Contacts of the helix formed by residues 252 - 261 (chain B) in PDB entry 5U03
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 ARG 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B HIS* 6.1 1.3 - - - -
247B VAL* 3.8 26.5 - - + +
248B SER* 3.0 29.4 + - - +
249B SER 2.9 13.4 + - - +
250B ILE 2.9 0.6 + - - -
251B TYR* 1.3 112.2 + - + +
253B VAL* 1.3 56.3 + - - +
254B PRO 3.5 0.2 - - - -
255B LEU* 3.2 13.7 + - + +
256B LEU* 2.9 26.4 + - - +
289B ALA* 5.4 2.2 - - - +
292B TYR 5.6 0.4 - - - -
293B ASP* 2.7 33.7 + - - -
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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
----------------------------------------------------------
18B ILE* 4.4 9.0 - - + -
19B ILE* 3.9 23.1 - - + -
22B SER* 3.4 23.3 - - - +
244B VAL* 4.5 8.1 - - + -
247B VAL* 3.9 24.9 - - + -
250B ILE* 2.8 21.8 + - - +
252B ARG* 1.3 72.9 - - - +
254B PRO* 1.3 69.3 - - + +
255B LEU 3.0 1.1 - - - -
256B LEU* 2.9 8.1 + - - +
257B LEU* 2.8 28.0 + - + +
601B ATP 4.1 15.7 - - + +
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Residues in contact with PRO 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.8 18.8 - - - +
25B THR* 4.9 0.4 - - + -
26B ILE* 4.3 18.2 - - + -
77B PHE* 4.4 2.5 - - + -
250B ILE 3.3 9.4 - - - +
251B TYR 3.3 12.8 - - - +
253B VAL* 1.3 96.8 - - + +
255B LEU* 1.3 54.7 + - - +
257B LEU* 3.3 7.0 + - + +
258B GLU 3.0 20.8 + - - -
280B LYS* 3.3 22.4 + - - +
285B TRP* 4.2 39.7 - - + +
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Residues in contact with LEU 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 TYR* 4.1 16.2 - - + +
252B ARG* 3.2 15.0 + - + +
253B VAL 3.0 0.8 - - - -
254B PRO* 1.3 74.1 - - - +
256B LEU* 1.3 67.2 + - - +
258B GLU* 3.0 23.5 + - - +
259B GLU* 2.9 29.3 + - + +
280B LYS* 4.9 1.8 - - - +
282B LEU* 4.4 13.5 - - + -
285B TRP* 3.9 27.1 - - + +
286B LYS* 4.5 8.1 - - + +
289B ALA* 3.8 28.9 - - + -
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Residues in contact with LEU 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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243B CYS 3.7 12.1 - - - +
244B VAL* 3.8 38.1 - - + -
245B HIS* 3.8 39.7 - - + +
247B VAL* 4.6 5.2 - - + -
252B ARG 2.9 13.1 + - - +
253B VAL* 3.3 9.9 - - - +
255B LEU* 1.3 75.7 - - - +
257B LEU* 1.3 67.1 + - + +
259B GLU* 2.9 31.4 + - - +
260B GLN* 2.9 32.0 + - + +
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Residues in contact with LEU 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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19B ILE* 4.8 10.8 - - + +
22B SER* 3.7 24.9 - - - -
23B VAL* 3.9 16.8 - - + -
26B ILE* 3.7 23.1 - - + -
215B VAL* 6.0 2.0 - - + -
242B ILE* 4.6 5.8 - - + -
244B VAL* 4.5 13.2 - - + -
253B VAL* 2.8 24.8 + - + +
254B PRO* 3.6 6.5 - - + +
256B LEU* 1.3 84.2 - - + +
258B GLU* 1.3 51.7 + - - +
260B GLN* 3.1 6.6 + - - +
261B GLY 2.7 29.3 + - - -
262B VAL* 3.4 37.4 + - + +
263B VAL* 5.8 0.4 - - - -
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Residues in contact with GLU 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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254B PRO 3.0 7.3 + - - +
255B LEU* 3.0 17.2 + - - +
257B LEU* 1.3 74.4 - - - +
259B GLU* 1.3 65.4 + - + +
261B GLY* 2.9 15.6 + - - +
263B VAL* 5.5 3.4 - - - -
278B PRO* 5.9 1.4 - - - +
279B ARG* 3.7 28.1 + - - +
280B LYS* 3.0 43.9 + - - +
282B LEU* 3.4 35.0 - - - +
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Residues in contact with GLU 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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245B HIS* 5.8 1.6 + - - -
255B LEU* 2.9 20.4 + - + +
256B LEU* 2.9 21.3 + - - +
258B GLU* 1.3 76.1 - - + +
260B GLN* 1.3 68.4 + - - +
261B GLY* 4.4 0.5 - - - -
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Residues in contact with GLN 260 (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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227B LYS* 5.3 10.3 + - - +
239B GLU* 5.0 13.5 - - - +
241B VAL 4.5 3.8 - - - +
242B ILE* 4.0 24.3 - - + +
243B CYS* 4.1 18.5 + - - +
256B LEU* 2.9 34.0 + - + +
257B LEU* 3.3 8.7 - - - +
258B GLU 3.1 0.2 - - - -
259B GLU* 1.3 83.1 + - - +
261B GLY* 1.3 61.9 + - - +
262B VAL* 3.6 16.2 - - + +
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Residues in contact with GLY 261 (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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239B GLU* 4.4 5.5 - - - +
257B LEU 2.7 9.8 + - - -
258B GLU* 2.9 13.6 + - - -
259B GLU 4.4 0.4 - - - -
260B GLN* 1.3 76.9 - - - +
262B VAL* 1.3 64.4 + - - +
263B VAL* 3.0 5.2 + - - -
264B ASP* 3.2 25.8 + - - +
265B TYR* 3.3 9.7 + - - +
279B ARG* 5.1 7.6 - - - -
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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