Contacts of the helix formed by residues 248 - 259 (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 PRO 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B PHE* 6.1 6.5 - - + -
243B THR* 5.3 6.7 - - + -
246B ASN 4.5 0.7 - - - +
247B LYS* 1.4 93.8 - - + +
249B ARG* 1.3 65.6 + - - +
250B ILE* 3.3 5.2 - - + +
251B ALA* 3.3 21.1 + - + +
252B GLU* 3.2 21.1 + - - +
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Residues in contact with ARG 249 (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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164B ASN* 3.4 34.6 + - - +
165B MET* 3.6 27.2 - - - +
203B ARG 4.8 4.2 + - - -
204B ARG* 3.2 42.6 + - - +
248B PRO* 1.3 72.8 - - - +
250B ILE* 1.3 69.1 + - + +
252B GLU* 3.4 27.1 + - - +
253B MET* 3.6 14.5 + - - +
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Residues in contact with ILE 250 (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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80B PHE* 3.9 42.4 - - + -
164B ASN* 4.6 26.7 - - + +
167B LEU* 4.1 15.9 - - + -
168B GLY* 5.4 8.3 - - - -
171B LEU* 4.8 6.5 - - + -
248B PRO* 3.3 5.1 - - + +
249B ARG* 1.3 82.2 - - + +
251B ALA* 1.3 62.0 + - - +
253B MET* 2.8 27.6 + - + +
254B ILE* 3.0 28.4 + - + +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 5.7 8.0 - - + -
240B ILE* 3.9 22.5 - - + +
247B LYS* 4.0 13.0 - - + +
248B PRO* 3.3 36.8 + - + +
250B ILE* 1.3 77.8 - - - +
252B GLU* 1.3 61.7 + - - +
254B ILE* 3.4 10.7 + - - +
255B CYS* 3.1 24.8 + - - +
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Residues in contact with GLU 252 (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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204B ARG* 3.5 27.4 + - - +
246B ASN* 6.1 0.2 - - - -
247B LYS* 3.6 30.5 + - + +
248B PRO 3.2 14.1 + - - +
249B ARG* 3.5 14.3 - - - +
250B ILE 3.1 0.4 - - - -
251B ALA* 1.3 76.8 - - - +
253B MET* 1.3 58.7 + - - +
255B CYS* 3.5 3.7 + - - +
256B ASN* 3.0 28.6 + - - +
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Residues in contact with MET 253 (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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165B MET* 6.6 0.2 - - - -
168B GLY* 3.8 30.7 - - - +
172B ALA* 4.0 19.1 - - + -
199B TYR* 5.5 9.6 - - + -
204B ARG* 3.4 55.2 - - + +
205B VAL* 4.1 13.2 - - + -
249B ARG* 3.6 13.4 + - - +
250B ILE* 2.8 17.0 + - + +
252B GLU* 1.3 77.0 - - - +
254B ILE* 1.3 69.8 + - + +
256B ASN* 3.5 7.3 + - + +
257B ILE* 3.4 25.0 + - + +
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Residues in contact with ILE 254 (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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80B PHE* 5.2 10.1 - - + -
171B LEU* 4.2 24.5 - - + -
172B ALA* 5.5 1.3 - - - +
175B TRP* 3.4 49.9 - - + +
236B LEU* 4.5 8.5 - - + -
237B ILE* 5.2 0.2 - - + -
240B ILE* 4.1 13.9 - - + -
250B ILE* 3.0 30.2 + - + +
251B ALA* 3.7 8.7 - - - +
252B GLU 3.3 0.4 - - - -
253B MET* 1.3 81.7 - - + +
255B CYS* 1.3 61.4 + - - +
257B ILE* 3.2 6.8 + - - +
258B ASP* 2.8 38.1 + - - +
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Residues in contact with CYS 255 (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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237B ILE* 6.2 0.7 - - - -
240B ILE* 4.0 11.4 - - + +
241B LYS* 4.8 19.7 - - - -
247B LYS* 4.0 20.9 - - - +
251B ALA 3.1 14.0 + - - +
252B GLU* 4.0 4.0 - - - +
254B ILE* 1.3 79.8 - - - +
256B ASN* 1.3 53.4 + - - +
258B ASP* 3.2 14.9 + - - +
259B THR* 2.7 37.8 + - - -
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Residues in contact with ASN 256 (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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198B LYS* 6.0 0.3 - - - -
199B TYR* 2.5 44.3 + - + +
202B GLN* 6.2 0.8 - - - +
204B ARG* 4.9 12.5 - - - +
252B GLU 3.0 18.4 + - - +
253B MET* 3.5 11.0 - - - +
254B ILE 3.2 0.4 - - - -
255B CYS* 1.3 77.0 - - - +
257B ILE* 1.3 60.4 + - - +
259B THR* 3.3 18.9 + - - -
260B TYR* 4.2 12.6 + - - -
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Residues in contact with ILE 257 (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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172B ALA* 4.2 21.3 - - + +
175B TRP* 3.6 44.1 - - + +
176B VAL* 3.7 24.9 - - + +
195B ARG* 5.8 1.3 - - - -
199B TYR* 3.4 37.0 - - + +
253B MET* 3.5 15.3 - - + +
254B ILE* 3.2 7.4 + - - +
256B ASN* 1.3 72.7 - - - +
258B ASP* 1.3 61.2 + - - +
259B THR 3.0 6.8 + - - -
260B TYR* 3.2 27.0 + - + +
261B ILE* 4.3 1.4 + - - +
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Residues in contact with ASP 258 (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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175B TRP* 3.7 17.0 - - - +
237B ILE* 3.3 49.8 - - + +
240B ILE* 4.3 1.0 - - - +
254B ILE* 2.8 33.3 + - - +
255B CYS* 3.2 13.4 + - - +
257B ILE* 1.3 73.5 - - - +
259B THR* 1.3 55.8 + - - +
260B TYR 3.0 9.7 + - - -
261B ILE* 3.2 26.9 - - - +
262B VAL* 4.4 2.3 + - - +
312B TYR* 4.2 4.8 + - - +
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Residues in contact with THR 259 (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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255B CYS* 2.7 27.4 + - - -
256B ASN* 3.3 14.0 + - - -
257B ILE 3.0 1.4 - - - -
258B ASP* 1.3 76.1 - - - +
260B TYR* 1.3 70.6 + - + +
262B VAL* 3.9 22.9 - - + +
12R C 5.2 2.1 - - - +
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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