ASP 5.6 0.2 - - - +
190B MET* 3.5 23.8 - - + +
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Residues in contact with ASN 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 LEU* 3.1 26.1 + - - +
23B PHE 3.1 5.1 + - - +
25B LEU* 1.3 76.2 - - - +
27B ARG* 1.3 55.9 + - - +
29B ARG* 3.0 23.0 + - - +
30B LEU* 2.9 25.3 + - - +
73B TRP* 2.9 78.6 + - + +
74B ALA* 4.8 0.4 - - - -
188B THR* 3.8 11.3 + - - +
191B GLU* 3.5 9.9 + - - +
284B PHE* 5.9 0.2 - - - -
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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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20B LEU 5.3 0.4 + - - -
23B PHE* 3.0 23.5 + - - +
24B ALA* 3.6 28.7 - - - +
25B LEU 3.2 0.2 - - - -
26B ASN* 1.3 74.9 - - - +
28B GLN* 1.3 63.6 + - - +
30B LEU* 3.3 6.6 + - - +
31B CYS* 3.0 29.0 + - - -
73B TRP* 5.2 1.1 - - - -
74B ALA* 2.9 38.6 + - - +
75B PHE* 3.9 29.0 + - - +
86B ILE* 3.8 27.9 - - + +
91B GLY* 5.4 4.4 + - - +
93B SER* 3.6 26.4 + - - -
121B TYR 4.4 5.3 + - - -
122B ALA 3.5 23.4 + - - -
123B VAL* 4.0 10.0 - - - +
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Residues in contact with GLN 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 ALA 2.9 13.6 + - - +
25B LEU* 3.2 27.0 + - - +
27B ARG* 1.3 75.3 - - - +
29B ARG* 1.3 57.5 + - + +
31B CYS* 3.2 7.9 + - - +
32B GLU* 2.8 60.6 + - + +
35B ARG* 5.1 3.5 + - - +
91B GLY* 6.3 1.8 - - - -
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Residues in contact with ARG 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 LEU* 2.8 35.6 + - + +
26B ASN* 3.0 25.6 + - - +
28B GLN* 1.3 76.3 - - + +
30B LEU* 1.3 62.5 + - - +
32B GLU* 3.3 16.9 + - - +
33B ARG* 3.0 23.7 + - - +
73B TRP* 3.6 16.8 - - - -
183B CYS* 3.1 29.0 + - - +
186B PHE* 2.8 33.9 + - - +
187B LYS 5.3 0.2 - - - -
188B THR* 3.5 26.9 - - - +
191B GLU* 4.2 2.8 + - - -
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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 ASN 2.9 16.7 + - - +
27B ARG* 3.6 4.9 - - - +
28B GLN 3.3 0.2 - - - -
29B ARG* 1.3 74.5 - - - +
31B CYS* 1.3 67.1 + - - +
33B ARG* 3.2 3.1 + - + +
34B LEU* 2.9 44.9 + - + +
46B VAL* 4.5 10.1 - - + -
48B LEU* 5.9 0.2 - - + -
73B TRP* 4.1 9.6 - - + -
74B ALA* 5.8 0.7 - - + -
86B ILE* 4.3 22.0 - - + -
176B LEU* 4.1 18.2 - - + -
179B GLU* 4.3 3.1 - - + -
180B ILE* 3.9 49.1 - - + +
183B CYS* 3.9 11.8 - - - -
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Residues in contact with CYS 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 ARG 3.0 17.8 + - - +
28B GLN* 3.2 9.8 + - - +
30B LEU* 1.3 77.1 - - - +
32B GLU* 1.3 57.7 + - - +
34B LEU* 3.2 8.1 + - - +
35B ARG* 2.8 55.4 + - - +
46B VAL* 6.1 0.9 - - - -
86B ILE* 3.5 29.4 - - - -
87B ASP 3.8 5.8 - - - -
88B VAL* 3.7 21.9 - - - +
91B GLY* 3.9 9.2 - - - -
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Residues in contact with GLU 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 GLN* 2.8 50.9 + - + +
29B ARG* 3.7 18.5 - - - +
31B CYS* 1.3 76.5 - - - +
33B ARG* 1.3 61.2 + - - +
35B ARG* 3.4 23.2 + - - +
36B LYS* 3.3 40.2 + - - +
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Residues in contact with ARG 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 ARG 3.0 16.4 + - - +
30B LEU 3.6 4.7 - - - +
32B GLU* 1.3 75.1 - - - +
34B LEU* 1.3 64.8 + - + +
36B LYS* 3.2 22.2 + - + +
37B ASN* 3.3 11.4 + - - +
179B GLU* 3.2 57.5 + - + +
182B GLU* 3.6 30.7 + - - +
183B CYS* 3.8 16.2 - - - +
186B PHE* 5.2 6.9 - - - -
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Residues in contact with LEU 34 (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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30B LEU* 2.9 36.9 + - + +
31B CYS* 3.8 4.7 - - - +
33B ARG* 1.3 76.4 - - - +
35B ARG* 1.3 62.9 + - - +
37B ASN* 3.1 18.5 + - - +
40B VAL* 3.5 23.4 - - + +
46B VAL* 3.7 29.8 - - + -
88B VAL* 3.9 22.4 - - + -
145B LEU* 4.3 6.3 - - + -
175B ILE* 4.0 26.7 - - + -
176B LEU* 4.3 6.5 - - + -
179B GLU* 4.0 22.7 - - + +
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Residues in contact with ARG 35 (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 GLN* 5.8 2.6 - - - +
31B CYS* 2.8 29.8 + - - +
32B GLU* 3.7 28.7 + - - +
34B LEU* 1.3 76.6 - - - +
36B LYS* 1.3 60.5 + - + +
37B ASN 3.2 4.1 + - - +
40B VAL* 5.6 0.9 - - - -
88B VAL* 2.8 36.4 + - + +
89B ASP* 3.5 21.9 + - - +
90B THR 3.7 3.4 + - - -
91B GLY* 3.4 20.8 - - - +
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Residues in contact with LYS 36 (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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32B GLU* 3.3 28.1 + - - +
33B ARG* 3.2 12.6 + - - +
34B LEU 3.2 0.8 - - - -
35B ARG* 1.3 76.5 - - + +
37B ASN* 1.3 60.8 + - - +
38B PRO* 3.4 10.4 - - - +
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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
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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