Contacts of the helix formed by residues 20 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.1 29.9 + - + +
8A SER* 3.7 3.6 - - - -
9A PHE* 3.6 30.3 - - + +
18A VAL 3.9 1.3 - - - +
19A PRO* 1.3 71.4 - - - +
21A ALA* 1.3 61.8 + - - +
22A LEU 3.0 0.4 - - - -
23A PHE* 3.1 31.6 + - + +
24A ALA* 3.3 8.9 + - - +
27A ARG* 5.3 0.9 + - - -
75A PHE 4.4 2.9 - - - +
120A LYS* 3.3 21.8 - - + +
121A TYR* 3.7 40.5 - - + +
122A ALA* 4.5 5.3 - - + +
282A TYR* 3.7 20.4 - - - +
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Residues in contact with ALA 21 (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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6A GLY* 6.6 0.4 - - - -
7A PRO* 4.8 0.8 + - - +
19A PRO* 4.0 8.9 - - + +
20A LEU* 1.3 76.7 - - - +
22A LEU* 1.3 63.7 + - - +
24A ALA* 3.6 10.9 - - + +
25A LEU* 2.9 24.6 + - - +
122A ALA* 5.7 1.9 - - - +
190A MET* 3.6 16.2 - - + +
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Residues in contact with LEU 22 (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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18A VAL* 3.8 23.1 - - + -
19A PRO* 3.0 16.3 + - + +
21A ALA* 1.3 77.5 - - - +
23A PHE* 1.3 81.2 + - + +
25A LEU* 3.4 4.0 + - - +
26A ASN* 3.1 43.2 + - - +
188A THR* 4.8 1.4 + - - +
190A MET* 3.6 52.6 - - + +
191A GLU* 3.9 17.7 - - + +
194A VAL* 4.0 7.9 - - + -
284A PHE* 4.1 9.9 - - + -
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Residues in contact with PHE 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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18A VAL* 4.6 1.6 - - + -
19A PRO 4.3 9.4 - - - -
20A LEU* 3.1 30.4 + - + +
22A LEU* 1.3 93.5 - - + +
24A ALA* 1.3 67.7 + - - +
26A ASN* 3.2 3.3 + - - +
27A ARG* 2.9 36.6 + - - +
72A HIS* 3.1 45.8 - + - -
73A TRP* 3.4 14.4 - - - -
74A ALA 3.6 12.2 - - - +
75A PHE 3.9 4.0 - - - +
76A GLY* 3.5 13.0 - - - -
121A TYR 6.1 0.4 - - - +
282A TYR* 3.6 40.2 - + - -
284A PHE* 4.4 4.9 - + - -
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Residues in contact with ALA 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 3.3 4.3 + - - +
21A ALA* 3.3 17.9 + - + +
23A PHE* 1.3 80.0 - - - +
25A LEU* 1.3 61.6 + - - +
27A ARG* 3.3 29.1 + - - +
28A GLN* 3.0 23.5 + - - +
122A ALA* 5.2 5.6 - - + +
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Residues in contact with LEU 25 (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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21A ALA 2.9 16.9 + - - +
22A LEU 3.6 4.9 - - - +
24A ALA* 1.3 73.0 - - - +
26A ASN* 1.3 60.6 + - - +
28A GLN* 3.2 27.1 + - - +
29A ARG* 2.9 50.7 + - + +
188A THR* 3.7 28.0 - - + +
190A MET* 3.6 23.1 - - + +
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Residues in contact with ASN 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 LEU* 3.1 26.6 + - - +
23A PHE 3.2 8.3 + - - +
25A LEU* 1.3 76.4 - - - +
27A ARG* 1.3 62.2 + - - +
29A ARG* 3.0 22.9 + - - +
30A LEU* 2.9 19.9 + - - +
73A TRP* 3.0 74.2 + - + +
74A ALA* 4.8 0.2 - - - -
188A THR* 3.8 10.7 - - - +
191A GLU* 3.5 9.8 + - - +
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Residues in contact with ARG 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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20A LEU 5.3 0.8 + - - -
23A PHE* 2.9 25.4 + - - +
24A ALA* 3.5 28.3 - - - +
25A LEU 3.3 0.2 - - - -
26A ASN* 1.3 74.6 - - - +
28A GLN* 1.3 62.9 + - - +
30A LEU* 3.3 6.9 + - - +
31A CYS* 3.0 29.2 + - - -
73A TRP* 5.3 1.1 - - - -
74A ALA* 2.9 38.3 + - - +
75A PHE* 3.9 28.4 + - - +
86A ILE* 3.9 29.1 - - + +
91A GLY 5.3 5.5 + - - +
93A SER* 3.5 26.8 + - - -
121A TYR 4.4 4.2 + - - -
122A ALA 3.5 23.0 + - - -
123A VAL* 4.0 8.8 - - - +
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Residues in contact with GLN 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 ALA 3.0 13.1 + - - +
