Contacts of the helix formed by residues 211 - 219 (chain A) in PDB entry 4LDR
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 LEU 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLN* 3.6 25.8 - - - +
21A LEU* 4.1 24.7 - - + -
46A ARG* 3.9 31.9 - - - +
169A ASN* 3.6 14.4 - - - +
173A LEU* 3.6 9.6 - - + +
207A GLN* 2.8 26.6 + - + +
210A ARG* 1.3 110.4 - - + +
212A THR* 1.3 59.8 + - - +
213A ALA 3.3 1.6 - - - -
214A PHE* 3.2 4.7 + - - +
215A GLU* 3.0 31.2 + - - +
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Residues in contact with THR 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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166A THR* 4.4 5.8 - - + -
168A CYS 2.6 27.4 + - - +
169A ASN* 3.0 20.7 + - - +
170A THR 4.5 0.5 + - - -
182A LEU* 4.1 19.2 - - + +
199A CYS* 3.6 24.7 - - + -
207A GLN 3.1 4.7 + - - -
208A GLY* 3.6 10.8 - - - -
211A LEU* 1.3 74.3 - - - +
213A ALA* 1.3 65.3 + - - +
215A GLU* 3.2 4.3 + - - +
216A LEU* 3.0 32.5 + - + +
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Residues in contact with ALA 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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199A CYS* 4.3 8.5 - - - -
208A GLY 3.0 11.5 + - - +
209A ALA* 3.4 23.1 - - - +
211A LEU 3.3 0.4 - - - -
212A THR* 1.3 75.6 - - - +
214A PHE* 1.3 64.3 + - - +
216A LEU* 3.4 1.7 + - - +
217A VAL* 3.0 28.8 + - - +
225A LEU* 5.0 1.6 - - + -
315B ALA* 3.8 9.4 - - + -
318B ILE* 3.7 34.5 - - + -
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Residues in contact with PHE 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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3A LEU* 4.0 21.1 - - + -
16A LEU* 4.9 2.9 - - + -
21A LEU* 3.7 19.5 - - + -
22A PRO* 3.7 30.5 - - + -
23A LYS 5.7 0.2 - - - -
24A GLN 5.4 0.4 - - - -
25A SER* 3.2 27.4 - - - -
173A LEU* 3.9 16.4 - - + -
210A ARG 3.3 15.9 - - - +
211A LEU* 3.2 11.7 + - + +
213A ALA* 1.3 79.4 - - - +
215A GLU* 1.3 60.7 + - - +
217A VAL* 3.8 4.1 - - - +
218A TYR* 2.9 52.5 + + - +
315B ALA* 3.3 12.6 - - + +
316B PRO* 5.6 1.1 - - + -
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Residues in contact with GLU 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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3A LEU* 3.5 16.2 - - + -
169A ASN* 2.9 22.3 + - - -
171A GLY* 3.2 2.1 - - - -
172A ALA* 2.7 26.5 + - - +
173A LEU* 3.1 26.2 + - + +
182A LEU* 3.4 20.2 - - + -
186A ARG* 2.9 24.6 + - - +
211A LEU 3.0 18.2 + - - +
212A THR 3.2 2.4 + - - +
214A PHE* 1.3 74.9 - - - +
216A LEU* 1.3 62.6 + - - +
218A TYR* 3.3 6.5 + - - +
219A GLU* 3.1 31.3 + - - +
221A ILE* 5.7 0.2 - - - -
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Residues in contact with LEU 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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166A THR* 5.7 1.6 - - + -
182A LEU* 3.9 22.2 - - + -
185A ILE* 4.2 6.7 - - + -
197A ALA* 4.4 9.9 - - + +
199A CYS* 4.1 18.6 - - + -
212A THR* 3.0 37.0 + - + +
213A ALA* 3.8 4.3 - - - +
215A GLU* 1.3 75.9 - - - +
217A VAL* 1.3 64.2 + - - +
220A GLN 3.1 2.4 + - - -
221A ILE* 2.9 65.7 + - + +
223A ALA* 3.6 28.7 - - + -
318B ILE* 4.4 1.8 - - + -
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Residues in contact with VAL 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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213A ALA 3.0 22.5 + - - +
214A PHE* 3.8 4.5 - - - +
216A LEU* 1.3 74.2 - - - +
218A TYR* 1.3 67.0 + - - +
220A GLN* 2.9 21.6 + - - +
221A ILE 5.2 0.9 - - - -
316B PRO 3.7 17.9 - - - +
317B GLY* 3.6 11.4 - - - +
318B ILE* 3.5 39.5 - - + +
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Residues in contact with TYR 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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2A THR 4.3 7.1 + - - -
3A LEU* 3.6 54.8 - - + +
4A GLU 5.1 0.9 + - - -
7A ARG* 4.5 13.9 + - - -
25A SER* 5.5 3.8 - - - -
27A TYR* 5.0 1.4 + - - -
214A PHE* 2.9 36.4 + + + +
215A GLU* 3.4 9.4 - - - +
217A VAL* 1.3 80.2 - - - +
219A GLU* 1.3 65.2 + - + +
220A GLN* 3.4 7.4 + - - +
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Residues in contact with GLU 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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2A THR* 3.3 12.4 - - - +
3A LEU* 2.7 31.3 + - - +
186A ARG* 2.8 40.2 + - - +
189A HIS* 4.2 8.0 + - - +
215A GLU 3.1 19.6 + - - +
218A TYR* 1.3 82.5 - - + +
220A GLN* 1.3 70.4 + - - +
221A ILE* 3.1 22.8 + - + +
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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