Contacts of the helix formed by residues 249 - 258 (chain B) in PDB entry 1U3W
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 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B LYS 4.3 2.7 - - - +
248B LYS* 1.3 89.8 - - + +
250B ILE* 1.3 66.8 + - - +
251B GLN* 3.4 30.3 - - + +
252B GLU* 3.0 42.8 + - - +
253B VAL* 3.2 8.1 + - - +
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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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198B PHE* 3.9 9.6 - - + -
222B VAL* 4.2 7.2 - - + -
241B ILE* 3.6 30.3 - - + -
243B PRO* 4.1 42.8 - - + +
246B TYR* 4.7 4.0 - - + -
248B LYS 3.5 2.5 + - - -
249B PRO* 1.3 71.7 - - - +
251B GLN* 1.3 63.5 + - - +
253B VAL* 3.4 13.1 - - + +
254B LEU* 2.8 41.6 + - + +
274B THR* 5.9 2.5 - - + -
277B ALA* 3.6 25.4 - - + -
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Residues in contact with GLN 251 (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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249B PRO* 3.4 28.2 - - + +
250B ILE* 1.3 83.3 + - - +
252B GLU* 1.3 64.2 + - + +
254B LEU* 3.5 1.6 + - - +
255B LYS* 3.0 35.8 + - + +
277B ALA* 3.6 36.3 - - - +
280B LEU* 3.7 38.7 - - + +
281B CYS* 3.9 14.7 - - + +
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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
----------------------------------------------------------
248B LYS* 3.7 25.8 - - + +
249B PRO* 3.0 39.0 + - + +
251B GLN* 1.3 81.9 + - + +
253B VAL* 1.3 66.1 + - - +
255B LYS* 3.3 9.7 + - + +
256B GLU* 3.0 41.4 + - - +
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Residues in contact with VAL 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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241B ILE* 4.2 7.2 - - + -
246B TYR* 3.6 52.7 - - + -
248B LYS* 4.0 20.8 - - + +
249B PRO 3.6 12.8 - - - +
250B ILE* 3.1 13.2 + - + +
252B GLU* 1.3 78.4 - - - +
254B LEU* 1.3 62.4 + - - +
256B GLU* 3.3 7.7 + - - +
257B MET* 3.1 44.1 + - + +
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Residues in contact with LEU 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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196B ALA* 4.4 9.0 - - + -
198B PHE* 3.5 34.8 - - + -
220B ILE* 3.6 42.8 - - + -
222B VAL* 4.4 4.3 - - + -
241B ILE* 3.6 14.6 - - + -
250B ILE* 2.8 27.0 + - + +
251B GLN 3.9 3.8 - - - +
253B VAL* 1.3 78.1 - - - +
255B LYS* 1.3 60.2 + - - +
257B MET* 3.2 12.2 + - - +
258B THR* 2.7 25.5 + - - +
261B GLY* 5.1 0.7 - - - -
262B VAL* 5.1 3.8 - - + -
281B CYS* 3.8 23.1 - - + +
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Residues in contact with LYS 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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251B GLN* 3.0 27.4 + - + +
252B GLU* 3.8 8.9 - - + +
254B LEU* 1.3 74.5 - - - +
256B GLU* 1.3 65.1 + - + +
258B THR* 3.1 12.0 + - - -
259B ASP 3.4 0.3 + - - -
260B GLY* 3.0 52.3 + - - +
261B GLY* 3.8 7.6 - - - +
280B LEU 3.6 18.8 + - - +
281B CYS 4.0 8.1 - - - +
282B CYS 5.7 0.2 - - - -
284B GLU 6.4 0.2 - - - +
312B ARG* 5.2 7.5 - - - +
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Residues in contact with GLU 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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248B LYS* 2.6 42.0 + - - +
252B GLU* 3.0 29.8 + - - +
253B VAL* 3.3 6.1 + - - +
255B LYS* 1.3 78.2 - - + +
257B MET* 1.3 60.3 + - - +
258B THR 3.6 0.3 + - - -
259B ASP 4.5 3.2 + - - -
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Residues in contact with MET 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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218B ARG* 3.0 23.3 + - - +
220B ILE* 4.1 11.7 - - + -
239B GLU* 3.3 36.8 - - - +
241B ILE* 4.0 31.6 - - + -
246B TYR* 5.5 0.2 - - - -
253B VAL* 3.1 34.5 + - + +
254B LEU* 3.2 15.0 + - - +
256B GLU* 1.3 76.6 - - - +
258B THR* 1.3 63.2 + - + +
259B ASP 3.8 0.9 - - - -
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Residues in contact with THR 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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101A ARG* 3.0 17.3 + - - -
194B THR* 4.8 10.3 + - - +
218B ARG* 4.0 14.1 - - - +
220B ILE* 3.6 29.6 - - + -
254B LEU 2.7 22.4 + - - +
255B LYS 3.1 1.6 + - - -
257B MET* 1.3 85.0 - - + +
259B ASP* 1.3 69.9 + - - +
260B GLY 3.2 0.4 + - - -
261B GLY* 3.0 29.1 + - - -
262B VAL* 3.6 13.6 + - + -
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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