Contacts of the helix formed by residues 260 - 272 (chain B) in PDB entry 5M7T
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 PRO 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B PRO* 3.9 10.5 - - + -
258B GLU* 3.4 19.5 - - + +
259B ILE* 1.4 85.7 - - - +
261B VAL* 1.3 64.6 + - - +
262B GLU* 3.2 30.5 - - + +
263B SER* 2.5 38.9 + - - +
264B ILE* 3.5 6.1 + - - +
303B LEU* 4.3 0.7 - - - -
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Residues in contact with VAL 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 ILE 3.5 2.2 + - - -
260B PRO* 1.3 70.5 - - - +
262B GLU* 1.3 72.1 + - + +
264B ILE* 3.1 6.8 + - - +
265B GLU* 3.1 39.0 + - - +
300B SER* 4.6 8.3 - - - -
302B GLU* 3.8 30.7 - - + -
303B LEU* 4.0 24.2 - - + +
306B ARG* 4.7 15.3 - - - +
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Residues in contact with GLU 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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260B PRO* 3.2 25.0 - - + +
261B VAL* 1.3 89.5 - - + +
263B SER* 1.3 62.8 + - - +
264B ILE 3.3 0.2 - - - -
265B GLU* 3.9 14.3 - - - +
266B GLU* 3.2 22.3 + - - +
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B VAL* 5.8 0.5 - - - +
249B TRP* 5.1 5.6 + - - -
252B PRO* 4.1 21.3 - - - +
259B ILE* 4.0 4.2 - - - +
260B PRO* 2.5 38.4 + - - +
262B GLU* 1.3 80.9 - - - +
264B ILE* 1.3 63.3 + - - +
266B GLU* 3.5 12.5 - - - +
267B VAL* 3.1 29.1 + - - +
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP* 4.0 27.8 - - + +
259B ILE* 3.8 19.3 - - + -
260B PRO 3.8 5.6 - - - +
261B VAL 3.1 7.5 + - - +
263B SER* 1.3 77.1 - - - +
265B GLU* 1.3 56.9 + - - +
267B VAL* 3.5 4.1 - - + +
268B SER* 2.8 49.9 + - - +
275B PRO* 4.2 5.4 - - + -
277B ILE* 4.1 11.2 - - + -
303B LEU* 3.6 26.9 - - + -
306B ARG* 3.8 28.3 - - + +
307B LEU* 3.9 12.1 - - + -
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Residues in contact with GLU 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 VAL* 3.1 23.0 + - - +
262B GLU* 3.9 13.4 - - - +
264B ILE* 1.3 75.7 - - - +
266B GLU* 1.3 64.7 + - - +
268B SER* 3.7 6.2 - - - -
269B LYS* 3.2 27.2 + - + +
306B ARG* 3.5 39.0 + - - +
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Residues in contact with GLU 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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228B VAL* 3.1 33.8 - - + +
229B SER* 3.8 21.9 + - - -
262B GLU 3.2 15.5 + - - +
263B SER* 3.5 12.9 - - - +
264B ILE 3.2 0.4 - - - -
265B GLU* 1.3 77.0 - - - +
267B VAL* 1.3 63.2 + - - +
269B LYS* 3.1 29.7 + - - +
270B ILE* 3.6 5.4 + - - +
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Residues in contact with VAL 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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228B VAL* 5.2 6.3 - - + -
234B LEU* 4.1 16.8 - - + -
249B TRP* 3.7 58.8 - - + +
263B SER 3.1 15.6 + - - +
264B ILE* 3.5 13.0 - - - +
266B GLU* 1.3 79.5 - - - +
268B SER* 1.3 67.0 + - - +
270B ILE* 3.1 8.0 + - - +
271B ILE* 3.0 36.2 + - + +
275B PRO* 4.5 11.7 - - + -
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Residues in contact with SER 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 ILE* 2.8 32.5 + - - +
265B GLU* 3.7 7.4 - - - -
267B VAL* 1.3 74.0 - - - +
269B LYS* 1.3 55.8 + - - +
271B ILE* 4.3 1.1 - - - -
272B LYS* 2.9 28.2 + - - -
273B ARG 3.3 24.9 + - - -
274B ALA* 3.8 4.4 - - - -
275B PRO* 3.4 16.3 - - - +
306B ARG 4.4 1.7 + - - -
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Residues in contact with LYS 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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229B SER* 6.6 0.4 - - - -
265B GLU 3.2 16.4 + - - +
266B GLU* 3.1 17.0 + - - +
268B SER* 1.3 76.3 - - - +
270B ILE* 1.3 63.5 + - - +
272B LYS* 3.3 20.0 + - - +
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Residues in contact with ILE 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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228B VAL 3.1 26.2 - - - +
229B SER* 3.5 24.2 - - - +
230B GLN* 4.6 0.4 - - - -
231B SER 3.9 20.6 - - - +
234B LEU* 3.6 32.2 - - + +
235B ARG* 3.9 29.2 - - + +
238B GLY* 3.6 12.8 - - - -
266B GLU 3.6 4.0 + - - +
267B VAL* 3.1 17.4 + - - +
269B LYS* 1.3 79.2 - - - +
271B ILE* 1.3 61.7 + - - +
272B LYS* 3.9 5.7 - - - +
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Residues in contact with ILE 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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234B LEU* 3.9 33.7 - - + +
237B VAL* 4.9 7.4 - - + -
238B GLY* 3.4 13.1 - - - +
247B VAL* 3.2 39.5 - - + -
249B TRP* 5.9 2.0 - - + -
267B VAL* 3.0 30.7 + - + +
268B SER* 4.6 0.2 - - - -
270B ILE* 1.3 79.4 - - + +
272B LYS* 1.3 62.9 + - - +
273B ARG* 2.6 52.6 + - - +
275B PRO* 4.1 16.6 - - + -
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Residues in contact with LYS 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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238B GLY* 3.5 23.8 - - - +
239B GLU* 3.9 27.0 + - - +
268B SER 2.9 15.1 + - - -
269B LYS 3.3 14.0 + - - +
270B ILE 3.9 6.1 - - - +
271B ILE* 1.3 81.8 - - - +
273B ARG* 1.3 64.8 + - - +
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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