Contacts of the helix formed by residues 16 - 25 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L PHE* 1.3 74.7 - - - +
17L PRO* 1.3 64.9 - - - +
18L PHE* 3.6 29.5 + - - +
19L GLU* 3.1 53.0 + - + +
20L GLU* 3.6 11.2 + - - +
115M VAL* 3.1 40.5 - - + +
116M MET 3.8 9.4 + - - +
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Residues in contact with PRO 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L PHE* 3.3 39.2 - - + +
16L GLU* 1.3 86.2 - - - +
18L PHE* 1.3 56.6 + - + +
19L GLU 3.2 0.3 + - - -
20L GLU* 3.3 2.2 + - + +
21L VAL* 2.7 41.7 + - + +
58M ASN* 4.0 14.4 - - + +
59M VAL 5.3 0.2 - - - +
62M VAL* 4.2 19.3 - - + -
115M VAL* 3.7 16.2 - - + -
139M LEU* 3.5 26.5 - - + -
142M LEU* 6.2 0.4 - - + -
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Residues in contact with PHE 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L GLU* 3.3 19.6 + - - +
17L PRO* 1.3 79.4 - - + +
19L GLU* 1.3 62.7 + - - +
21L VAL* 4.2 16.8 - - + -
22L LYS* 3.2 35.0 + - + +
62M VAL* 3.6 34.3 - - + -
66M MET* 5.3 1.6 - - + -
116M MET 4.8 0.4 - - - -
117M PRO* 3.5 15.3 - - + -
118M LEU* 3.1 62.1 - - + -
121M PHE* 4.6 10.1 - + - -
135M LEU* 4.8 15.7 - - + -
139M LEU* 5.4 4.7 - - + -
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L GLU* 3.1 34.7 - - + +
17L PRO 3.1 0.8 - - - -
18L PHE* 1.3 83.1 - - - +
20L GLU* 1.3 65.2 + - + +
22L LYS* 3.3 28.6 + - - +
23L LYS* 4.1 7.6 + - - +
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Residues in contact with GLU 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L PHE* 3.3 33.1 - - + -
16L GLU 3.9 10.5 + - - +
17L PRO 3.3 4.3 + - - +
19L GLU* 1.3 77.0 - - + +
21L VAL* 1.3 65.1 + - - +
22L LYS 3.2 1.6 - - - -
23L LYS* 3.2 17.9 + - - +
24L GLU* 3.3 9.9 + - - +
142M LEU* 3.5 35.0 - - + +
145M GLU* 5.4 1.4 - - - +
146M LYS* 4.1 16.2 + - - -
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Residues in contact with VAL 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L PRO 2.7 27.8 + - - +
18L PHE* 4.2 11.7 - - + -
20L GLU* 1.3 66.8 - - - +
22L LYS* 1.3 63.7 + - - +
23L LYS 2.9 5.4 - - - -
24L GLU* 4.2 1.6 - - - +
25L LEU* 2.8 26.7 + - + +
135M LEU* 3.7 31.4 - - + +
138M SER* 4.0 11.0 - - - -
139M LEU* 3.6 38.1 - - + +
142M LEU* 3.7 22.2 - - + -
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Residues in contact with LYS 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PHE* 3.2 28.5 + - + +
19L GLU* 3.3 24.5 + - - +
21L VAL* 1.3 78.4 - - - +
23L LYS* 1.3 57.8 + - + +
25L LEU* 4.6 3.9 - - - +
26L ASP* 3.2 22.9 - - - +
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Residues in contact with LYS 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L GLU 4.7 6.7 - - - +
20L GLU* 3.2 12.7 + - - +
21L VAL 2.9 0.4 - - - -
22L LYS* 1.3 81.1 - - + +
24L GLU* 1.3 62.6 + - - +
25L LEU 3.4 0.2 - - - -
26L ASP* 3.5 15.6 + - - +
27L LEU* 3.5 19.2 - - + +
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Residues in contact with GLU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L GLU 3.3 2.9 + - - +
21L VAL 3.1 2.5 + - - +
23L LYS* 1.3 76.4 - - - +
25L LEU* 1.3 56.9 + - - +
26L ASP 3.0 5.6 - - - -
27L LEU* 2.9 40.4 + - + +
28L VAL* 3.5 5.5 + - - +
39L GLN* 4.3 7.3 + - - +
138M SER* 3.0 22.2 + - - +
141M LYS* 3.2 35.3 - - + +
142M LEU* 2.8 44.0 + - + +
145M GLU* 5.4 2.9 - - - +
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 2.8 22.6 + - + +
22L LYS* 4.6 4.7 - - - +
24L GLU* 1.3 76.7 - - - +
26L ASP* 1.3 66.6 + - - +
27L LEU 3.3 0.9 - - - -
28L VAL* 3.0 24.6 - - + +
126M LYS* 5.9 4.5 - - - -
131M HIS* 4.0 19.5 - - + +
134M GLU* 3.8 47.1 - - + +
135M LEU* 3.5 25.6 - - + +
138M SER* 3.1 13.8 + - - +
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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