25A LEU* 3.5 29.7 - - - +
27A ARG* 1.3 77.8 - - - +
29A ARG* 1.3 57.3 + - - +
31A CYS* 3.3 6.9 + - - +
32A GLU* 2.9 59.4 + - + +
35A ARG* 5.2 1.7 + - - +
91A GLY* 6.2 1.8 - - - -
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Residues in contact with ARG 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 LEU* 2.9 36.1 + - + +
26A ASN* 3.0 25.2 + - - +
28A GLN* 1.3 75.3 - - + +
30A LEU* 1.3 62.2 + - - +
32A GLU* 3.4 16.3 + - - +
33A ARG* 3.1 23.0 + - - +
73A TRP* 3.5 16.8 - - - -
183A CYS* 2.9 40.0 + - - +
186A PHE* 3.0 25.3 + - - +
188A THR* 3.5 26.6 - - - +
191A GLU* 4.3 2.6 + - - -
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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 ASN 2.9 16.9 + - - +
27A ARG* 3.6 5.2 - - - +
29A ARG* 1.3 73.9 - - - +
31A CYS* 1.3 66.0 + - - +
33A ARG* 3.3 2.1 + - + +
34A LEU* 2.9 46.3 + - + +
46A VAL* 4.5 9.9 - - + -
48A LEU* 5.8 0.4 - - + -
73A TRP* 4.2 9.6 - - + -
74A ALA* 5.8 1.6 - - + -
86A ILE* 4.3 21.5 - - + -
176A LEU* 4.1 14.4 - - + -
179A GLU* 4.2 6.3 - - + +
180A ILE* 3.8 54.1 - - + +
183A CYS* 3.8 8.2 - - - -
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Residues in contact with CYS 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 ARG 3.0 18.7 + - - +
28A GLN* 3.7 9.0 - - - +
30A LEU* 1.3 77.8 - - - +
32A GLU* 1.3 58.7 + - - +
34A LEU* 3.2 8.6 + - - +
35A ARG* 2.9 54.9 + - - +
46A VAL* 6.0 0.4 - - - -
86A ILE* 3.5 29.8 - - - -
87A ASP 3.9 2.2 - - - -
88A VAL* 3.8 21.5 - - - +
91A GLY* 3.9 12.8 - - - -
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Residues in contact with GLU 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 GLN* 2.9 50.2 + - + +
29A ARG* 3.6 16.5 - - - +
31A CYS* 1.3 77.7 - - - +
33A ARG* 1.3 61.2 + - - +
35A ARG* 3.5 22.6 + - - +
36A LYS* 3.5 25.0 + - - +
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ARG 3.1 14.0 + - - +
30A LEU 3.7 5.8 - - - +
32A GLU* 1.3 73.1 - - - +
34A LEU* 1.3 66.2 + - - +
36A LYS* 3.1 17.3 + - + +
37A ASN 3.4 7.4 + - - -
179A GLU* 3.0 58.2 + - + +
182A GLU* 3.6 30.2 + - - +
183A CYS* 4.0 13.6 - - - +
186A PHE* 5.2 8.9 - - - -
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Residues in contact with LEU 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* 2.9 36.7 + - + +
31A CYS* 3.7 5.2 - - - +
33A ARG* 1.3 75.7 - - - +
35A ARG* 1.3 63.6 + - - +
37A ASN* 3.0 19.4 + - - +
40A VAL* 3.3 21.8 - - + +
46A VAL* 3.6 31.0 - - + -
88A VAL* 4.0 21.3 - - + -
145A LEU* 4.3 6.3 - - + -
175A ILE* 4.0 20.9 - - + -
176A LEU* 4.3 8.1 - - + -
179A GLU* 3.9 28.3 - - + -
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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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28A GLN* 5.2 1.8 + - - +
31A CYS* 2.9 32.0 + - - +
32A GLU* 3.8 27.4 - - - +
33A ARG 3.3 0.2 - - - -
34A LEU* 1.3 76.3 - - - +
36A LYS* 1.3 62.7 + - + +
37A ASN 3.5 3.6 + - - +
40A VAL* 5.2 2.9 - - - +
88A VAL* 2.8 37.5 + - + +
89A ASP* 3.5 23.6 + - - +
90A THR 3.8 2.8 - - - -
91A GLY* 3.6 16.8 - - - +
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU 3.5 13.9 + - - +
33A ARG* 3.1 12.0 + - + +
34A LEU 3.1 0.6 - - - -
35A ARG* 1.3 77.4 - - + +
37A ASN* 1.3 61.9 + - - +
38A PRO* 3.4 11.1 - - - +
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Residues in contact with ASN 37 (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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33A ARG 3.4 3.8 + - - +
34A LEU* 3.0 14.0 + - - +
35A ARG 4.4 3.5 - - - +
36A LYS* 1.3 76.2 - - - +
38A PRO* 1.3 72.1 - - - +
39A ALA* 2.9 26.2 + - - +
40A VAL* 3.0 28.6 + - + +
175A ILE* 4.0 17.6 + - - +
179A GLU* 2.8 33.3 + - - +
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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
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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