Contacts of the helix formed by residues 211 - 219 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLN* 3.9 16.8 - - - +
21B LEU* 4.3 13.5 - - + -
46B ARG* 3.7 43.1 - - - +
169B ASN* 3.6 13.2 - - + +
173B LEU* 3.7 16.9 - - + +
207B GLN* 2.8 29.4 + - + +
210B ARG* 1.3 110.3 - - + +
212B THR* 1.3 59.5 + - - +
213B ALA 3.3 1.6 - - - -
214B PHE* 3.2 4.1 + - + +
215B GLU* 2.9 31.4 + - - +
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B THR* 4.3 5.2 - - + -
168B CYS 2.6 28.5 + - - +
169B ASN* 3.2 19.3 + - - +
170B THR 4.6 0.7 + - - -
182B LEU* 4.0 19.8 - - + +
199B CYS* 3.7 25.1 - - + -
207B GLN 3.0 4.5 + - - -
208B GLY* 3.4 10.7 + - - -
211B LEU* 1.3 75.7 - - - +
213B ALA* 1.3 63.2 + - - +
215B GLU* 3.2 4.8 + - - +
216B LEU* 2.9 33.5 + - + +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA* 3.6 10.8 - - + -
318A ILE* 3.8 33.6 - - + +
199B CYS* 4.3 6.5 - - - -
208B GLY 3.0 11.0 + - - +
209B ALA* 3.2 25.4 - - - +
211B LEU 3.3 0.2 - - - -
212B THR* 1.3 76.3 - - - +
214B PHE* 1.3 56.4 + - - +
216B LEU* 3.3 1.6 + - - +
217B VAL* 2.9 35.6 + - - +
225B LEU* 5.1 0.9 - - + -
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Residues in contact with PHE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ALA* 3.2 12.0 - - + +
316A PRO* 5.4 2.0 - - + -
3B LEU* 4.2 24.2 - - + -
16B LEU* 5.0 2.2 - - + -
21B LEU* 3.8 18.6 - - + -
22B PRO* 3.9 27.8 - - + -
25B SER* 3.8 30.1 - - - -
173B LEU* 4.0 16.8 - - + -
210B ARG 3.5 16.2 - - - +
211B LEU* 3.2 11.0 + - + +
213B ALA* 1.3 79.2 - - - +
215B GLU* 1.3 67.8 + - - +
217B VAL* 3.4 3.9 + - - +
218B TYR* 2.9 37.9 + + + +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.6 18.8 - - + -
169B ASN* 3.0 18.3 + - - +
171B GLY* 3.1 1.0 - - - -
172B ALA* 2.7 24.6 + - - +
173B LEU* 2.9 31.4 + - + +
182B LEU* 3.5 22.0 - - + -
186B ARG* 2.9 26.3 + - - +
211B LEU 2.9 17.5 + - - +
212B THR 3.2 3.3 + - - +
214B PHE* 1.3 77.5 - - - +
216B LEU* 1.3 62.3 + - - +
218B TYR* 3.3 1.8 + - - +
219B GLU* 3.0 31.3 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.3 2.5 - - + -
166B THR* 5.7 1.3 - - + -
182B LEU* 4.1 20.4 - - + -
185B ILE* 4.4 2.9 - - + -
197B ALA* 4.3 16.4 - - + +
199B CYS* 3.9 19.1 - - + -
212B THR* 2.9 38.5 + - + +
213B ALA 3.7 3.6 - - - +
215B GLU* 1.3 77.8 - - - +
217B VAL* 1.3 60.5 + - - +
219B GLU* 3.5 1.6 + - - -
220B GLN 3.1 2.4 + - - -
221B ILE* 3.0 62.9 + - + +
223B ALA* 3.6 29.2 - - + -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ALA 5.3 0.2 - - - +
316A PRO 3.7 17.0 - - - +
317A GLY* 3.7 9.6 - - - +
318A ILE* 3.6 39.5 - - + +
213B ALA 2.9 21.5 + - - +
214B PHE* 3.9 4.5 - - - +
216B LEU* 1.3 75.5 - - - +
218B TYR* 1.3 66.5 + - - +
220B GLN* 3.0 21.7 + - - +
221B ILE 5.4 0.4 - - - -
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Residues in contact with TYR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 3.5 45.2 + - + +
3B LEU* 3.6 34.5 - - + -
214B PHE* 2.9 33.4 + + + +
215B GLU* 3.5 6.3 - - - +
217B VAL* 1.3 80.0 - - - +
219B GLU* 1.3 71.8 + - + +
220B GLN* 3.2 11.8 + - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 3.8 16.2 + - - +
3B LEU* 3.4 23.9 + - - +
186B ARG* 2.8 44.5 + - - +
189B HIS* 4.3 7.1 + - - -
215B GLU 3.0 18.6 + - - +
216B LEU 4.2 0.2 - - - +
218B TYR* 1.3 82.4 - - + +
220B GLN* 1.3 71.9 + - - +
221B ILE* 3.2 27.4 + - + +
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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