Contacts of the helix formed by residues 259 - 273 (chain B) in PDB entry 4IYM
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 ASP 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A PRO* 3.7 31.7 - - + +
482A SER 5.3 0.5 + - - -
258B ALA* 1.3 69.6 - - - +
260B LEU* 1.3 58.3 + - - +
261B ASP* 3.4 17.3 + - - +
262B GLN* 3.3 42.7 + - + +
263B ALA* 2.9 26.7 + - - +
414B TYR* 4.6 4.4 - - + -
416B ARG* 3.3 21.8 + - - +
436B ASN* 5.7 0.8 + - - -
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Residues in contact with LEU 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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254B ILE* 3.7 28.3 - - + -
255B MSE 4.5 1.8 - - - +
256B PRO 5.2 6.3 - - - +
258B ALA* 3.1 20.8 + - + +
259B ASP* 1.3 69.5 + - - +
261B ASP* 1.3 60.7 + - - +
263B ALA* 3.7 3.9 - - - +
264B ALA* 2.9 31.0 + - - +
292B THR* 3.8 24.9 - - + +
295B ARG* 3.5 52.9 - - + +
296B LEU* 4.2 9.9 - - + +
299B LYS* 3.7 17.3 - - + +
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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 ASP* 3.5 11.7 - - - +
260B LEU* 1.3 76.3 + - - +
262B GLN* 1.3 58.7 + - + +
264B ALA* 3.4 3.2 + - - +
265B ASN* 3.0 36.9 + - - +
299B LYS* 2.9 29.6 + - - +
303B MSE 5.6 0.2 - - - +
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Residues in contact with GLN 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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481A PRO* 3.6 22.2 - - - +
482A SER 5.8 0.6 - - - +
259B ASP* 3.3 34.7 + - + +
261B ASP* 1.3 76.6 - - + +
263B ALA* 1.3 65.5 + - - +
265B ASN* 3.5 7.3 + - - +
266B ALA* 3.0 26.3 + - - +
414B TYR* 4.2 10.6 - - + -
436B ASN* 6.1 0.7 - - - +
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Residues in contact with ALA 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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252B MSE 4.0 2.3 - - - +
254B ILE* 4.0 34.8 - - + -
259B ASP 2.9 16.5 + - - +
260B LEU* 3.4 6.7 + - - +
262B GLN* 1.3 74.6 - - - +
264B ALA* 1.3 58.3 + - - +
266B ALA* 3.4 2.6 + - - +
267B LEU* 3.0 34.2 + - - +
296B LEU* 4.5 4.5 - - + -
414B TYR* 3.8 24.7 - - + -
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Residues in contact with ALA 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 LEU 2.9 19.1 + - - +
261B ASP* 3.7 5.2 - - - +
263B ALA* 1.3 73.9 - - - +
265B ASN* 1.3 64.8 + - - +
267B LEU* 3.1 4.9 + - - +
268B ILE* 3.0 24.9 + - - +
296B LEU* 4.1 11.2 - - + -
299B LYS* 3.9 21.1 - - + -
300B LEU* 3.7 12.5 - - + +
303B MSE 3.9 19.5 - - + -
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Residues in contact with ASN 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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261B ASP* 3.0 24.6 + - - +
262B GLN* 3.9 7.8 - - - +
264B ALA* 1.3 75.0 - - - +
266B ALA* 1.3 63.0 + - - +
268B ILE* 3.1 8.5 + - - +
269B GLY* 3.0 19.8 + - - -
303B MSE 3.5 24.7 - - - +
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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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252B MSE 3.9 6.1 - - + -
262B GLN 3.0 19.5 + - - +
263B ALA 3.6 4.5 - - - +
264B ALA 3.3 0.2 - - - -
265B ASN* 1.3 77.1 - - - +
267B LEU* 1.3 57.6 + - - +
269B GLY* 3.8 1.3 - - - +
270B ALA* 2.8 35.4 + - - +
414B TYR* 3.4 24.7 - - + +
