Contacts of the helix formed by residues 206 - 218 (chain A) in PDB entry 1LI5
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 HIS 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PHE* 4.0 17.2 - + + +
182A VAL 5.0 2.3 + - - -
204A GLY* 3.3 0.4 - - - -
205A TRP* 1.3 101.5 + + + +
207A ILE* 1.3 63.1 + - - +
208A GLU* 3.4 4.1 + - - -
209A CYS* 3.8 9.0 + - - +
210A SER 4.2 0.3 + - - -
233A PRO* 4.2 8.8 - - + +
234A HIS* 3.1 52.5 + - + +
237A ASN* 3.1 40.2 + - + -
238A GLU* 4.1 8.9 - - - +
241A GLN* 2.9 24.8 - - - +
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Residues in contact with ILE 207 (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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121A ILE* 3.5 35.7 - - + +
124A LEU* 3.9 30.5 - - + -
125A THR* 4.0 15.9 - - - +
128A LEU* 4.7 1.6 - - + -
182A VAL 5.5 0.6 + - - -
183A LEU* 3.6 29.2 - - + +
203A PRO* 3.7 16.6 - - + -
204A GLY 3.8 4.7 - - - +
205A TRP 3.9 0.2 - - - -
206A HIS* 1.3 74.9 - - - +
208A GLU* 1.3 68.5 + - - +
209A CYS 3.4 0.2 - - - -
210A SER 3.5 1.4 + - - -
211A ALA* 3.0 20.1 + - - +
241A GLN* 3.2 28.1 - - + +
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Residues in contact with GLU 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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66A ASN* 3.0 18.8 + - - +
67A ILE 4.1 0.5 - - - +
68A THR* 2.8 46.5 + - - +
70A ILE* 4.4 5.2 - - - +
114A ALA* 4.0 20.7 + - + +
121A ILE* 3.8 23.8 - - + -
203A PRO* 5.3 3.9 - - + +
204A GLY 4.8 5.8 + - - +
205A TRP 4.4 15.1 - - - +
206A HIS 5.0 0.9 - - - +
207A ILE* 1.3 80.3 - - + +
209A CYS* 1.3 73.8 + - + +
211A ALA* 3.3 0.7 + - - -
212A MET* 2.8 42.0 + - - +
234A HIS* 5.7 2.2 - - + -
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Residues in contact with CYS 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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26A TYR* 2.6 39.2 + - + +
66A ASN* 3.8 17.7 - - - -
206A HIS 3.8 3.0 + - - +
207A ILE 3.4 0.8 - - - -
208A GLU* 1.3 82.5 - - + +
210A SER* 1.3 58.3 + - - +
213A ASN* 2.9 38.4 + - - +
234A HIS* 4.0 2.2 - - - +
238A GLU* 3.4 18.8 - - + +
963A ZN 2.3 37.0 - - - -
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Residues in contact with SER 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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124A LEU* 3.4 19.2 - - - +
206A HIS 4.2 1.0 + - - -
207A ILE 3.5 3.4 + - - -
208A GLU 3.3 0.2 - - - -
209A CYS* 1.3 78.5 - - - +
211A ALA* 1.3 62.9 + - - +
213A ASN* 3.4 16.4 - - - +
214A CYS* 3.6 15.1 + - - +
238A GLU* 3.2 18.6 + - - +
241A GLN* 3.0 29.6 + - - +
242A SER* 3.0 24.3 + - - -
246A HIS* 5.1 0.9 + - - -
250A TYR* 4.1 1.7 + - - -
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Residues in contact with ALA 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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120A GLU* 3.6 40.4 - - + +
121A ILE* 3.6 24.0 - - + -
124A LEU* 3.2 13.9 - - + +
207A ILE 3.0 18.1 + - - +
208A GLU 3.8 0.4 - - - +
210A SER* 1.3 78.7 - - - +
212A MET* 1.3 61.0 + - - +
214A CYS* 3.4 17.5 - - - -
215A LYS* 4.0 4.0 + - - +
