Contacts of the helix formed by residues 260 - 273 (chain B) in PDB entry 1UNN
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 CYS 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B ALA 3.3 4.0 + - - -
259B GLY* 1.3 70.1 - - - +
261B ASP* 1.3 64.8 + - - +
263B LEU* 3.8 1.3 - - - +
264B LYS* 2.9 31.7 + - - +
328B LEU* 3.5 33.7 - - - +
331B LEU* 4.5 0.4 - - - -
332B LYS* 4.2 11.0 - - - -
333B CYS 3.1 27.8 - - - +
334B GLU 2.7 12.6 + - - +
336B VAL* 3.7 32.5 - - + -
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Residues in contact with ASP 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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259B GLY* 3.3 0.6 - - - -
260B CYS* 1.3 83.4 - - - +
262B LEU* 1.3 62.4 + - - +
264B LYS* 3.3 16.3 + - - +
265B GLN* 2.9 55.6 + - - +
333B CYS 4.8 1.9 + - - +
334B GLU* 4.3 3.6 + - - +
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Residues in contact with LEU 262 (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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258B ALA* 6.1 0.2 - - + -
259B GLY* 3.4 20.7 + - - +
260B CYS 3.4 0.2 - - - -
261B ASP* 1.3 77.9 - - - +
263B LEU* 1.4 64.2 + - - +
265B GLN* 3.4 5.0 + - + +
266B ALA* 3.0 24.9 + - - +
269B ARG* 5.1 3.2 + - - +
306B LEU* 4.1 24.5 - - + +
307B ASP 5.7 4.3 - - - +
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Residues in contact with LEU 263 (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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256B LEU* 5.3 0.7 - - + -
258B ALA* 3.9 14.1 - - + +
259B GLY 2.9 16.6 + - - +
260B CYS 3.8 3.4 - - - +
262B LEU* 1.4 75.8 - - - +
264B LYS* 1.3 63.2 + - - +
266B ALA* 3.2 4.2 + - - +
267B PHE* 2.9 60.5 + - + -
290B LEU* 3.3 27.6 - - + -
292B ILE* 4.2 0.4 - - + -
306B LEU* 3.7 16.5 - - + +
328B LEU* 3.9 11.4 - - + -
336B VAL* 3.5 28.0 - - + -
338B MET* 4.3 16.8 - - + -
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Residues in contact with LYS 264 (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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260B CYS* 2.9 20.7 + - - +
261B ASP* 3.3 25.9 + - - +
263B LEU* 1.3 77.3 - - - +
265B GLN* 1.3 68.4 + - - +
267B PHE 3.4 0.3 + - - -
268B ALA* 2.9 29.2 + - + +
325B LEU* 3.4 17.3 - - + +
328B LEU* 3.6 34.9 + - + +
329B ASN* 3.0 39.7 + - - +
332B LYS* 5.5 6.7 - - - +
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Residues in contact with GLN 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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81A GLY* 4.6 9.4 - - - +
83A PRO* 6.6 0.4 - - + -
261B ASP* 2.9 53.7 + - - +
262B LEU* 4.0 5.8 - - + +
264B LYS* 1.3 92.1 - - - +
266B ALA* 1.3 57.6 + - - +
268B ALA* 3.7 11.4 - - - +
269B ARG* 3.0 52.9 + - - +
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Residues in contact with ALA 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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262B LEU 3.0 18.3 + - - +
263B LEU 3.6 4.0 - - - +
265B GLN* 1.3 74.6 - - - +
267B PHE* 1.3 61.1 + - - +
269B ARG* 3.4 14.1 + - - +
270B ALA* 2.9 28.9 + - - +
292B ILE* 4.0 5.8 - - + -
304B GLU* 3.5 30.7 - - + +
306B LEU* 3.8 22.0 - - + -
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Residues in contact with PHE 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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263B LEU* 2.9 55.2 + - + +
