Contacts of the helix formed by residues 16 - 27 (chain A) in PDB entry 1W3U
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 PRO 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 1.3 91.8 - - + +
17A LEU* 1.3 64.3 + - - +
18A GLU 4.4 1.1 - - - +
19A VAL* 3.0 30.4 + - + +
20A LEU* 3.1 11.7 + - - +
251A VAL* 4.3 11.9 - - + -
254A TRP* 3.3 61.7 - - + +
341A ALA* 3.5 17.9 - - + +
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Residues in contact with LEU 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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4A ARG* 4.0 47.8 - - + +
15A LEU 3.3 3.2 + - - -
16A PRO* 1.3 71.4 - - - +
18A GLU* 1.3 58.3 + - - +
20A LEU* 3.1 11.6 + - + +
21A GLU* 2.8 59.6 + - + +
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Residues in contact with GLU 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 PRO* 3.2 0.8 - - - +
17A LEU* 1.3 80.2 - - - +
19A VAL* 1.3 57.2 + - - +
21A GLU* 3.3 11.7 + - - +
22A ARG* 2.9 73.0 + - + +
254A TRP* 3.3 19.5 - - + +
257A GLU* 2.6 25.6 - - - +
258A ARG* 3.9 4.3 + - - -
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Residues in contact with VAL 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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15A LEU* 4.3 5.2 - - + -
16A PRO* 3.0 24.7 + - + +
18A GLU* 1.3 74.2 - - + +
20A LEU* 1.3 66.1 + - - +
22A ARG* 3.3 11.2 + - - +
23A ALA* 3.0 23.6 + - - +
247A MET* 3.8 23.8 - - + -
250A GLU* 3.7 30.4 - - + +
251A VAL* 4.1 14.4 - - + -
254A TRP* 3.7 30.5 - - + -
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Residues in contact with LEU 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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4A ARG* 3.6 37.5 - - - +
15A LEU* 4.1 31.6 - - + +
16A PRO 3.1 13.6 + - - +
17A LEU* 3.1 15.5 + - + +
19A VAL* 1.3 76.4 - - - +
21A GLU* 1.3 60.1 + - + +
23A ALA* 4.0 4.1 - - - +
24A GLN* 2.8 30.9 + - - +
247A MET* 4.7 6.3 - - + -
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Residues in contact with GLU 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 LEU* 2.8 50.1 + - + +
18A GLU* 3.8 11.4 - - + +
20A LEU* 1.3 78.4 - - - +
22A ARG* 1.3 58.5 + - + +
24A GLN* 3.5 15.9 + - - +
25A ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 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 GLU* 2.9 58.0 + - + +
19A VAL* 3.8 7.6 - - - +
21A GLU* 1.3 74.7 - - + +
23A ALA* 1.3 64.6 + - - +
25A ALA* 3.1 14.7 + - - +
26A GLU* 3.3 20.5 + - - +
246A TYR* 4.5 1.6 - - - -
250A GLU* 3.8 27.8 + - - +
253A LYS* 4.8 13.3 - - - +
254A TRP* 4.8 4.9 - - - +
257A GLU* 2.8 32.9 + - - -
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Residues in contact with ALA 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 VAL 3.0 16.3 + - - +
20A LEU* 4.0 2.9 - - - +
22A ARG* 1.3 73.7 - - - +
24A GLN* 1.4 68.7 + - - +
26A GLU* 3.4 1.9 + - - +
27A PHE* 2.9 27.8 + - + +
243A PHE* 4.8 4.9 - - + -
246A TYR* 3.3 22.2 + - + +
247A MET* 3.6 32.8 - - + -
250A GLU* 5.3 2.8 + - + +
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Residues in contact with GLN 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 2.8 22.8 + - - +
21A GLU* 3.6 15.9 - - - +
23A ALA* 1.4 72.4 - - - +
25A ALA* 1.3 67.1 + - - +
27A PHE* 3.2 21.7 + - + +
28A VAL* 4.8 0.9 + - - +
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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
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21A GLU 2.9 18.5 + - - +
22A ARG* 3.1 8.8 + - - +
24A GLN* 1.3 79.7 - - - +
26A GLU* 1.3 60.4 + - - +
27A PHE 3.8 0.2 + - - -
28A VAL 5.0 1.4 + - - -
29A ASP 4.9 2.1 + - - +
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Residues in contact with GLU 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 ARG* 3.5 11.6 - - - +
23A ALA 4.0 0.4 - - - +
25A ALA* 1.3 79.0 - - + +
27A PHE* 1.3 62.8 + - - +
28A VAL 3.3 3.4 + - - -
29A ASP 3.4 29.1 - - - +
30A TYR* 3.5 34.4 + - + +
31A GLN* 4.4 12.0 + - - +
36A SER* 4.9 0.7 - - - -
37A ILE* 5.0 1.2 + - - +
246A TYR* 2.5 39.5 + - + +
250A GLU* 4.5 7.8 - - - +
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Residues in contact with PHE 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 ALA* 2.9 18.3 + - + +
24A GLN* 3.2 17.9 + - + +
26A GLU* 1.3 78.0 - - - +
28A VAL* 1.3 68.5 + - + +
36A SER* 2.7 32.1 + - - -
37A ILE* 6.0 1.6 - - - +
38A MET* 4.0 23.6 - - + -
243A PHE* 3.6 41.3 - + - -
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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