Contacts of the helix formed by residues 247 - 258 (chain B) in PDB entry 3UDB
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 SER 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 2.5 35.2 + - - -
246B ILE* 1.3 77.4 - - - +
248B PRO* 1.3 67.1 - - - +
249B GLU* 2.9 23.7 + - - -
250B CYS* 3.1 11.1 + - - +
251B ARG* 3.0 21.3 + - - +
276B TRP* 3.7 1.9 - - - -
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Residues in contact with PRO 248 (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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246B ILE 3.5 1.8 - - - +
247B SER* 1.3 88.4 - - - +
249B GLU* 1.3 70.3 + - - +
251B ARG* 3.5 13.1 - - + +
252B HIS* 2.8 28.9 + - - +
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Residues in contact with GLU 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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247B SER* 2.9 26.0 + - - +
248B PRO* 1.3 90.7 - - - +
250B CYS* 1.3 62.2 + - - +
252B HIS* 3.2 5.1 + - - -
253B LEU* 3.0 19.8 + - - +
274B HIS* 3.3 18.5 - - + -
275B GLU* 3.4 27.6 - - + +
276B TRP* 4.1 19.7 - - + +
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Residues in contact with CYS 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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114B GLU* 3.8 3.6 - - - +
207B LEU* 5.2 2.0 - - - -
211B LEU* 3.5 25.6 - - - -
246B ILE* 3.2 24.7 - - + -
247B SER* 3.1 18.6 + - - +
249B GLU* 1.3 79.6 - - - +
251B ARG* 1.3 61.3 + - - +
253B LEU* 3.4 3.1 + - - +
254B ILE* 3.2 26.4 + - - +
276B TRP* 3.3 38.5 - - - +
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Residues in contact with ARG 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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238B TYR* 5.6 0.2 + - - -
240B ILE* 4.1 37.6 + - + +
244B VAL 4.4 8.5 + - - -
245B HIS* 4.9 1.2 - - - +
246B ILE* 3.6 40.3 + - + +
247B SER 3.0 11.6 + - - +
248B PRO* 3.2 15.0 + - + +
250B CYS* 1.3 76.9 - - - +
252B HIS* 1.3 61.5 + - - +
254B ILE* 3.8 8.3 + - - +
255B SER* 3.3 21.3 + - - -
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO 2.8 16.4 + - - +
249B GLU* 3.5 8.1 - - - +
250B CYS 3.1 0.4 - - - -
251B ARG* 1.3 76.0 - - - +
253B LEU* 1.3 65.0 + - - +
255B SER* 2.7 28.8 + - - -
256B ARG* 3.0 38.4 + - + +
274B HIS* 3.0 26.8 + + + +
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Residues in contact with LEU 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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121B PHE* 4.0 21.3 - - + -
207B LEU* 4.4 6.1 - - + -
249B GLU 3.0 12.7 + - - +
250B CYS* 3.7 8.7 - - - +
252B HIS* 1.3 76.3 - - - +
254B ILE* 1.3 63.0 + - - +
256B ARG* 3.0 12.8 + - - +
257B ILE* 3.1 29.1 + - + +
266B ILE* 4.3 15.5 - - + -
271B ILE* 4.4 14.4 - - + -
274B HIS* 3.7 30.8 + - + +
276B TRP* 3.6 33.2 - - + -
277B PHE* 5.2 1.8 - - + -
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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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204B GLY* 5.7 2.7 - - - +
207B LEU* 3.8 22.4 - - + -
208B TYR* 5.0 13.9 - - + +
211B LEU* 3.9 26.9 - - + -
238B TYR* 4.0 16.4 - - + +
240B ILE* 4.4 19.7 - - + -
246B ILE* 5.1 0.9 - - + -
250B CYS* 3.2 18.4 + - - +
251B ARG* 4.0 6.3 - - - +
253B LEU* 1.3 77.9 - - - +
255B SER* 1.3 63.2 + - - +
257B ILE* 3.2 9.1 + - + +
258B PHE* 3.1 48.8 + - + +
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Residues in contact with SER 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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238B TYR* 3.9 16.8 - - - -
251B ARG 3.3 10.5 + - - -
252B HIS* 2.7 33.8 + - - -
254B ILE* 1.3 79.1 - - - +
256B ARG* 1.3 61.7 + - - +
257B ILE 3.6 0.2 + - - -
258B PHE* 3.8 8.1 + - - +
259B VAL* 3.5 15.2 - - - +
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Residues in contact with ARG 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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252B HIS* 3.0 46.9 + - + +
253B LEU* 3.0 9.6 + - - +
255B SER* 1.3 80.2 - - - +
257B ILE* 1.3 60.6 + - - +
259B VAL* 3.5 17.7 - - - +
264B LYS 3.2 24.7 + - - -
265B ARG* 3.9 0.4 - - - -
266B ILE* 3.2 66.2 + - + +
270B GLU* 4.3 12.3 + - - -
274B HIS* 5.4 0.4 - - - +
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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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121B PHE* 4.4 16.6 - - + -
200B VAL* 3.6 29.2 - - + +
201B TRP* 3.9 11.2 - - - -
203B CYS* 5.9 0.2 - - + -
204B GLY* 3.6 27.8 - - - +
207B LEU* 4.8 3.8 - - + -
253B LEU* 3.1 33.7 + - + +
254B ILE* 3.2 9.2 + - - +
256B ARG* 1.3 77.5 - - - +
258B PHE* 1.3 61.6 + - + +
259B VAL 2.9 12.3 + - - -
265B ARG* 3.3 21.6 + - - -
266B ILE* 3.7 20.9 - - + -
271B ILE* 4.4 5.2 - - + -
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Residues in contact with PHE 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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201B TRP* 3.8 35.4 - + + -
204B GLY* 3.6 26.2 - - - -
205B VAL* 3.7 28.3 - - + -
208B TYR* 4.4 17.3 - + + -
216B PRO* 4.5 11.7 - - + -
217B PHE* 4.5 7.2 - + - -
236B VAL* 3.3 26.4 - - + +
238B TYR* 3.8 25.0 + + + +
254B ILE* 3.1 37.3 + - + +
255B SER 3.9 6.0 - - - +
256B ARG 3.5 0.4 - - - -
257B ILE* 1.3 77.5 - - + +
259B VAL* 1.3 61.1 + - - +
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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