Contacts of the helix formed by residues 15 - 23 (chain J) in PDB entry 3STJ
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 LEU 15 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J SER* 1.4 75.3 + - - +
16J ALA* 1.4 58.2 + - - +
17J PRO* 3.5 2.0 - - - -
18J MET* 3.3 16.7 + - + +
19J LEU* 3.0 41.7 + - + +
142J VAL* 3.6 25.6 - - + -
156J SER* 3.9 17.9 - - - +
194J LEU* 3.6 28.3 - - + -
138K GLY 3.1 11.9 + - - +
140K PHE* 3.8 19.7 - - + -
158K ILE* 4.0 21.8 - - + -
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Residues in contact with ALA 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J SER* 3.0 16.4 + - - +
15J LEU* 1.4 73.1 - - - +
17J PRO* 1.4 67.3 - - + +
19J LEU* 4.4 0.4 - - - -
20J GLU* 2.9 27.7 + - - +
136K ARG* 3.7 28.9 - - + -
137K VAL 3.2 23.0 - - - +
138K GLY* 3.7 2.6 - - - -
139K ASP* 3.5 13.5 - - - +
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Residues in contact with PRO 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J SER* 3.6 21.1 - - - +
15J LEU 3.6 3.8 - - - -
16J ALA* 1.4 92.5 - - + +
18J MET* 1.4 59.8 + - - +
20J GLU* 3.6 17.9 - - - +
21J LYS* 3.6 24.3 - - - +
136K ARG* 4.1 14.6 - - - +
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Residues in contact with MET 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J LEU* 3.3 20.6 + - + +
17J PRO* 1.4 75.8 - - - +
19J LEU* 1.3 96.5 + - + +
20J GLU 3.2 0.7 - - - -
21J LYS* 3.2 26.0 + - - +
22J VAL* 3.3 19.2 + - + +
142J VAL* 4.1 19.1 - - + -
192J LEU* 5.0 1.8 - - + -
193J ASN 3.6 20.0 - - - +
194J LEU* 3.5 22.7 - - - +
195J ASN* 4.7 8.3 - - - +
196J GLY* 3.5 25.1 - - - -
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Residues in contact with LEU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J LEU* 3.0 29.6 + - + +
16J ALA 3.3 0.6 + - - +
18J MET* 1.3 97.5 - - + +
20J GLU* 1.3 57.3 + - - +
22J VAL* 3.1 2.2 + - + -
23J LEU* 2.7 68.4 + - + +
142J VAL* 4.0 24.7 - - + -
144J VAL* 4.4 0.4 - - + -
154J ALA* 4.5 9.9 - - + -
192J LEU* 4.3 12.1 - - + -
137K VAL* 3.8 9.9 - - + +
138K GLY* 3.6 27.1 - - - +
158K ILE* 5.1 0.7 - - + -
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Residues in contact with GLU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ALA 2.9 13.7 + - - +
17J PRO* 3.6 13.1 - - - +
19J LEU* 1.3 76.5 - - - +
21J LYS* 1.4 60.4 + - + +
23J LEU* 4.6 4.3 - - - +
24J PRO* 3.7 15.4 - - - +
136K ARG* 3.1 44.3 + - - -
137K VAL 5.4 0.2 + - - -
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Residues in contact with LYS 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J PRO* 3.6 23.6 - - - +
18J MET* 3.2 17.9 + - + +
20J GLU* 1.4 77.1 - - + +
22J VAL* 1.3 65.5 + - + +
24J PRO* 3.8 7.8 - - - +
125J THR* 3.8 15.9 - - - +
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Residues in contact with VAL 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J MET* 3.3 19.1 - - + +
19J LEU* 3.1 5.6 + - + +
21J LYS* 1.3 81.5 - - + +
23J LEU* 1.4 66.4 + - - +
24J PRO* 3.3 4.3 - - - -
25J ALA* 2.9 26.8 + - - +
26J VAL* 4.2 3.9 + - + +
125J THR* 5.3 0.7 - - - -
127J ILE* 3.9 11.7 - - + -
192J LEU* 3.5 32.1 - - + -
195J ASN 4.5 4.0 - - - +
196J GLY* 3.5 35.7 - - - +
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Residues in contact with LEU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J LEU* 2.7 62.4 + - + +
20J GLU* 4.6 3.4 - - - +
22J VAL* 1.4 72.4 - - + +
24J PRO* 1.4 64.1 - - + +
26J VAL* 3.0 14.2 + - - +
95J ASN* 3.5 16.8 - - - +
144J VAL* 3.8 20.2 - - + -
152J GLN* 2.9 40.8 - - - +
154J ALA* 4.6 6.5 - - + -
137K VAL* 3.9 26.2 - - + +
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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