Contacts of the helix formed by residues 16 - 26 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115J VAL* 3.7 31.2 - - + +
14N ILE 6.2 0.4 - - - +
15N PHE* 1.3 77.3 - - - +
17N PRO* 1.3 69.7 - - + +
18N PHE 3.3 1.6 - - - +
19N GLU* 3.0 48.0 + - + +
20N GLU* 3.3 15.7 + - - +
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Residues in contact with PRO 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J ASN* 3.9 15.9 - - + +
59J VAL* 5.3 0.9 - - + +
62J VAL* 4.2 20.2 - - + -
115J VAL* 3.7 17.3 - - + -
139J LEU* 4.1 21.3 - - + -
142J LEU* 4.3 1.3 - - + +
15N PHE* 3.5 40.1 - - + +
16N GLU* 1.3 82.9 - - - +
18N PHE* 1.3 58.0 + - + +
20N GLU* 3.4 2.6 + - + +
21N VAL* 2.8 40.3 + - - +
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Residues in contact with PHE 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J VAL* 3.6 33.9 - - + -
66J MET* 5.2 1.6 - - + -
115J VAL* 6.1 1.3 - - + -
116J MET 4.9 3.1 - - - -
117J PRO* 3.6 18.4 - - + -
118J LEU* 3.0 66.9 - - + -
121J PHE* 4.4 10.8 - + - -
135J LEU* 4.7 10.5 - - + -
139J LEU* 5.4 4.5 - - + -
16N GLU* 3.3 1.4 - - - +
17N PRO* 1.3 83.1 - - + +
19N GLU* 1.3 67.0 + - + +
21N VAL* 3.4 23.2 - - + +
22N LYS* 3.7 19.6 + - - +
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Residues in contact with GLU 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N GLU* 3.0 47.2 + - + +
18N PHE* 1.3 79.6 - - + +
20N GLU* 1.3 62.9 + - + +
22N LYS* 3.4 25.0 - - - +
23N LYS* 4.6 3.1 + - - +
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Residues in contact with GLU 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 3.3 29.6 - - + +
145J GLU* 5.4 4.5 - - - +
146J LYS* 3.4 26.4 + - - -
15N PHE* 3.5 28.1 - - + -
16N GLU 3.3 12.0 + - - +
17N PRO 4.1 2.5 - - - +
19N GLU* 1.3 78.7 - - + +
21N VAL* 1.3 58.2 + - - +
22N LYS 3.6 0.4 - - - -
23N LYS* 3.1 32.1 - - + +
24N GLU 3.8 0.5 + - - -
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Residues in contact with VAL 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 4.3 14.4 - - + +
138J SER* 3.6 22.2 - - - -
139J LEU* 3.9 19.5 - - + +
142J LEU* 3.3 18.8 - - + -
17N PRO 2.8 20.8 + - - +
18N PHE* 3.4 34.1 - - + +
20N GLU* 1.3 77.3 - - - +
22N LYS* 1.3 60.4 + - + +
23N LYS 3.2 2.7 - - - -
24N GLU* 3.1 1.0 + - - +
25N LEU* 2.7 33.8 + - - +
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Residues in contact with LYS 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 6.1 0.4 - - - -
18N PHE 3.7 14.1 - - - +
19N GLU* 3.4 21.5 - - - +
21N VAL* 1.3 83.9 - - + +
23N LYS* 1.3 64.3 + - + +
25N LEU* 3.6 9.3 + - - +
26N ASP* 3.4 20.8 + - - +
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Residues in contact with LYS 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 5.2 3.3 - - + +
145J GLU* 5.6 2.0 + - - -
19N GLU 4.9 2.5 - - - +
20N GLU* 3.1 28.3 - - + +
22N LYS* 1.3 83.9 - - + +
24N GLU* 1.3 91.7 + - - +
26N ASP* 2.5 28.1 - - - +
27N LEU* 3.2 30.5 - - - +
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Residues in contact with GLU 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J SER* 3.5 34.1 + - - +
141J LYS* 3.6 29.2 - - + +
142J LEU* 3.8 27.9 - - + +
145J GLU* 4.9 3.5 - - - +
20N GLU 4.0 2.0 - - - +
21N VAL 3.1 8.4 + - - +
23N LYS* 1.3 103.7 + - - +
25N LEU* 1.3 63.9 + - - +
27N LEU* 3.0 28.9 + - - +
28N VAL* 3.5 7.0 + - + +
39N GLN* 4.6 5.2 + - - +
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Residues in contact with LEU 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J LYS* 5.2 9.9 - - - -
131J HIS* 5.2 9.4 - - + +
134J GLU* 3.5 41.1 - - + +
135J LEU* 3.7 23.3 - - + +
138J SER* 3.2 17.7 - - - +
21N VAL 2.7 20.5 + - - +
22N LYS* 3.8 10.1 - - - +
23N LYS 3.3 0.2 - - - -
24N GLU* 1.3 74.6 - - - +
26N ASP* 1.3 62.9 + - + +
27N LEU 3.2 0.7 + - - -
28N VAL* 3.5 17.1 + - + +
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Residues in contact with ASP 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N LYS 3.4 12.4 + - - +
23N LYS* 2.5 28.4 - - - +
24N GLU 3.2 1.0 - - - -
25N LEU* 1.3 80.5 - - + +
27N LEU* 1.3 71.4 + - - +
28N VAL 3.4 5.0 - - - +
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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