Contacts of the helix formed by residues 212 - 226 (chain B) in PDB entry 4UFT
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 GLU 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B ARG* 6.1 0.9 - - - -
144B PHE 4.4 0.2 - - - -
145B GLY* 3.3 29.4 + - - -
146B TRP 3.8 24.7 + - - +
147B PHE* 4.9 0.4 - - - +
148B GLU* 4.1 16.9 + - - +
150B LYS* 4.6 11.3 + - - -
210B ARG 4.0 1.0 + - - -
211B LEU* 1.3 76.2 - - - +
213B ARG* 1.3 65.6 + - + +
214B LYS* 3.2 30.0 + - + +
215B TRP* 3.2 21.4 + - + +
216B LEU* 3.3 11.5 + - - +
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Residues in contact with ARG 213 (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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210B ARG* 6.4 0.7 - - - +
211B LEU 3.9 0.8 + - - -
212B GLU* 1.3 71.8 - - + +
214B LYS* 1.3 75.0 + - + +
216B LEU* 3.3 14.3 + - + +
217B ASP* 2.8 30.1 + - - +
220B ARG* 4.9 1.4 + - - -
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Residues in contact with LYS 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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143B ARG* 4.1 33.3 - - - +
144B PHE 5.8 3.4 - - - +
212B GLU* 3.1 26.6 - - + +
213B ARG* 1.3 95.7 - - + +
215B TRP* 1.3 61.2 + - - +
217B ASP* 3.3 17.1 + - + +
218B VAL* 3.4 14.6 + - - +
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Residues in contact with TRP 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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56B VAL* 3.3 38.9 + - + +
59B ILE* 3.7 28.9 - - + -
60B GLY* 3.6 25.6 - - - +
76B ILE* 6.0 1.1 - - + -
144B PHE 5.0 4.9 + - - -
145B GLY 5.1 9.2 - - - +
146B TRP* 6.0 2.0 - - - +
170B ILE* 4.5 13.5 - - + -
173B GLN* 5.7 3.6 - - + -
174B ILE* 3.9 27.1 - - + -
177B LEU* 6.2 0.4 - - + -
211B LEU* 3.6 32.1 - - + -
212B GLU* 3.2 21.2 + - + +
214B LYS* 1.3 77.8 - - - +
216B LEU* 1.3 74.9 + - + +
218B VAL* 3.4 11.6 - - - +
219B VAL* 3.3 28.9 - - + +
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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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173B GLN* 3.6 26.9 - - + +
177B LEU* 3.4 26.7 - - + +
192B GLU* 3.8 33.7 - - + +
210B ARG* 4.8 8.1 - - - +
211B LEU* 3.8 16.6 - - + +
212B GLU 3.3 15.9 - - - +
213B ARG* 3.3 13.6 + - + +
215B TRP* 1.3 90.5 - - + +
217B ASP* 1.3 60.2 + - - +
219B VAL* 4.6 0.7 - - - -
220B ARG* 2.9 40.2 + - - +
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Residues in contact with ASP 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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187B THR* 4.9 6.9 - - - +
213B ARG 2.8 18.2 + - - +
214B LYS* 3.5 15.2 - - + +
215B TRP 3.2 0.4 - - - -
216B LEU* 1.3 76.8 - - - +
218B VAL* 1.3 62.0 + - - +
220B ARG* 3.2 30.5 + - - +
221B ASN* 3.0 35.8 + - - +
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Residues in contact with VAL 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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59B ILE* 3.9 25.1 - - + +
60B GLY* 4.9 4.3 - - - -
61B ASN 5.7 2.2 - - - +
64B VAL* 5.9 5.8 - - + -
69B LEU* 4.5 15.0 - - + +
214B LYS 3.4 9.0 + - - +
215B TRP* 3.4 16.2 - - - +
217B ASP* 1.3 83.6 + - - +
219B VAL* 1.3 68.5 + - + +
221B ASN* 4.0 5.5 - - - +
222B ARG* 3.5 20.6 + - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 3.7 28.7 - - + -
69B LEU* 5.8 2.0 - - + -
73B LEU* 4.0 16.6 - - + +
174B ILE* 3.9 22.0 - - + -
177B LEU* 4.1 7.0 - - + -
