Contacts of the helix formed by residues 16 - 26 (chain W) in PDB entry 3A68
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 GLU 16 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL* 4.0 24.1 - - + +
14W ILE 5.9 1.3 - - - +
15W PHE* 1.3 82.0 - - - +
17W PRO* 1.3 69.1 - - - +
18W PHE 3.3 1.8 - - - -
19W GLU* 3.1 52.4 + - + +
20W GLU* 3.2 20.5 + - + +
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Residues in contact with PRO 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN* 3.7 23.6 - - + +
59D VAL* 5.8 1.1 - - + -
62D VAL* 4.2 24.9 - - + -
115D VAL* 3.7 11.2 - - + -
139D LEU* 4.3 14.1 - - + -
142D LEU* 4.0 3.4 - - + +
15W PHE* 3.5 43.0 - - + +
16W GLU* 1.3 83.5 - - - +
18W PHE* 1.3 61.7 + - + +
20W GLU 3.4 0.7 + - - -
21W VAL* 2.8 35.4 + - - +
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Residues in contact with PHE 18 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.6 33.7 - - + -
115D VAL* 6.0 2.0 - - + -
116D MET 4.9 2.2 - - - -
117D PRO* 3.5 19.3 - - + -
118D LEU* 3.1 66.6 - - + -
121D PHE* 4.2 6.7 - + - -
135D LEU* 3.9 24.7 - - + -
139D LEU* 5.8 1.6 - - + -
16W GLU* 3.3 1.0 - - - +
17W PRO* 1.3 81.8 - - + +
19W GLU* 1.3 61.0 + - + +
21W VAL* 3.6 18.2 - - + +
22W LYS* 3.0 35.9 - - - +
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Residues in contact with GLU 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16W GLU* 3.1 48.5 + - + +
18W PHE* 1.3 79.1 - - + +
20W GLU* 1.3 65.6 + - + +
21W VAL 3.5 0.2 + - - -
22W LYS* 3.5 36.3 + - - +
23W LYS* 4.4 1.7 + - - +
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Residues in contact with GLU 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.0 21.4 - - + +
145D GLU* 4.8 2.3 - - - +
146D LYS* 2.8 32.0 + - - -
14W ILE 4.7 2.9 - - - +
15W PHE* 3.3 26.2 - - - -
16W GLU* 3.2 19.2 + - + +
17W PRO 4.2 2.0 - - - +
19W GLU* 1.3 78.4 - - + +
21W VAL* 1.3 61.2 + - - +
22W LYS 3.3 0.4 + - - -
23W LYS* 3.9 14.6 + - - +
24W GLU* 4.0 8.3 + - - +
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Residues in contact with VAL 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 4.0 20.9 - - + -
138D SER* 3.5 39.5 - - - +
139D LEU* 3.9 18.2 - - + +
142D LEU* 4.4 5.8 - - + +
17W PRO 2.8 20.8 + - - +
18W PHE* 3.6 20.9 - - + +
20W GLU* 1.3 74.7 - - - +
22W LYS* 1.3 65.6 + - + +
23W LYS 3.2 1.1 - - - -
24W GLU* 2.9 4.8 + - - -
25W LEU* 2.8 32.8 + - + +
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Residues in contact with LYS 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W PHE* 3.0 29.3 + - - +
19W GLU* 3.5 27.8 - - - +
20W GLU 3.3 0.2 - - - -
21W VAL* 1.3 80.9 - - + +
23W LYS* 1.3 61.6 + - - +
25W LEU* 3.5 6.1 + - - +
26W ASP* 3.3 32.3 + - - +
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Residues in contact with LYS 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLU* 5.3 6.0 + - - -
19W GLU 4.4 1.5 + - - +
20W GLU* 3.9 11.2 + - - +
21W VAL 3.2 0.2 - - - -
22W LYS* 1.3 79.1 - - - +
24W GLU* 1.3 75.6 + - - +
26W ASP* 3.5 8.4 + - - +
27W LEU* 3.2 48.2 + - + +
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Residues in contact with GLU 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D SER* 3.5 37.6 + - - +
141D LYS* 4.0 26.7 - - + +
142D LEU* 4.3 16.8 + - + +
145D GLU* 4.5 9.9 - - - +
20W GLU 4.0 3.7 + - - +
21W VAL* 2.9 18.1 + - + +
23W LYS* 1.3 91.3 + - - +
25W LEU* 1.3 65.1 + - - +
27W LEU* 3.1 29.1 + - - +
28W VAL* 3.6 7.1 + - - +
39W GLN* 4.7 5.9 + - - +
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Residues in contact with LEU 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LYS* 4.1 12.0 + - - +
131D HIS* 4.1 26.0 - - + +
134D GLU* 4.0 35.2 - - + +
135D LEU* 4.7 15.9 - - + -
138D SER* 3.1 16.7 + - - +
21W VAL* 2.8 21.0 + - + +
22W LYS* 3.9 7.2 - - - +
24W GLU* 1.3 72.2 - - - +
26W ASP* 1.3 67.0 + - - +
27W LEU 3.0 1.4 + - - -
28W VAL* 3.2 19.0 + - + +
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Residues in contact with ASP 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22W LYS* 3.3 20.2 + - - +
23W LYS* 3.8 8.1 - - - +
24W GLU 3.2 0.6 - - - -
25W LEU* 1.3 83.2 - - - +
27W LEU* 1.3 65.4 + - + +
28W VAL 3.4 2.8 + - - +
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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