Contacts of the helix formed by residues 204 - 217 (chain A) in PDB entry 1L0N
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 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.9 23.8 + - - +
203A LEU* 1.3 76.6 - - - +
205A HIS* 1.3 66.1 + - - +
206A ARG* 3.1 11.6 - - + +
207A GLN* 2.8 43.0 + - + +
208A LEU* 3.5 2.3 + - - +
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Residues in contact with HIS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 3.1 55.1 + - + +
16A VAL 4.2 0.4 - - - -
17A SER* 3.2 25.5 - - - -
25A VAL* 3.3 23.5 + - + -
26A ALA* 4.2 2.5 - - - -
27A SER* 2.8 30.4 + - - +
29A GLN* 5.0 3.8 + - - +
203A LEU 4.0 1.6 + - - -
204A GLU* 1.3 70.9 - - - +
206A ARG* 1.3 58.9 + - + +
208A LEU* 3.2 8.6 + - - +
209A LEU* 2.9 35.6 + - + +
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLU* 3.0 11.3 + - + +
205A HIS* 1.3 76.2 - - + +
207A GLN* 1.3 56.0 + - + +
209A LEU* 3.5 8.5 - - + +
210A ASP* 2.8 46.2 + - - +
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Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.1 20.3 - - + +
107A PRO* 5.1 8.8 - - - +
203A LEU* 5.3 0.7 - - - -
204A GLU* 2.8 36.4 + - + +
206A ARG* 1.3 76.9 - - + +
208A LEU* 1.3 56.2 + - - +
210A ASP* 3.5 6.2 - - - +
211A LEU* 2.8 47.0 + - + +
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.7 17.5 - - + -
26A ALA 3.6 24.9 - - - +
27A SER* 3.7 13.5 - - - -
37A VAL* 4.5 2.7 - - + -
106A LEU* 4.7 11.5 - - + +
110A VAL* 4.2 18.2 - - + -
197A LEU* 3.8 24.9 - - + +
199A ALA* 3.7 26.9 - - + +
203A LEU* 5.2 3.4 - - + -
204A GLU 3.5 2.7 + - - +
205A HIS* 3.2 14.9 + - - +
207A GLN* 1.3 79.0 - - - +
209A LEU* 1.3 56.7 + - - +
211A LEU* 3.4 3.9 + - - +
212A ALA* 2.8 30.7 + - - +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.4 30.1 - - - +
18A GLN 5.3 1.6 - - - +
19A LEU* 3.8 16.6 - - + -
25A VAL* 3.7 18.8 - - + +
205A HIS* 2.9 25.9 + - + +
206A ARG* 3.2 12.5 + - + +
208A LEU* 1.3 72.4 - - - +
210A ASP* 1.3 68.6 + - - +
212A ALA* 2.9 5.3 + - - +
213A GLN* 2.8 26.7 + - + +
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Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ARG* 2.8 29.4 + - - +
207A GLN* 3.5 6.4 - - - +
209A LEU* 1.3 74.3 - - - +
211A LEU* 1.3 61.1 + - + +
213A GLN* 3.1 5.0 + - - +
214A LYS* 2.8 32.0 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.9 26.5 - - + -
107A PRO* 3.7 42.6 - - + +
110A VAL* 3.7 23.6 - - + +
207A GLN* 2.8 29.1 + - + +
208A LEU* 3.7 4.0 - - - +
210A ASP* 1.3 75.5 - - + +
212A ALA* 1.3 55.8 + - - +
214A LYS* 4.3 8.5 - - + +
215A HIS* 2.9 55.3 + - + +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.4 20.1 - - + +
23A LEU* 4.7 2.5 - - + -
25A VAL* 4.1 17.9 - - + -
110A VAL* 4.7 0.4 - - - +
197A LEU* 4.0 17.7 - - + -
208A LEU 2.8 21.3 + - - +
209A LEU 2.9 4.5 + - - +
211A LEU* 1.3 70.0 - - - +
213A GLN* 1.3 60.3 + - - +
216A PHE* 3.0 41.7 + - + +
217A SER 3.7 0.2 + - - -
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.5 33.4 - - + +
20A ASP* 4.1 22.0 + - - +
21A ASN* 5.2 2.0 + - - +
209A LEU* 2.8 14.6 + - + +
210A ASP* 3.8 7.9 - - - +
212A ALA* 1.3 74.8 - - - +
214A LYS* 1.3 67.1 + - - +
217A SER* 3.0 37.6 + - - -
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP 2.8 18.0 + - - +
211A LEU* 3.8 10.7 - - + +
213A GLN* 1.3 81.7 - - - +
215A HIS* 1.3 92.0 + - + +
217A SER* 4.7 4.5 + - - +
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Residues in contact with HIS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 4.5 1.8 - - + -
110A VAL* 4.3 3.5 - - + +
111A GLU* 3.6 47.9 - - + +
114A ALA* 3.4 19.0 - - + +
118A GLN* 3.1 20.4 + - - +
211A LEU* 2.9 37.8 + - + +
214A LYS* 1.3 115.0 - - + +
216A PHE* 1.3 62.8 + - + +
217A SER 3.6 2.8 - - - +
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Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.3 3.1 - - + -
21A ASN* 3.8 8.3 + - - +
23A LEU* 3.5 28.3 - - + -
39A VAL* 4.1 17.9 - - + -
110A VAL* 3.8 25.8 - - + -
113A LEU* 4.3 1.3 - - + -
114A ALA* 3.7 23.6 - - + -
117A VAL* 3.6 23.8 - - + -
118A GLN* 3.9 12.6 - - - +
195A MET* 3.9 17.0 - - + -
197A LEU* 4.1 14.6 - - + -
212A ALA* 3.0 28.8 + - - +
215A HIS* 1.3 80.4 - - + +
217A SER* 1.3 66.3 + - - +
218A GLY* 3.0 4.9 + - - -
219A LEU* 3.6 20.3 + - + +
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Residues in contact with SER 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 4.3 10.8 - - - +
118A GLN* 5.1 1.2 - - - +
212A ALA 3.7 2.0 + - - -
213A GLN* 3.0 35.5 + - - -
214A LYS 4.8 3.7 - - - +
215A HIS 3.6 3.0 - - - +
216A PHE* 1.3 75.8 + - - +
218A GLY* 1.3 58.2 + - - +
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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