Contacts of the helix formed by residues 264 - 275 (chain B) in PDB entry 5UQ9
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 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B ASN 4.3 11.9 - - - -
189B GLY* 4.1 3.3 - - - -
192B TYR* 3.2 33.5 + - - -
262B GLY 3.1 3.0 - - - -
263B THR* 1.3 76.6 - - - +
265B LYS* 1.3 63.8 + - - +
266B TRP 3.2 0.2 - - - -
267B THR* 3.3 21.0 + - - -
268B ALA 3.9 0.9 + - - -
281B ILE* 4.3 0.7 - - - +
285B VAL* 3.7 13.2 - - - +
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Residues in contact with LYS 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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272A LEU* 3.1 34.0 - - + +
273A GLU* 4.2 16.1 + - - +
192B TYR* 4.8 0.8 - - - -
260B GLN 4.6 2.4 + - - +
261B LYS* 3.4 38.2 + - - +
262B GLY 3.2 22.1 + - - +
264B GLY* 1.3 78.3 - - - +
266B TRP* 1.3 92.8 + - + +
268B ALA* 2.9 7.4 + - - +
269B ILE* 2.9 33.7 + - + +
285B VAL* 3.6 31.8 - - + +
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Residues in contact with TRP 266 (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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273A GLU* 4.9 14.4 - - + -
185B MET* 3.6 14.9 - - + +
263B THR* 3.3 36.3 - - - +
264B GLY 3.2 0.6 - - - -
265B LYS* 1.3 104.3 - - + +
267B THR* 1.3 56.3 + - - +
269B ILE* 3.6 37.5 - - + +
270B SER* 2.9 32.1 + - - -
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Residues in contact with THR 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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185B MET* 2.8 31.8 + - - +
186B VAL* 3.8 26.5 - - + +
188B ASN* 4.6 0.5 - - - +
189B GLY* 3.1 23.2 + - - -
190B ILE* 6.0 0.4 - - + -
263B THR 4.5 0.9 + - - -
264B GLY* 3.3 12.2 + - - -
265B LYS 3.1 0.8 - - - -
266B TRP* 1.3 79.1 - - - +
268B ALA* 1.3 57.4 + - - +
270B SER* 3.5 0.9 + - - -
271B ALA* 3.1 21.0 + - - +
278B VAL* 5.3 3.9 - - + +
281B ILE* 4.1 11.2 - - + -
341B LEU* 3.7 20.6 - - + +
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Residues in contact with ALA 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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272A LEU* 3.7 20.9 - - + -
286A PHE* 4.3 5.9 - - + -
264B GLY 3.9 0.8 + - - -
265B LYS 2.9 10.4 + - - +
267B THR* 1.3 75.8 - - - +
269B ILE* 1.3 60.9 + - - +
271B ALA* 3.2 9.8 + - - +
272B LEU* 3.0 30.7 + - - +
278B VAL* 5.2 1.3 - - - +
281B ILE* 4.0 11.1 - - + +
282B GLY* 3.9 26.9 - - - +
285B VAL* 4.7 2.7 - - + -
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Residues in contact with ILE 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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269A ILE* 4.0 22.7 - - + +
272A LEU* 3.7 27.4 - - + -
273A GLU* 4.0 23.8 - - + +
265B LYS* 2.9 24.6 + - + +
266B TRP* 3.6 41.1 - - + +
267B THR 3.3 0.2 - - - -
268B ALA* 1.3 74.4 - - - +
270B SER* 1.3 59.2 + - - +
272B LEU* 3.2 5.6 + - - +
273B GLU* 2.8 47.5 + - - +
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Residues in contact with SER 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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106B TYR* 4.1 12.8 + - - -
107B ARG* 5.1 0.9 + - - -
182B PHE* 4.7 5.4 - - - -
185B MET* 3.2 29.2 - - - +
266B TRP 2.9 19.9 + - - -
267B THR 3.8 5.4 - - - -
269B ILE* 1.3 76.9 - - - +
271B ALA* 1.3 60.8 + - - +
273B GLU* 3.9 12.5 + - - +
274B TYR* 3.1 34.7 + - - +
341B LEU* 3.7 8.9 - - - +
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Residues in contact with ALA 271 (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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286A PHE* 4.0 7.5 - - + -
267B THR 3.1 11.8 + - - +
268B ALA* 3.3 10.8 - - - +
269B ILE 3.2 0.4 - - - -
270B SER* 1.3 77.4 - - - +
272B LEU* 1.3 57.3 + - - +
274B TYR 3.5 0.3 + - - -
275B GLY* 2.8 8.8 + - - -
276B VAL 2.8 45.5 + - - +
278B VAL* 3.6 27.8 - - + -
341B LEU* 3.9 11.4 - - + +
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Residues in contact with LEU 272 (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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265A LYS* 3.6 23.6 - - + +
268A ALA* 3.6 29.8 - - + -
269A ILE* 3.7 22.7 - - + +
272A LEU* 3.6 28.9 - - + -
282A GLY 4.9 1.1 - - - +
285A VAL* 3.7 29.7 - - + +
286A PHE* 3.5 29.4 - - + -
289A CYS* 6.0 0.9 - - - -
268B ALA 3.0 11.7 + - - +
269B ILE* 3.7 4.9 - - - +
271B ALA* 1.3 73.2 - - - +
273B GLU* 1.3 67.3 + - - +
275B GLY* 3.4 10.3 + - - +
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Residues in contact with GLU 273 (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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265A LYS* 4.2 16.7 + - - +
269A ILE* 4.0 17.7 - - + +
106B TYR* 4.4 1.2 + - - -
107B ARG* 2.6 32.9 + - - -
269B ILE* 2.8 33.8 + - - +
270B SER* 3.9 13.5 + - - +
272B LEU* 1.3 77.3 - - - +
274B TYR* 1.3 72.0 + - + +
275B GLY 3.8 0.2 + - - -
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Residues in contact with TYR 274 (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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106B TYR* 3.0 26.5 + - - -
107B ARG* 4.6 6.5 + - - -
182B PHE* 4.0 19.3 - + - -
270B SER* 3.1 25.3 + - - +
273B GLU* 1.3 84.8 - - + +
275B GLY* 1.3 64.6 + - - +
276B VAL* 3.4 18.0 + - + +
341B LEU* 4.1 12.1 - - + -
344B GLN* 3.9 21.8 + - + +
345B ALA* 4.5 10.3 - - + -
348B GLU* 4.2 29.8 - - + -
349B PHE* 3.1 29.4 - + - -
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Residues in contact with GLY 275 (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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289A CYS* 3.4 36.7 - - - +
293A LEU* 5.7 3.6 - - - +
271B ALA 2.8 9.6 + - - -
272B LEU 3.4 9.5 + - - -
273B GLU 3.4 0.8 + - - -
274B TYR* 1.3 79.4 - - - +
276B VAL* 1.3 58.1 + - - +
277B PRO* 4.1 1.9 - - - +
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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