Contacts of the helix formed by residues 261 - 270 (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 GLY 261 (chain B).
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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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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 5.6 2.2 - - + -
26B ILE* 5.2 2.5 - - + -
213B LEU* 4.6 3.1 - - + -
239B GLU* 6.0 0.9 - - - +
242B ILE* 3.7 30.7 - - + -
257B LEU* 3.4 40.1 + - + +
260B GLN* 3.6 24.2 - - + +
261B GLY* 1.3 76.4 - - - +
263B VAL* 1.3 69.8 + - + +
265B TYR* 3.2 10.3 + - - +
266B PHE* 2.9 48.6 + - + -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.6 29.2 - - + -
27B LEU* 6.2 1.8 - - + -
30B CYS* 4.0 23.6 - - - -
257B LEU 5.4 2.0 - - - +
258B GLU* 5.5 2.5 - - - -
261B GLY* 3.0 1.5 - - - -
262B VAL* 1.3 84.4 - - + +
264B ASP* 1.3 60.9 - - - +
266B PHE* 2.9 14.5 + - + +
267B LEU* 2.8 41.5 + - + +
274B ILE* 4.6 0.7 - - + -
279B ARG* 3.7 32.5 - - + -
280B LYS* 4.5 10.1 - - + -
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLU* 5.7 0.2 - - - +
261B GLY* 3.2 12.5 + - - +
263B VAL* 1.3 78.7 - - - +
265B TYR* 1.3 63.0 + - - +
267B LEU* 3.1 20.8 + - - +
268B ARG* 3.0 42.3 + - - +
279B ARG* 2.9 45.0 + - - +
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Residues in contact with TYR 265 (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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212B ASP* 2.9 22.2 + - + +
213B LEU* 3.6 33.4 - - + -
239B GLU* 3.8 28.3 - - + +
240B GLN* 2.9 39.9 + - + -
261B GLY 3.3 4.1 + - - +
262B VAL* 3.2 15.0 + - - +
263B VAL 3.1 0.2 - - - -
264B ASP* 1.3 77.6 - - - +
266B PHE* 1.3 56.2 + + - +
268B ARG* 2.9 20.3 + - + +
269B ARG* 2.7 68.5 + - + +
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.7 9.6 - - + -
23B VAL* 4.2 29.2 - - + -
26B ILE* 6.4 0.7 - - + -
27B LEU* 5.1 14.1 - - + -
176B CYS* 3.6 30.7 - - - -
178B ILE* 4.0 11.7 - - + -
213B LEU* 3.6 22.4 - - + -
262B VAL* 2.9 43.5 + - + -
263B VAL* 2.9 13.4 + - + +
265B TYR* 1.3 79.9 - + - +
267B LEU* 1.3 59.4 + - + +
269B ARG* 4.2 2.2 - - + +
270B LEU* 2.7 55.4 + - + +
272B LEU* 5.2 3.4 - - + -
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Residues in contact with LEU 267 (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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30B CYS* 5.6 3.8 - - + -
263B VAL* 2.8 26.4 + - + +
264B ASP* 3.1 27.8 + - - +
266B PHE* 1.3 76.1 - - + +
268B ARG* 1.3 60.8 + - + +
271B ASP* 3.1 7.4 + - - -
272B LEU* 3.0 55.8 + - + +
273B PRO 3.9 4.7 - - - +
274B ILE* 3.5 44.4 - - + -
279B ARG* 5.7 0.4 - - + -
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Residues in contact with ARG 268 (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 ARG* 5.5 1.4 + - - -
239B GLU* 2.7 39.0 + - - -
264B ASP* 3.0 35.7 + - - +
265B TYR* 2.9 20.3 + - + +
267B LEU* 1.3 79.8 - - + +
269B ARG* 1.3 58.9 + - - +
271B ASP* 3.1 20.9 - - - +
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Residues in contact with ARG 269 (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 ARG* 2.9 63.6 + - - +
173B GLU* 3.5 10.0 - - - +
175B PHE* 3.1 22.8 + - - -
176B CYS* 4.8 5.2 - - - -
212B ASP* 2.8 37.8 + - + +
265B TYR* 2.7 50.9 + - + +
266B PHE* 3.9 3.6 - - - +
268B ARG* 1.3 75.9 - - - +
270B LEU* 1.3 67.1 + - + +
271B ASP* 3.3 2.8 + - - +
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Residues in contact with LEU 270 (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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2B LYS* 2.8 44.9 + - + -
4B ILE* 4.2 19.1 - - + -
27B LEU* 5.8 2.2 - - + -
142B VAL* 5.4 0.7 - - + -
173B GLU 3.1 25.1 - - - +
175B PHE 4.3 8.7 - - - +
176B CYS* 4.1 20.0 - - + -
266B PHE* 2.7 41.4 + - + +
269B ARG* 1.3 77.0 - - + +
271B ASP* 1.3 71.5 + - - +
272B LEU* 3.7 26.2 - - + -
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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