Contacts of the helix formed by residues 265 - 272 (chain A) in PDB entry 5TE0
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A PHE 3.0 15.3 + - - +
263A GLY 4.0 0.2 + - - -
264A GLU* 1.3 75.8 - - - +
266A GLN* 1.3 57.4 + - - +
267A VAL* 3.7 3.5 + - - +
268A ALA* 3.1 26.7 + - - +
269A ILE* 3.0 30.9 + - - +
406A GOL 3.3 21.8 + - - -
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Residues in contact with GLN 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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218A LYS* 4.9 14.1 - - - +
223A LEU* 3.8 28.2 - - + +
226A ARG* 4.9 4.6 - - - +
231A VAL* 3.8 27.8 + - + +
264A GLU 3.3 1.2 + - - +
265A SER* 1.3 69.1 - - - +
267A VAL* 1.3 61.2 + - + +
269A ILE* 3.5 7.1 + - - +
270A CYS* 3.0 34.1 + - - -
406A GOL 3.0 34.3 + - - +
410A GOL 5.2 2.2 + - - -
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Residues in contact with VAL 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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265A SER* 3.3 7.1 - - - +
266A GLN* 1.3 74.5 - - + +
268A ALA* 1.3 65.3 + - - +
270A CYS* 3.2 6.7 + - - +
271A ASP* 3.0 39.0 + - - +
406A GOL 3.7 16.9 - - - +
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Residues in contact with ALA 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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262A PHE* 3.6 13.2 - - + +
265A SER* 3.1 28.6 + - - +
267A VAL* 1.3 78.4 - - - +
269A ILE* 1.4 55.8 + - - +
271A ASP* 3.3 1.5 + - - -
272A GLY* 2.9 8.5 + - - -
273A ASN* 2.9 58.6 + - + +
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Residues in contact with ILE 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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223A LEU* 3.5 41.7 - - + +
224A SER* 4.7 5.6 - - - +
226A ARG 3.3 23.6 - - - +
228A PRO* 3.6 11.2 - - + +
231A VAL* 3.9 14.6 - - + -
246A TRP* 3.4 26.0 - - + +
262A PHE* 3.6 30.5 - - + -
263A GLY 5.0 0.9 - - - +
265A SER 3.0 23.5 + - - +
266A GLN* 3.6 8.7 - - - +
268A ALA* 1.4 74.6 - - - +
270A CYS* 1.4 58.7 + - - +
272A GLY 3.0 15.4 + - - -
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Residues in contact with CYS 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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228A PRO* 3.9 15.6 - - + +
231A VAL* 3.6 28.0 - - - -
232A ASN* 3.8 27.1 - - + +
266A GLN 3.0 20.9 + - - +
267A VAL* 4.0 3.8 - - - +
269A ILE* 1.4 76.0 - - - +
271A ASP* 1.3 63.2 + - - +
272A GLY 3.5 0.5 + - - -
296A PRO* 3.5 17.2 - - - +
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Residues in contact with ASP 271 (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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267A VAL* 3.0 34.6 + - - +
268A ALA* 3.9 4.2 - - - +
270A CYS* 1.3 77.0 - - - +
272A GLY* 1.3 60.6 + - - +
273A ASN* 3.3 16.5 + - + +
296A PRO* 3.9 8.6 - - - +
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Residues in contact with GLY 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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246A TRP* 4.0 6.5 - - - -
262A PHE* 3.6 12.1 - - - -
268A ALA 2.9 6.0 + - - -
269A ILE 3.0 11.4 + - - -
270A CYS 3.3 0.8 + - - -
271A ASP* 1.3 78.0 - - - +
273A ASN* 1.3 58.1 + - - +
274A PHE* 3.3 20.7 + - - +
291A ARG* 5.7 2.3 + - - -
294A LEU 4.8 3.3 - - - +
296A PRO* 3.7 17.2 - - - +
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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