Contacts of the helix formed by residues 15 - 23 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 1.3 76.5 + - - +
16D ALA* 1.3 52.0 + - - +
17D PRO* 3.5 2.5 - - - -
18D MET* 3.3 15.5 + - + +
19D LEU* 2.9 49.3 + - + +
142D VAL* 3.8 23.8 - - + -
156D SER* 3.9 17.5 - - - +
194D LEU* 3.6 28.9 - - + -
138E GLY 3.1 12.1 + - - +
140E PHE* 3.8 19.1 - - + -
158E ILE* 4.0 22.9 - - + -
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 3.0 16.2 + - - +
15D LEU* 1.3 73.7 - - - +
17D PRO* 1.4 65.9 - - + +
20D GLU* 3.0 28.1 + - - +
136E ARG* 3.6 28.7 - - + -
137E VAL 3.2 24.6 - - - +
138E GLY* 3.7 2.8 - - - -
139E ASP* 3.6 12.1 - - - +
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Residues in contact with PRO 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D SER* 3.5 24.2 - - - +
15D LEU 3.6 0.9 - - - -
16D ALA* 1.4 91.8 - - + +
18D MET* 1.4 61.2 + - - +
20D GLU* 3.6 23.1 - - - +
21D LYS* 3.6 21.1 - - - +
136E ARG* 4.1 13.9 - - - +
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Residues in contact with MET 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.3 20.5 + - + +
17D PRO* 1.4 78.8 - - - +
19D LEU* 1.3 94.4 + - + +
20D GLU 3.5 0.2 + - - -
21D LYS* 3.5 19.7 + - + +
22D VAL* 3.4 25.5 + - - +
142D VAL* 3.9 20.2 - - + -
192D LEU* 4.8 2.0 - - + -
193D ASN 3.4 22.4 - - - +
194D LEU* 3.6 22.9 - - + +
195D ASN 4.9 5.2 - - - +
196D GLY* 3.5 26.9 - - - -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 2.9 30.6 + - + +
16D ALA 4.2 2.2 - - - +
18D MET* 1.3 97.9 - - + +
20D GLU* 1.4 60.1 + - - +
22D VAL* 4.5 2.7 - - + -
23D LEU* 2.8 64.8 + - + +
142D VAL* 3.9 24.5 - - + -
144D VAL* 4.5 0.7 - - + -
154D ALA* 4.6 9.4 - - + -
192D LEU* 4.3 12.6 - - + -
137E VAL* 3.9 7.6 - - + +
138E GLY* 3.6 26.2 - - - +
158E ILE* 5.1 1.1 - - + -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ALA 3.0 13.0 + - - +
17D PRO* 3.6 12.6 - - - +
19D LEU* 1.4 76.8 - - - +
21D LYS* 1.4 61.2 + - + +
23D LEU* 4.8 3.9 - - - +
24D PRO* 3.8 14.6 - - - +
136E ARG* 3.0 45.1 + - - -
137E VAL 5.6 0.2 + - - -
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO* 3.6 23.3 + - - +
18D MET* 3.8 16.1 - - - +
19D LEU 3.3 0.6 - - - -
20D GLU* 1.4 78.9 - - + +
22D VAL* 1.3 65.4 + - + +
24D PRO* 3.7 9.1 - - - +
125D THR* 3.8 16.3 - - - +
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET* 3.4 17.5 - - - +
19D LEU* 3.3 5.3 + - + +
21D LYS* 1.3 79.8 - - + +
23D LEU* 1.4 66.4 + - - +
24D PRO* 3.4 3.8 - - - -
25D ALA* 3.0 23.3 + - - +
26D VAL* 4.2 3.8 + - + +
125D THR* 5.4 1.1 - - - -
127D ILE* 3.7 13.7 - - + -
192D LEU* 3.6 25.6 - - + -
195D ASN 4.5 4.3 - - - +
196D GLY* 3.4 39.0 - - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 2.8 51.3 + - + +
20D GLU* 4.8 2.9 - - - +
22D VAL* 1.4 72.9 - - - +
24D PRO* 1.4 59.5 - - + +
26D VAL* 2.9 22.5 + - - +
95D ASN* 3.6 8.1 - - - +
144D VAL* 3.7 32.5 - - + -
152D GLN* 3.0 41.3 - - + +
154D ALA* 4.6 9.2 - - + -
192D LEU* 6.0 0.2 - - + -
137E VAL* 4.0 24.7 - - + +
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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