215B TRP* 3.3 31.0 - - + +
216B LEU* 3.4 7.5 + - - +
217B ASP 3.2 0.4 - - - -
218B VAL* 1.3 76.6 - - + +
220B ARG* 1.3 65.5 + - - +
221B ASN 3.2 0.2 - - - -
222B ARG* 3.2 6.0 + - - +
223B ILE* 3.1 39.8 + - + +
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Residues in contact with ARG 220 (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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177B LEU* 3.8 24.7 - - + +
180B LYS* 3.6 26.7 - - - +
181B ALA* 4.8 5.6 - - + +
185B PRO* 4.1 18.3 + - - +
187B THR* 4.2 24.1 + - - +
190B ASP* 5.3 8.7 + - - -
213B ARG 4.9 1.0 + - - -
216B LEU* 2.9 39.5 + - - +
217B ASP* 3.2 32.8 + - - +
219B VAL* 1.3 76.6 - - - +
221B ASN* 1.3 61.4 + - - +
223B ILE* 3.5 9.1 + - - +
224B ALA* 3.3 22.1 + - + +
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Residues in contact with ASN 221 (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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217B ASP* 3.0 23.7 + - - +
218B VAL* 4.0 8.1 - - + +
219B VAL 3.2 0.2 - - - -
220B ARG* 1.3 77.6 - - - +
222B ARG* 1.3 56.8 + - - +
224B ALA* 3.5 5.6 + - - +
225B GLU* 3.0 30.2 + - - +
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Residues in contact with ARG 222 (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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66B GLY* 3.4 31.7 + - - -
67B PRO* 5.0 0.8 - - - +
69B LEU* 3.8 27.3 - - + +
70B THR* 3.2 25.2 + - - +
73B LEU* 5.2 4.5 - - + -
218B VAL 3.5 15.1 + - - +
219B VAL* 3.2 6.3 + - - +
221B ASN* 1.3 76.6 - - - +
223B ILE* 1.3 60.1 + - - +
225B GLU* 3.5 30.6 + - - +
226B ASP* 2.9 43.2 + - - +
229B LEU* 4.5 15.8 - - + +
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Residues in contact with ILE 223 (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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73B LEU* 4.7 3.8 - - + -
174B ILE* 4.8 9.6 - - + +
177B LEU* 4.2 20.0 - - + +
178B VAL* 5.1 5.4 - - + -
181B ALA* 3.9 19.5 - - + -
219B VAL* 3.1 42.1 + - + +
220B ARG* 3.7 10.1 - - - +
222B ARG* 1.3 77.0 - - - +
224B ALA* 1.3 51.6 + - - +
226B ASP 3.0 9.9 - - - +
229B LEU* 3.8 22.7 - - + -
230B ARG* 2.7 47.1 + - + +
233B MET* 3.9 17.9 - - + -
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Residues in contact with ALA 224 (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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181B ALA* 3.8 26.7 - - - +
182B VAL* 5.3 2.0 - - - -
220B ARG* 3.3 13.8 + - + +
221B ASN* 3.9 5.6 - - - +
223B ILE* 1.3 81.2 - - - +
225B GLU* 1.3 60.0 + - - +
230B ARG* 3.0 18.6 + - - +
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Residues in contact with GLU 225 (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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221B ASN* 3.0 22.8 + - - +
222B ARG* 3.2 33.5 + - - +
224B ALA* 1.3 81.6 - - - +
226B ASP* 1.3 79.5 + - - +
227B LEU* 3.8 1.6 + - - +
230B ARG* 4.5 0.7 + - - -
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Residues in contact with ASP 226 (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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70B THR* 4.2 14.9 + - - +
222B ARG* 2.9 32.6 + - - +
223B ILE 3.0 6.6 - - - +
225B GLU* 1.3 85.1 + - - +
227B LEU* 1.3 68.5 + - - +
228B SER* 3.5 11.5 + - - -
229B LEU* 3.2 31.9 + - + +
230B ARG* 2.9 23.7 + - - +
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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