Contacts of the helix formed by residues 215 - 223 (chain A) in PDB entry 3LXC
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 ASN 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A MET* 5.3 1.2 - - - +
213A LYS 3.3 4.0 + - - +
214A PRO* 1.3 72.4 - - - +
216A TYR* 1.3 60.9 + - - +
217A THR* 3.0 16.3 + - - -
218A GLU* 3.2 23.3 + - - +
219A ILE* 3.1 24.3 + - - +
1D NAG 1.4 67.3 + - + +
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Residues in contact with TYR 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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205A PRO* 4.0 11.2 - - + +
214A PRO* 3.7 29.8 + - + +
215A ASN* 1.3 69.6 + - - +
217A THR* 1.3 60.1 + - - +
219A ILE* 3.7 11.9 - - + -
220A ARG* 2.9 32.7 + - - +
226A TRP* 3.8 30.0 - + - -
228A ASN* 2.7 30.7 + - - +
245A TRP* 4.8 0.9 - - - -
252A ARG* 3.7 40.0 + - + -
253A ILE* 3.6 19.2 - - + +
256A VAL* 3.4 30.1 - - + +
263A ASN* 4.5 2.0 - - - -
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Residues in contact with THR 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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215A ASN* 3.0 11.1 + - - -
216A TYR* 1.3 78.7 - - - +
218A GLU* 1.3 59.5 + - - +
220A ARG* 4.0 7.0 - - - +
221A GLN* 3.3 22.0 + - - +
256A VAL* 4.4 6.0 - - - +
1D NAG 3.8 18.6 - - - -
2D NAG 3.6 32.1 - - + +
5D FUC 5.9 3.4 - - + +
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Residues in contact with GLU 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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181A ALA* 5.1 2.5 - - - +
185A LYS* 2.9 41.5 + - - +
204A TRP* 4.2 15.5 - - + -
215A ASN* 3.2 30.3 + - - +
217A THR* 1.3 78.6 - - - +
219A ILE* 1.3 65.2 + - - +
221A GLN* 3.1 18.5 + - - +
222A TYR* 3.2 23.5 - - + -
1D NAG 4.3 13.2 + - - +
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Residues in contact with ILE 219 (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 TRP* 3.8 44.0 - - + +
205A PRO* 3.9 20.0 - - + -
208A MET* 4.9 1.1 - - - -
214A PRO* 3.8 28.5 - - + -
215A ASN 3.1 19.6 + - - +
216A TYR* 3.9 11.9 - - + +
218A GLU* 1.3 75.8 - - + +
220A ARG* 1.3 58.3 + - - +
222A TYR* 3.1 4.3 + - - -
223A CYS* 2.9 30.6 + - - +
226A TRP* 3.9 36.1 - - + -
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Residues in contact with ARG 220 (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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32A LEU* 2.6 38.5 + - - +
216A TYR 2.9 19.1 + - - +
217A THR* 4.0 5.6 - - - +
219A ILE* 1.3 74.0 - - - +
221A GLN* 1.3 63.2 + - - +
222A TYR 3.0 2.9 + - - -
223A CYS 3.4 1.8 - - - +
226A TRP* 3.8 22.8 - - + -
256A VAL* 3.0 24.6 + - + -
257A ALA 3.5 0.2 - - - -
258A GLY* 3.0 41.8 + - - +
259A PRO* 3.3 17.6 + - - +
260A GLY 4.0 2.4 - - - -
261A GLY* 3.2 18.7 + - - +
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Residues in contact with GLN 221 (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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32A LEU* 3.2 21.2 - - - +
33A ASP 4.7 1.0 + - - -
217A THR* 3.3 12.7 + - - +
218A GLU* 3.1 16.9 + - - +
220A ARG* 1.3 79.5 - - - +
222A TYR* 1.3 86.6 + - + +
1D NAG 5.5 7.3 - - - -
2D NAG 6.2 2.2 - - - +
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Residues in contact with TYR 222 (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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32A LEU* 3.3 9.0 - - - +
184A TYR 4.9 0.7 - - - +
185A LYS* 3.7 53.1 + - + +
188A SER* 2.7 42.6 + - - +
189A LEU* 4.3 24.9 - - + +
200A TYR* 3.1 12.3 - - - -
204A TRP* 4.3 13.2 - + + -
218A GLU* 3.2 29.4 - - + -
219A ILE 3.1 5.8 + - - +
220A ARG 3.0 0.2 - - - -
221A GLN* 1.3 111.1 + - + +
223A CYS* 1.3 60.2 + - - +
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Residues in contact with CYS 223 (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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32A LEU* 3.1 23.0 + - - -
184A TYR* 5.0 0.9 - - - -
200A TYR* 4.0 5.4 - - - -
202A CYS* 2.0 50.0 - - + -
204A TRP* 4.1 18.2 - - - -
219A ILE* 2.9 18.0 + - - +
220A ARG 3.4 4.1 + - - +
222A TYR* 1.3 82.2 - - - +
224A ASN* 1.3 60.6 + - - +
225A HIS 3.8 9.2 - - - +
226A TRP* 3.5 18.2 - - + -
260A GLY 3.6 0.2 - - - +
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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