Contacts of the helix formed by residues 221 - 228 (chain L) in PDB entry 3D1N
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 GLN 221 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219L GLY* 2.7 2.6 + - - -
220L GLN* 1.3 78.4 - - - +
222L ASN* 1.3 70.5 + - - +
223L LEU 3.4 1.1 - - - -
224L MSE 3.4 17.9 - - + +
225L GLU* 3.1 33.0 + - - +
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Residues in contact with ASN 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L ARG* 3.1 22.6 - - + +
218L GLU* 2.9 53.0 + - - +
219L GLY* 2.7 7.5 + - - +
221L GLN* 1.3 86.1 + - - +
223L LEU* 1.3 63.6 + - - +
224L MSE 3.1 0.4 - - - -
225L GLU* 2.9 36.6 + - - +
226L PHE* 3.2 16.1 + - - +
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Residues in contact with LEU 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L LEU* 3.6 39.3 - - + +
163L LEU* 4.8 9.2 - - + -
212L ALA* 3.2 35.2 - - + +
215L ARG* 3.7 6.8 + - + -
216L ASN* 3.2 37.0 - - + +
219L GLY 3.8 1.4 + - - -
220L GLN* 4.6 10.5 - - + +
222L ASN* 1.3 77.1 - - - +
224L MSE 1.3 60.9 + - - +
226L PHE* 3.0 5.0 + - + +
227L VAL* 2.9 41.6 + - + +
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Residues in contact with MSE 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LEU* 6.1 3.6 - - - -
167L GLN* 4.3 18.8 - - - +
220L GLN 5.2 3.1 - - - +
221L GLN* 3.4 25.8 + - + +
222L ASN 3.1 0.4 - - - -
223L LEU* 1.3 84.5 - - - +
225L GLU* 1.3 66.0 + - - +
226L PHE 3.3 0.2 + - - -
227L VAL* 4.5 8.3 - - + +
228L GLY 3.3 19.4 + - - -
229L GLY* 3.5 40.0 + - - +
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Residues in contact with GLU 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L ARG* 5.2 5.7 + - - +
218L GLU* 4.5 1.2 - - - +
221L GLN* 3.1 24.2 + - - +
222L ASN* 2.9 49.8 + - - +
224L MSE 1.3 77.1 - - - +
226L PHE* 1.3 63.4 + - + +
227L VAL 3.5 0.5 + - - -
228L GLY 4.4 6.2 + - - +
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Residues in contact with PHE 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L ALA* 4.3 5.5 - - - +
175L THR* 5.8 8.3 - - + -
208L TRP* 3.4 45.5 - + - -
211L GLU* 3.3 35.9 - - + -
212L ALA* 3.4 38.1 - - + -
215L ARG* 3.4 28.9 - - + +
222L ASN 3.2 10.0 + - - +
223L LEU* 3.0 9.7 + - + +
225L GLU* 1.3 81.0 - - - +
227L VAL* 1.3 65.6 + - + +
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Residues in contact with VAL 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LEU* 4.3 26.9 - - + -
167L GLN* 3.8 42.2 - - + +
170L GLN* 4.8 2.3 - - + +
171L ALA* 3.5 29.0 + - + +
208L TRP* 4.9 7.0 - - + -
223L LEU* 2.9 28.3 + - + +
224L MSE 3.3 8.9 + - - +
225L GLU 4.5 0.7 - - - -
226L PHE* 1.3 82.5 - - + +
228L GLY* 1.3 64.2 + - - +
229L GLY* 4.4 8.1 - - - +
231L PRO* 6.2 0.4 - - + -
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Residues in contact with GLY 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L GLN* 5.9 1.1 - - - -
224L MSE 3.3 6.2 + - - -
225L GLU 4.9 3.6 - - - +
227L VAL* 1.3 85.5 - - - +
229L GLY* 1.3 55.4 + - - -
230L GLU 3.4 4.5 - - - -
231L PRO* 3.7 23.3 - - - +
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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