Contacts of the helix formed by residues 16 - 29 (chain A) in PDB entry 4X4W
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
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Residue Dist Surf HB Arom Phob DC
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13A SER 4.3 10.5 - - - +
14A LEU* 2.9 15.9 + - - +
15A PHE* 1.3 76.4 - - - +
17A GLU* 1.3 65.7 + - - +
18A GLY 3.6 0.8 + - - -
19A LEU* 3.2 13.2 + - - +
20A LYS* 3.0 23.3 + - - +
92A GLU* 2.7 35.2 + - - +
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Residues in contact with GLU 17 (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* 1.3 74.0 - - - +
18A GLY* 1.3 57.5 + - - +
20A LYS* 3.5 10.2 + - + +
21A SER* 2.9 32.2 + - - -
90A HIS* 3.6 34.8 + - + +
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Residues in contact with GLY 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* 3.1 4.3 + - - -
17A GLU* 1.3 77.1 - - - +
19A LEU* 1.3 60.1 + - - +
21A SER* 3.3 3.1 + - - -
22A LEU* 2.8 29.3 + - - +
89A LEU* 3.7 27.6 - - - +
90A HIS* 3.8 13.8 + - - +
92A GLU* 4.4 2.2 + - - -
94A PHE* 3.5 12.2 - - - -
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Residues in contact with LEU 19 (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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14A LEU* 3.3 44.9 - - + +
15A PHE* 4.2 17.9 - - + -
16A THR* 3.2 13.4 + - - +
18A GLY* 1.3 76.3 - - - +
20A LYS* 1.3 58.3 + - - +
22A LEU* 3.1 11.2 + - + +
23A THR* 2.9 51.5 + - + +
35A ILE* 5.9 0.2 - - + -
52A ILE* 6.1 0.9 - - + -
54A PHE* 3.8 34.5 - - + -
94A PHE* 3.5 15.1 - - + -
136A PHE* 4.0 15.0 - - + -
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Residues in contact with LYS 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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12A GLN* 5.6 3.5 - - - +
15A PHE* 3.7 37.8 + - + +
16A THR 3.0 22.2 + - - +
17A GLU* 3.8 9.4 - - + +
19A LEU* 1.3 76.9 - - - +
21A SER* 1.3 61.3 + - - +
23A THR* 3.3 7.6 + - - -
24A GLU* 3.1 42.7 + - - +
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Residues in contact with SER 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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17A GLU 2.9 18.8 + - - -
18A GLY 3.7 4.3 - - - -
20A LYS* 1.3 75.9 - - - +
22A LEU* 1.3 63.8 + - - +
24A GLU* 3.4 12.7 + - - +
25A LEU* 3.1 23.0 + - - +
89A LEU* 3.7 16.4 - - - +
90A HIS* 3.3 22.6 + - - -
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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 GLY 2.8 19.7 + - - +
19A LEU* 3.1 13.0 + - + +
21A SER* 1.3 74.3 - - - +
23A THR* 1.3 64.0 + - - +
25A LEU* 3.2 4.5 + - + +
26A PHE* 3.2 49.7 + - + -
33A LEU* 4.1 19.1 - - + -
54A PHE* 5.1 3.8 - - + -
67A PHE* 3.9 14.1 - - + -
87A ALA* 4.8 0.4 - - + -
89A LEU* 3.8 27.5 - - + +
94A PHE* 3.8 34.8 - - + -
96A ILE* 4.0 16.8 - - + -
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Residues in contact with THR 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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15A PHE* 5.4 4.3 - - + -
19A LEU* 2.9 29.4 + - + +
20A LYS* 3.3 12.6 + - - +
22A LEU* 1.3 75.5 - - - +
24A GLU* 1.3 65.8 + - - +
26A PHE* 3.4 2.9 + - - +
27A VAL* 3.1 28.9 + - - +
33A LEU* 4.4 8.1 - - + -
136A PHE* 3.5 50.6 - - + +
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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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20A LYS* 3.1 35.0 + - - +
21A SER* 3.8 11.8 + - - +
23A THR* 1.3 80.3 - - - +
25A LEU* 1.3 56.3 + - - +
27A VAL* 3.4 8.0 + - - +
28A LYS* 2.9 30.0 + - - +
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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 SER 3.1 13.4 + - - +
22A LEU* 3.2 9.8 + - + +
24A GLU* 1.3 77.0 - - - +
26A PHE* 1.3 58.5 + - + +
28A LYS* 3.3 16.8 + - + +
29A GLU* 3.0 50.1 + - + +
66A MET* 4.0 19.5 - - + -
67A PHE* 3.9 22.2 - - + -
70A ALA* 4.1 18.6 - - + -
72A ILE* 3.5 31.0 - - + -
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Residues in contact with PHE 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* 3.2 46.2 + - + +
23A THR 4.0 3.4 - - - +
25A LEU* 1.3 78.8 - - + +
27A VAL* 1.3 65.7 + - + +
29A GLU* 3.3 4.2 + - - +
30A ASN 3.0 17.5 + - - -
31A HIS* 3.1 40.1 + + + +
33A LEU* 3.9 27.6 - - + -
56A THR* 3.5 28.5 - - + -
58A ALA* 4.4 9.6 - - + -
63A MET* 4.0 22.0 - - + -
66A MET* 4.5 12.1 - - + -
67A PHE* 3.8 16.8 - + - -
96A ILE* 4.2 9.0 - - + -
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Residues in contact with VAL 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 THR* 3.1 18.6 + - - +
24A GLU* 3.6 10.3 - - - +
26A PHE* 1.3 75.9 - - - +
28A LYS* 1.3 65.9 + - - +
30A ASN* 3.0 23.6 + - - +
31A HIS 4.4 2.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 18.8 + - - +
25A LEU* 3.3 18.3 + - + +
27A VAL* 1.3 82.0 - - - +
29A GLU* 1.3 77.2 + - - +
30A ASN* 3.2 11.1 + - - +
70A ALA* 6.3 0.2 - - - +
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Residues in contact with GLU 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* 3.0 25.8 + - + +
26A PHE 3.3 1.1 + - - +
27A VAL 3.2 0.2 - - - -
28A LYS* 1.3 100.7 + - - +
30A ASN* 1.3 73.0 + - - +
31A HIS* 3.3 32.3 + - + +
66A MET* 3.7 28.7 - - + +
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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