Contacts of the helix formed by residues 261 - 272 (chain A) in PDB entry 1MF8
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 SER 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 4.1 9.6 - - - -
239A PHE* 3.7 6.7 - - - -
242A GLU* 3.6 16.6 - - - -
246A GLU 2.8 28.9 + - - -
247A HIS* 3.3 7.6 + - - -
260A TYR* 1.3 76.3 - - - +
262A TYR* 1.3 65.9 + - - +
263A PRO* 2.9 16.8 - - - +
264A ALA* 3.3 9.7 + - - +
265A VAL* 3.0 25.5 + - - +
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Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 3.8 17.7 - + + -
240A GLY* 3.5 12.3 - - - +
242A GLU* 3.1 25.7 + - - +
245A GLN* 5.9 1.6 - - - -
261A SER* 1.3 73.9 - - - +
263A PRO* 1.4 65.7 - - + +
265A VAL* 3.7 1.7 + - - +
266A CYS* 3.2 45.2 + - + -
292A ARG* 3.4 61.0 + - + -
293A LYS 2.9 20.4 + - - -
294A SER* 3.6 0.3 - - - -
295A GLN* 3.4 19.7 + - + +
301A SER* 3.7 20.2 - - - -
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Residues in contact with PRO 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLU* 4.0 6.1 - - + +
244A THR 4.6 2.2 - - - +
245A GLN* 3.5 55.2 - - - +
247A HIS* 5.0 7.4 - - + +
261A SER* 2.9 19.1 - - - +
262A TYR* 1.4 98.4 - - + +
264A ALA* 1.3 64.5 + - - +
265A VAL 3.2 1.8 - - - -
266A CYS* 3.4 4.6 + - + +
267A GLU* 3.0 27.5 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 4.3 3.8 - - + +
247A HIS* 3.9 32.2 - - + -
248A PHE* 4.2 18.0 - - + -
260A TYR* 4.3 4.9 - - + -
261A SER* 3.3 28.2 + - - +
263A PRO* 1.3 78.8 - - - +
265A VAL* 1.3 63.1 + - - +
267A GLU* 3.3 3.5 + - - +
268A PHE* 3.2 22.5 + - - +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 3.9 13.2 - - + -
239A PHE* 3.4 23.3 - - + -
260A TYR* 3.8 18.6 - - + -
261A SER 3.0 17.9 + - - +
262A TYR 3.8 4.9 - - - +
263A PRO 3.2 0.4 - - - -
264A ALA* 1.3 76.1 - - - +
266A CYS* 1.3 56.6 + - - +
267A GLU 3.1 0.5 + - - -
268A PHE* 3.1 2.9 + - - +
269A LEU* 2.7 44.6 + - + +
277A ILE* 3.7 30.5 - - + -
301A SER* 4.1 13.2 - - - +
302A LEU* 4.9 2.0 - - + -
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Residues in contact with CYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A TYR* 3.2 50.7 + - + +
263A PRO* 3.4 6.0 + - + +
265A VAL* 1.3 78.6 - - - +
267A GLU* 1.3 53.8 + - - +
269A LEU* 3.9 9.0 - - - -
270A GLN* 2.7 51.3 + - - +
294A SER* 4.2 18.2 - - - -
295A GLN* 5.1 1.8 - - - -
301A SER* 4.3 11.0 - - - -
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ASN* 5.9 1.4 + - - -
247A HIS* 3.1 30.8 + - - -
263A PRO 3.0 16.7 + - - +
264A ALA* 3.6 5.6 - - - +
266A CYS* 1.3 74.8 - - - +
268A PHE* 1.3 65.1 + - - +
270A GLN* 4.2 3.9 - - - +
271A HIS* 3.1 29.8 + - + +
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Residues in contact with PHE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 3.5 26.5 - - + -
202A LEU* 4.0 20.6 - - + -
206A ILE* 3.5 29.2 - - + -
207A ASN* 3.3 20.4 - - - -
208A THR 4.3 1.8 - - - -
209A LEU* 3.8 16.4 - - + -
212A ILE* 5.1 1.8 - - + -
264A ALA 3.2 9.9 + - - +
265A VAL 3.1 6.3 + - - +
267A GLU* 1.3 76.3 - - - +
269A LEU* 1.3 73.0 + - - +
271A HIS* 4.6 1.3 - - - -
272A ASN* 2.7 52.3 + - - +
274A LEU* 3.3 23.3 - - + -
277A ILE* 4.4 11.4 - - + -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 2.7 34.7 + - + +
266A CYS* 4.1 9.4 - - - +
268A PHE* 1.3 79.5 - - - +
270A GLN* 1.3 58.7 + - + +
272A ASN 3.3 0.3 + - - -
273A ASN 2.9 7.4 + - - -
274A LEU* 2.7 56.6 + - + +
275A LEU 3.5 18.4 - - - +
276A SER* 4.1 9.9 - - - -
277A ILE* 3.5 30.3 - - + -
294A SER* 5.2 4.9 - - - +
301A SER* 3.5 29.2 - - - +
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A CYS* 2.7 39.4 + - - +
267A GLU* 4.2 3.9 - - - +
269A LEU* 1.3 71.8 - - + +
271A HIS* 1.3 60.0 + - - +
272A ASN 3.0 1.3 - - - -
273A ASN* 2.7 26.1 + - - +
274A LEU 5.2 0.4 - - - -
294A SER* 5.2 4.4 + - - +
295A GLN* 6.1 2.2 - - - +
296A THR* 3.9 24.5 + - + +
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 3.6 27.0 - - + +
208A THR* 3.4 23.8 - - + +
267A GLU* 3.1 20.8 + - + +
268A PHE* 3.9 2.9 - - - +
270A GLN* 1.3 78.8 - - - +
272A ASN* 1.3 62.1 + - - +
273A ASN* 3.6 1.2 + - - +
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Residues in contact with ASN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ASN 2.8 23.0 + - - -
208A THR* 3.3 9.9 - - - -
209A LEU* 3.2 34.0 + - + +
268A PHE* 2.7 49.3 + - - +
271A HIS* 1.3 81.3 - - - +
273A ASN* 1.3 71.0 + - - +
274A LEU* 3.1 25.4 + - + +
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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