Contacts of the helix formed by residues 16 - 26 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13R VAL* 3.7 18.0 - - + +
14R ILE 5.7 0.2 - - - -
15R PHE* 1.3 84.5 - - - +
17R PRO* 1.3 67.1 - - - +
18R PHE 3.3 2.0 - - - -
19R GLU* 3.0 35.8 + - + +
20R GLU* 3.1 21.1 + - + +
115S VAL* 4.0 20.5 - - + +
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Residues in contact with PRO 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R PHE* 3.7 28.0 - - + +
16R GLU* 1.3 85.5 - - - +
18R PHE* 1.3 63.3 + - + +
20R GLU 3.2 0.7 + - - -
21R VAL* 2.9 37.4 + - - +
58S ASN* 3.4 29.6 - - + +
59S VAL* 5.9 0.2 - - + -
62S VAL* 4.1 22.2 - - + -
115S VAL* 4.0 9.6 - - + +
117S PRO* 6.2 0.4 - - + -
139S LEU* 4.0 22.4 - - + -
142S LEU* 4.3 2.5 - - + -
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Residues in contact with PHE 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R GLU 3.2 1.2 + - - -
17R PRO* 1.3 88.9 - - + +
19R GLU* 1.3 65.8 + - + +
21R VAL* 3.6 15.9 - - + +
22R LYS* 3.3 25.4 - - - +
62S VAL* 3.8 34.3 - - + -
115S VAL* 6.3 0.9 - - + -
116S MET 5.0 2.2 - - - -
117S PRO* 3.7 13.5 - - + -
118S LEU* 3.2 66.9 - - + -
121S PHE* 4.1 15.5 - + - -
135S LEU* 4.9 15.0 - - + -
139S LEU* 5.6 5.2 - - + -
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Residues in contact with GLU 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R GLU* 3.0 35.6 + - + +
18R PHE* 1.3 84.1 - - + +
20R GLU* 1.3 66.3 + - + +
21R VAL 3.6 0.2 + - - -
22R LYS* 3.3 44.3 + - - +
23R LYS* 5.0 2.1 + - - +
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Residues in contact with GLU 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ILE 4.5 2.8 - - - +
15R PHE* 3.3 26.2 - - - -
16R GLU* 3.1 20.9 + - + +
19R GLU* 1.3 81.4 - - + +
21R VAL* 1.3 61.9 + - - +
22R LYS 3.3 1.2 + - - -
23R LYS* 4.0 14.7 + - - +
24R GLU* 4.2 6.4 + - - +
142S LEU* 3.9 25.4 - - + +
146S LYS* 3.2 32.5 + - - -
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Residues in contact with VAL 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R PRO 2.9 26.3 + - - +
18R PHE* 3.6 27.4 - - + +
20R GLU* 1.3 73.9 - - - +
22R LYS* 1.3 56.7 + - + +
23R LYS 3.2 3.4 - - - -
24R GLU* 2.8 9.0 + - - +
25R LEU* 2.7 54.7 + - + +
135S LEU* 5.3 2.0 - - + +
138S SER* 4.2 8.5 - - - +
139S LEU* 3.5 40.2 - - + +
142S LEU* 3.5 15.0 - - + -
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Residues in contact with LYS 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R PHE* 3.3 22.4 - - - +
19R GLU* 3.3 37.9 + - - +
20R GLU 3.3 1.0 - - - -
21R VAL* 1.3 77.6 - - + +
23R LYS* 1.3 62.2 + - + +
25R LEU* 3.3 12.1 + - + +
26R ASP* 2.9 31.0 + - - +
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Residues in contact with LYS 23 (chain R).
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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19R GLU 5.7 1.6 - - - +
20R GLU* 4.0 12.2 + - - +
21R VAL 3.2 0.4 - - - -
22R LYS* 1.3 77.8 - - + +
24R GLU* 1.3 66.0 - - - +
25R LEU 3.2 0.2 + - - -
26R ASP* 2.9 27.9 + - - +
27R LEU* 3.2 20.1 - - + +
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Residues in contact with GLU 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R GLU 4.2 2.7 + - - +
21R VAL* 2.8 15.9 + - - +
23R LYS* 1.3 81.3 - - - +
25R LEU* 1.3 60.1 + - - +
27R LEU* 3.8 21.4 + - - +
28R VAL* 3.6 9.9 + - - +
39R GLN* 3.9 10.7 + - - +
138S SER* 3.3 38.0 + - - +
141S LYS* 3.6 34.0 - - + +
142S LEU* 3.9 19.6 - - + +
145S GLU* 4.2 11.4 - - - +
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Residues in contact with LEU 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R VAL* 2.7 33.0 + - + +
22R LYS* 3.6 11.4 - - + +
24R GLU* 1.3 76.2 - - - +
26R ASP* 1.3 57.8 + - - +
27R LEU 3.0 6.1 + - - -
28R VAL* 2.9 24.4 + - + +
126S LYS* 5.7 4.5 - - - +
131S HIS* 5.5 3.1 - - + +
134S GLU* 3.8 22.0 - - + +
135S LEU* 3.2 38.8 - - + -
138S SER* 3.1 24.9 - - - +
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Residues in contact with ASP 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R LYS* 2.9 20.8 + - - +
23R LYS* 2.9 19.7 - - - +
25R LEU* 1.3 74.3 - - - +
27R LEU* 1.3 68.5 + - - +
28R VAL 3.5 1.6 - - - -
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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