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Residues in contact with MET 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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26A TYR* 4.9 5.6 - - + +
66A ASN* 4.5 11.2 - - - -
112A PRO* 3.1 42.4 - - + +
113A ARG 3.0 22.2 - - - +
114A ALA* 3.5 14.8 - - - +
117A HIS* 2.9 45.8 - - + +
120A GLU* 5.2 2.5 - - - -
121A ILE* 5.5 0.9 - - + -
208A GLU* 2.8 33.8 + - - +
209A CYS 4.3 1.8 - - - +
211A ALA* 1.3 75.2 - - + +
213A ASN* 1.3 64.4 + - - +
215A LYS* 3.4 5.5 + - - +
216A GLN* 3.2 26.4 + - + +
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Residues in contact with ASN 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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26A TYR* 3.4 47.2 - - + -
209A CYS 2.9 27.3 + - - +
210A SER 3.4 6.4 - - - +
212A MET* 1.3 76.1 - - - +
214A CYS* 1.3 61.5 + - - +
216A GLN* 2.9 6.9 + - - -
217A LEU* 2.6 38.4 + - + -
218A GLY 4.3 1.8 - - - -
221A PHE* 3.6 25.2 - - + -
224A HIS* 3.7 4.2 - - - -
238A GLU* 3.8 0.8 + - - -
250A TYR* 3.0 32.9 + - - -
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Residues in contact with CYS 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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120A GLU* 6.0 1.8 - - - -
124A LEU* 5.1 3.6 - - - -
210A SER 3.6 12.3 + - - +
211A ALA* 3.4 18.6 - - - -
213A ASN* 1.3 81.2 + - - +
215A LYS* 1.3 64.9 + - - +
218A GLY* 3.0 36.6 + - - +
219A ASN* 3.3 27.7 + - - +
246A HIS* 4.0 17.5 - - + +
250A TYR* 6.4 0.7 - - + -
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Residues in contact with LYS 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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117A HIS* 5.9 2.0 - - + -
120A GLU* 4.7 17.0 - - + +
211A ALA 4.0 9.9 - - - +
212A MET* 3.4 8.9 + - - +
213A ASN 3.2 0.4 - - - -
214A CYS* 1.3 85.3 - - - +
216A GLN* 1.3 71.3 + - + +
218A GLY 4.7 0.5 + - - -
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Residues in contact with GLN 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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62A LYS* 2.9 36.1 + - - +
64A VAL* 4.0 27.4 - - + -
110A MET* 3.1 48.8 - - - +
112A PRO* 5.0 10.7 - - + +
117A HIS* 4.7 15.5 + - + -
212A MET* 3.2 17.7 + - - +
213A ASN* 2.9 4.2 + - - +
215A LYS* 1.3 85.6 - - + +
217A LEU* 1.3 60.2 + - + +
218A GLY 3.8 0.2 - - - -
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Residues in contact with LEU 217 (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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24A GLY* 3.8 20.9 - - - -
25A MET 3.8 23.3 - - - +
26A TYR* 3.9 10.8 - - + -
62A LYS* 3.9 27.4 - - + +
64A VAL* 4.1 12.6 - - + -
213A ASN* 2.6 19.1 + - + +
216A GLN* 1.3 83.0 - - + +
218A GLY* 1.3 59.6 + - - +
220A HIS 3.8 12.5 - - - +
221A PHE* 3.7 42.8 - - + +
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Residues in contact with GLY 218 (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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214A CYS* 3.0 32.8 + - - -
215A LYS 4.5 0.4 - - - -
216A GLN 3.8 1.0 - - - -
217A LEU* 1.3 80.5 - - - +
219A ASN* 1.3 64.9 + - - -
220A HIS 3.1 4.8 + - - -
221A PHE* 3.8 10.7 - - - -
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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