438B PRO* 3.6 20.1 - - + +
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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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252B MSE 3.7 24.2 - - + -
254B ILE* 4.4 0.7 - - + -
263B ALA 3.0 19.2 + - - +
264B ALA 3.1 8.2 + - - +
266B ALA* 1.3 73.7 - - - +
268B ILE* 1.3 60.1 + - - +
270B ALA* 4.9 0.2 - - - -
271B GLY* 2.8 29.3 + - - +
272B TYR* 4.0 3.3 - - - -
282B ILE* 3.7 30.5 - - + -
285B ALA* 3.9 21.5 - - + -
296B LEU* 3.8 31.0 - - + -
300B LEU* 3.8 22.4 - - + -
387B LEU* 4.3 13.3 - - + +
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Residues in contact with ILE 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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264B ALA 3.0 17.2 + - - +
265B ASN* 3.1 8.9 + - - +
267B LEU* 1.3 75.1 - - - +
269B GLY* 1.3 62.6 + - - +
272B TYR* 3.1 31.0 + - + +
273B GLY 3.9 0.9 + - - -
300B LEU* 4.0 12.3 - - + +
303B MSE 3.8 42.2 - - + +
304B VAL* 3.6 33.2 - - + +
307B LEU* 4.1 22.6 - - + +
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Residues in contact with GLY 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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265B ASN 3.0 13.2 + - - -
266B ALA* 3.8 2.5 - - - -
268B ILE* 1.3 77.9 - - - +
270B ALA* 1.3 56.9 + - - +
273B GLY* 2.9 30.6 + - - -
439B ILE* 5.1 4.1 - - - +
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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 2.8 23.4 + - - +
269B GLY* 1.3 71.3 - - - +
271B GLY* 1.3 62.9 + - - +
273B GLY 4.6 2.8 + - - +
278B ARG* 5.8 1.4 - - - -
281B ALA* 3.4 13.5 - - - +
282B ILE* 3.2 44.5 + - + +
438B PRO* 4.0 6.5 - - + +
439B ILE* 3.8 30.5 - - + +
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Residues in contact with GLY 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 LEU* 2.8 19.5 + - - +
270B ALA* 1.3 80.6 - - - +
272B TYR* 1.3 70.2 + - - +
276B GLY* 3.7 17.1 - - - -
281B ALA* 5.0 1.2 - - - +
282B ILE* 3.3 20.4 + - - +
384B GLY 4.5 1.9 - - - +
385B PRO* 4.5 4.5 - - - +
386B VAL 5.0 2.6 + - - +
387B LEU* 5.0 6.8 - - - +
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Residues in contact with TYR 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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267B LEU 4.0 4.7 - - - -
268B ILE* 3.1 23.9 + - + +
271B GLY* 1.3 77.2 - - - +
273B GLY* 1.3 68.3 + - - +
274B SER 3.5 0.2 + - - -
275B ALA* 3.0 17.5 + - - -
276B GLY 3.9 3.1 - - - +
304B VAL* 3.5 31.4 - - + +
307B LEU* 3.7 33.0 - - + -
318B ASP 4.9 0.8 - - - +
319B MSE 3.5 14.6 - - - +
365B GLY* 3.9 4.7 - - - -
366B CYS 2.6 38.7 + - - -
367B LEU* 3.6 5.7 - - - +
385B PRO* 3.5 32.5 - - + -
386B VAL 4.4 0.9 - - - -
387B LEU* 3.4 33.2 - - + +
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Residues in contact with GLY 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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95B ASP* 5.6 2.5 - - - -
268B ILE 3.9 1.2 + - - -
269B GLY* 2.9 22.0 + - - +
270B ALA 4.9 3.3 - - - +
271B GLY 3.8 0.2 - - - -
272B TYR* 1.3 75.8 + - - +
274B SER* 1.3 63.2 + - - -
276B GLY* 3.0 19.2 + - - -
278B ARG* 4.4 9.8 - - - -
318B ASP 5.0 7.0 - - - -
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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