Contacts of the helix formed by residues 21 - 34 (chain A) in PDB entry 1GM5
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 1.3 85.7 - - - +
22A LEU* 1.3 68.7 + - - +
23A GLU* 2.8 5.8 + - + +
24A GLU* 2.8 20.4 + - + +
25A PHE* 2.8 19.1 + - - +
49A LEU* 4.9 4.7 - - - +
50A ASP* 3.6 23.6 - - - +
51A ASP* 3.7 16.4 - - + +
154A ARG* 3.5 59.2 - - + +
155A LYS* 3.6 33.9 - - + +
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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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21A LEU* 1.3 70.6 - - - +
23A GLU* 1.3 53.6 + - - +
25A PHE* 2.7 19.4 + - + +
26A LEU* 2.5 68.7 + - + +
49A LEU* 4.4 12.3 - - + +
51A ASP* 3.7 17.0 + - - +
53A LEU* 4.8 11.9 - - + -
54A LEU* 4.8 11.9 - - + -
59A LEU* 4.0 34.3 - - + -
63A LEU* 5.1 10.5 - - + -
95A LEU* 6.3 0.4 - - + -
99A PHE* 4.9 4.5 - - + -
100A LEU* 4.2 22.0 - - + -
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Residues in contact with GLU 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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21A LEU* 2.8 8.7 + - + +
22A LEU* 1.3 73.0 - - - +
24A GLU* 1.3 88.6 + - + +
25A PHE 3.0 0.2 + - - -
26A LEU* 4.4 2.7 - - - -
27A ASN* 2.5 32.5 + - - +
53A LEU* 5.9 0.2 - - - +
100A LEU* 4.0 28.8 - - + +
154A ARG* 2.6 34.5 + - - +
313A THR* 3.7 7.5 - - - +
314A PHE* 3.1 35.7 + - - +
315A TYR* 3.3 12.1 + - + +
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Residues in contact with GLU 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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17A ALA* 3.6 15.4 - - - +
18A LEU* 2.9 23.5 - - - +
19A PRO 2.5 21.7 - - - +
20A THR 3.4 1.4 + - - +
21A LEU* 2.8 25.2 + - + +
23A GLU* 1.3 80.8 - - + +
25A PHE* 1.3 57.8 + - - +
27A ASN* 2.3 43.9 - - - +
28A GLU* 3.0 10.7 + - + +
154A ARG* 5.4 2.0 + - - +
155A LYS* 2.0 37.5 + - - +
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Residues in contact with PHE 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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20A THR 5.5 2.8 - - - +
21A LEU 2.8 11.2 + - - +
22A LEU* 2.7 30.9 + - + +
24A GLU* 1.3 68.6 - - - +
26A LEU* 1.3 84.6 + - + +
27A ASN 2.8 1.0 + - - -
28A GLU* 3.0 5.7 + - - +
29A VAL* 2.9 29.9 + - + +
42A ILE* 4.5 8.3 - - + -
45A LEU* 2.9 49.4 - - + -
46A LEU* 3.4 32.3 - - + -
49A LEU* 3.7 21.5 - - + -
63A LEU* 4.7 9.4 - - + -
67A LEU* 3.6 24.5 - - + -
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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 LEU* 2.5 41.3 + - + +
23A GLU* 3.7 5.4 - - - +
25A PHE* 1.3 86.5 - - + +
27A ASN* 1.3 70.0 + - - +
29A VAL* 2.8 14.4 + - + +
30A GLU* 3.1 8.7 + - - +
63A LEU* 5.1 3.6 - - + -
66A PHE* 5.0 7.9 - - + -
67A LEU* 6.1 1.3 - - + -
92A ILE* 4.2 28.0 - - + +
95A LEU* 3.7 46.0 - - + -
96A ARG* 4.2 17.7 - - - +
100A LEU* 4.8 7.0 - - + -
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Residues in contact with ASN 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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23A GLU* 2.5 22.0 + - - +
24A GLU* 2.3 39.7 - - - +
25A PHE 2.8 0.2 + - - -
26A LEU* 1.3 83.0 - - - +
28A GLU* 1.3 53.9 + - + +
30A GLU* 2.6 29.3 + - - +
31A LYS* 3.1 27.0 + - + +
96A ARG* 4.0 15.2 + - - +
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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
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18A LEU* 4.5 24.2 - - - +
24A GLU* 3.0 15.4 + - - +
25A PHE* 3.5 5.2 - - - +
27A ASN* 1.3 81.7 - - + +
29A VAL* 1.3 51.9 + - - +
31A LYS* 2.8 20.0 + - + +
32A MET* 2.3 39.3 + - + +
41A ARG* 2.7 46.7 + - - +
45A LEU* 4.1 21.3 - - + +
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Residues in contact with VAL 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 PHE* 2.9 40.1 + - + +
26A LEU* 2.8 18.1 + - + +
28A GLU* 1.3 76.1 - - - +
30A GLU* 1.3 57.9 + - - +
32A MET* 2.3 49.4 + - + +
33A LEU* 2.8 7.5 + - + +
42A ILE* 5.1 14.1 - - + -
45A LEU* 4.9 5.6 - - + -
66A PHE* 4.5 21.3 - - + -
67A LEU* 5.8 4.9 - - + -
70A VAL* 5.0 11.7 - - + -
92A ILE* 4.6 6.3 - - + -
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Residues in contact with GLU 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 3.1 4.1 + - - +
27A ASN* 2.6 17.7 + - - +
29A VAL* 1.3 72.2 - - - +
31A LYS* 1.3 67.0 + - + +
33A LEU* 3.0 2.2 + - - +
34A LYS* 2.9 57.0 + - - +
89A LEU* 3.9 20.2 - - + +
92A ILE* 3.6 23.8 - - + +
93A GLU* 3.8 4.8 - - - +
96A ARG* 2.4 40.9 + - - -
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Residues in contact with LYS 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 ASN* 3.1 30.4 + - + +
28A GLU* 2.8 26.5 + - + +
30A GLU* 1.3 80.9 - - - +
32A MET* 1.3 70.4 + - - +
34A LYS* 4.5 13.2 - - - +
35A ASN* 2.8 27.7 + - - +
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Residues in contact with MET 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 2.3 23.8 + - - +
29A VAL* 2.3 43.3 + - + +
31A LYS* 1.3 69.4 - - - +
33A LEU* 1.3 52.6 + - + +
35A ASN* 3.7 0.2 - - - +
36A GLN* 2.7 35.3 + - - +
37A VAL* 2.6 42.2 - - + +
41A ARG* 3.4 49.6 - - + +
42A ILE* 4.2 22.7 - - + +
45A LEU* 4.8 8.7 - - + -
70A VAL* 5.7 1.8 - - + -
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Residues in contact with LEU 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 VAL* 2.8 13.1 + - + +
30A GLU* 3.6 6.5 - - - +
32A MET* 1.3 69.1 - - + +
34A LYS* 1.3 116.1 - - + +
35A ASN 1.9 41.6 + - - +
37A VAL* 4.8 9.6 - - + +
70A VAL* 6.3 3.8 - - + -
84A ARG* 5.4 1.8 - - - +
85A ILE* 2.4 59.5 - - + +
88A SER* 5.2 5.6 - - - +
89A LEU* 2.9 37.9 - - + +
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Residues in contact with LYS 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 GLU* 2.9 51.5 + - + +
31A LYS* 4.0 11.9 - - - +
33A LEU* 1.3 113.1 - - + +
35A ASN* 1.3 75.4 + - - +
89A LEU* 4.5 11.0 - - + -
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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