264B LYS 3.7 4.0 - - - +
266B ALA* 1.3 75.6 - - - +
268B ALA* 1.3 57.8 + - - +
270B ALA* 3.3 3.4 + - - +
271B ALA* 2.8 30.1 + - - +
281B VAL* 4.1 5.4 - - + -
283B LEU* 3.8 41.7 - - + -
290B LEU* 4.5 0.9 - - + -
292B ILE* 3.6 28.5 - - + -
321B VAL* 3.4 24.2 - - + +
324B VAL* 3.6 30.7 - - + -
325B LEU* 3.8 13.5 - - + -
328B LEU* 3.8 3.1 - - + -
338B MET* 5.3 3.8 - - - -
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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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81A GLY* 6.5 1.1 - - - -
264B LYS* 2.9 18.3 + - + +
265B GLN* 3.7 14.8 - - - +
267B PHE* 1.3 80.6 - - - +
269B ARG* 1.3 61.5 + - + +
271B ALA* 3.5 10.8 + - - +
272B ILE* 3.5 14.3 - - - +
325B LEU* 3.9 19.2 - - + +
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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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78A ILE 4.4 2.9 - - - +
81A GLY* 2.8 50.2 + - - +
82A LEU* 3.5 29.9 - - - +
83A PRO* 4.0 10.1 - - - +
104A SER* 3.5 8.5 + - - -
106A PHE* 3.8 20.2 - - + -
262B LEU* 5.1 3.0 + - - +
265B GLN* 3.0 33.6 + - - +
266B ALA* 3.6 15.1 - - - +
268B ALA* 1.3 71.7 - - + +
270B ALA* 1.3 67.4 + - - +
271B ALA 3.0 2.4 + - - -
272B ILE* 3.1 29.6 + - + +
273B LEU 4.1 0.3 + - - -
302B ALA* 4.6 0.2 - - - +
304B GLU* 2.8 44.6 + - - +
306B LEU* 5.7 2.8 - - - +
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Residues in contact with ALA 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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266B ALA 2.9 18.0 + - - +
267B PHE* 3.7 4.7 - - - +
269B ARG* 1.3 75.9 - - - +
271B ALA* 1.4 64.3 + - - +
273B LEU* 3.0 14.4 + - - +
281B VAL* 4.3 4.5 - - + -
292B ILE* 3.5 29.4 - - + +
293B THR 5.0 0.4 - - - -
294B ALA* 3.1 29.6 - - + +
302B ALA* 4.0 14.6 - - + -
304B GLU* 4.6 7.1 + - + -
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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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267B PHE 2.8 18.4 + - - +
268B ALA* 3.5 11.2 - - - +
269B ARG 3.0 0.6 - - - -
270B ALA* 1.4 78.2 - - - +
272B ILE* 1.3 63.5 + - - +
274B SER* 2.9 27.0 + - - +
279B ARG* 3.3 23.7 + - - +
281B VAL* 4.9 0.2 - - - -
321B VAL* 3.6 26.0 - - + -
325B LEU* 4.5 3.4 - - + -
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Residues in contact with ILE 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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74A LYS* 4.0 44.9 - - + +
77A ASP* 3.3 48.2 - - + +
78A ILE* 3.4 17.9 - - + +
81A GLY* 5.5 0.4 - - - -
268B ALA 3.5 9.6 - - - +
269B ARG* 3.1 28.0 + - + +
271B ALA* 1.3 77.8 - - - +
273B LEU* 1.3 67.8 + - + +
274B SER 3.6 4.2 + - - +
279B ARG* 5.4 0.2 - - - +
296B ASN* 4.9 0.3 + - - -
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Residues in contact with LEU 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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74A LYS* 4.1 9.2 - - + -
78A ILE* 4.3 1.8 - - + -
106A PHE* 3.9 21.1 - - + -
107A SER 3.8 12.6 - - - +
108A LEU* 3.6 27.6 - - + -
270B ALA 3.0 11.3 + - - +
272B ILE* 1.3 93.3 - - + +
274B SER* 1.3 59.9 + - - +
294B ALA* 3.8 1.8 - - - -
295B ASN* 3.2 26.5 - - - -
296B ASN* 3.4 10.9 + - - +
300B GLU* 3.8 18.4 - - + +
301B GLU* 3.2 35.9 - - - +
302B ALA* 4.2 9.2 - - + +
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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