Contacts of the helix formed by residues 215 - 224 (chain A) in PDB entry 3L2P
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 ASP 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ASP 5.1 2.6 + - - -
174A CYS* 3.9 8.5 - - - -
214A GLY* 1.3 69.2 - - - -
216A VAL* 1.3 63.1 + - - +
217A TYR* 3.3 7.5 + - - +
218A LEU* 2.8 51.9 + - + +
219A THR* 2.9 29.5 + - - +
287A ILE* 4.9 3.6 - - + +
288A GLN* 3.8 22.4 + - - +
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Residues in contact with VAL 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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203A LEU* 5.1 15.5 - - + +
214A GLY 4.0 11.2 - - - +
215A ASP* 1.3 70.5 + - - +
217A TYR* 1.3 71.7 + - - +
218A LEU 3.1 0.9 - - - -
219A THR* 3.0 18.0 + - - -
220A VAL* 3.2 19.0 + - + +
346A LEU* 4.8 13.7 - - + -
364A VAL* 4.0 18.4 - - + -
368A LEU* 4.1 27.6 - - + -
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Residues in contact with TYR 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 ASP* 3.3 6.4 + - - +
216A VAL* 1.3 81.3 - - - +
218A LEU* 1.3 68.7 + - + +
220A VAL* 3.6 1.7 + - - +
221A LYS* 3.0 59.6 + - + +
228A ILE* 5.1 2.8 - - - +
360A LEU* 3.4 30.2 - - + +
361A GLN* 3.7 44.7 + - + +
364A VAL* 4.2 21.6 - - + +
368A LEU* 5.8 0.6 - - + +
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Residues in contact with LEU 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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215A ASP* 2.8 30.3 + - - +
217A TYR* 1.3 82.9 - - + +
219A THR* 1.3 60.3 + - - +
221A LYS* 4.2 13.9 - - + -
222A LEU* 2.7 38.8 + - + +
287A ILE* 3.8 16.4 - - + +
288A GLN* 3.8 42.6 - - + +
291A ASP* 3.6 36.1 - - + +
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Residues in contact with THR 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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173A ASP 4.4 13.0 - - - +
179A PHE* 3.9 18.2 - - + -
182A LEU* 5.3 2.7 - - + -
202A PHE* 4.4 16.2 - - + -
203A LEU* 3.9 19.7 - - - +
215A ASP 2.9 20.5 + - - +
216A VAL* 3.0 12.1 + - - -
218A LEU* 1.3 75.0 - - - +
220A VAL* 1.3 56.7 + - - +
222A LEU 3.8 0.3 - - - -
223A LEU* 2.7 40.8 + - - +
287A ILE* 3.7 19.1 - - + -
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Residues in contact with VAL 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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199A ILE* 5.7 0.2 - - + -
203A LEU* 4.2 25.8 - - + -
216A VAL* 3.2 18.7 + - + +
217A TYR* 3.9 3.8 - - - +
219A THR* 1.3 78.8 + - - +
221A LYS* 1.3 65.0 + - - +
223A LEU* 3.3 11.3 + - + +
224A LEU* 3.3 27.4 + - + +
342A VAL* 4.5 11.7 - - + +
343A LEU* 4.3 13.2 - - + -
346A LEU* 4.5 18.4 - - + -
360A LEU* 3.8 29.4 - - + -
364A VAL* 5.0 1.8 - - + -
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Residues in contact with LYS 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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217A TYR* 3.0 50.6 + - + +
218A LEU* 3.7 7.4 - - + +
219A THR 3.3 0.2 - - - -
220A VAL* 1.3 73.3 - - - +
222A LEU* 1.3 68.9 + - + +
223A LEU 3.0 1.6 - - - -
224A LEU* 2.8 30.0 + - - +
225A PRO* 3.8 0.9 - - - +
228A ILE* 3.9 32.5 - - + +
291A ASP* 3.0 30.4 + - - +
360A LEU* 3.9 13.7 - - + +
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Residues in contact with LEU 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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179A PHE* 3.5 22.0 - - + -
218A LEU* 2.7 31.8 + - + +
221A LYS* 1.3 91.7 - - + +
223A LEU* 1.3 61.5 + - - +
224A LEU 3.2 0.9 + - - -
225A PRO* 3.4 13.8 - - - +
287A ILE* 3.7 44.6 - - + +
290A VAL* 5.0 7.0 - - + -
291A ASP* 4.4 17.0 - - + +
294A LEU* 5.6 5.6 - - + -
328A LEU* 4.5 22.3 - - + +
333A LEU* 3.5 10.9 - - - +
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Residues in contact with LEU 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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179A PHE* 3.8 20.9 - - + -
182A LEU* 4.4 17.5 - - + -
183A CYS* 4.1 16.2 - - - -
186A VAL* 6.3 0.2 - - + -
199A ILE* 3.8 38.4 - - + -
203A LEU* 5.7 0.9 - - + -
219A THR* 2.7 30.0 + - - +
220A VAL* 3.4 10.3 - - + +
221A LYS 3.0 0.2 - - - -
222A LEU* 1.3 79.5 - - - +
224A LEU* 1.3 63.0 + - - +
225A PRO* 3.4 7.7 - - - +
333A LEU* 4.0 8.5 - - + +
335A MET* 4.7 12.1 - - - +
337A SER 4.7 5.5 - - - +
342A VAL* 3.8 24.2 - - + +
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Residues in contact with LEU 224 (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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220A VAL* 3.3 25.3 + - + +
221A LYS 2.8 12.6 + - - +
222A LEU 3.1 0.2 - - - -
223A LEU* 1.3 80.9 - - - +
225A PRO* 1.3 65.1 - - - +
226A GLY 3.0 3.6 + - - +
227A VAL* 3.1 24.2 + - + -
228A ILE* 3.0 27.5 + - + +
337A SER 4.7 0.7 - - - +
338A GLY* 3.5 30.7 - - - +
339A ALA* 3.5 20.0 - - + +
342A VAL* 3.6 24.7 - - + -
343A LEU* 4.5 12.8 - - + -
354A PHE* 6.1 0.4 - - + -
360A LEU* 5.0 6.3 - - + -
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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