Contacts of the helix formed by residues 271 - 279 (chain A) in PDB entry 5I1U
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 GLN 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A LEU* 3.7 9.9 - - + +
264A ARG* 5.0 6.9 + - - +
267A ASP* 3.3 27.8 + - - +
268A LEU* 3.0 29.8 + - - +
270A ASP* 1.3 77.8 - - + +
272A LEU* 1.3 64.7 + - - +
273A PRO* 3.4 1.8 - - - -
274A ASP* 3.3 12.8 + - + +
275A ALA* 3.1 21.1 + - - +
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Residues in contact with LEU 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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202A LEU* 4.1 12.1 - - + -
203A PHE* 3.5 27.1 - - + -
206A LEU* 4.9 4.9 - - + -
268A LEU 3.2 5.0 + - - +
269A ARG* 3.2 21.2 + - - +
271A GLN* 1.3 73.6 - - - +
273A PRO* 1.4 81.0 - - + +
275A ALA* 3.0 3.8 + - - +
276A CYS* 2.9 35.5 + - - -
286A ARG* 4.2 4.5 - - - +
289A ALA 4.2 4.3 - - - +
290A GLU* 4.2 23.3 - - + +
293A ALA* 3.4 33.0 - - + -
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Residues in contact with PRO 273 (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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269A ARG 3.9 4.0 - - - +
270A ASP* 3.6 16.2 - - - +
271A GLN 3.7 0.9 - - - -
272A LEU* 1.4 96.5 - - + +
274A ASP* 1.3 56.5 + - - +
276A CYS* 3.2 1.7 + - - +
277A ARG* 2.9 54.4 + - - +
286A ARG* 3.4 31.3 + - - +
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Residues in contact with ASP 274 (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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270A ASP 6.0 0.9 - - - -
271A GLN* 3.3 12.8 + - + +
272A LEU 3.3 0.6 - - - -
273A PRO* 1.3 78.8 - - - +
275A ALA* 1.3 59.2 + - - +
277A ARG* 2.5 38.1 + - - +
278A SER* 2.9 30.7 + - - -
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Residues in contact with ALA 275 (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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200A HIS* 3.9 28.5 + - + +
202A LEU* 3.9 14.6 - - + -
203A PHE* 4.9 6.7 - - + -
271A GLN 3.1 12.6 + - - +
272A LEU* 3.0 9.5 + - - +
274A ASP* 1.3 77.0 - - - +
276A CYS* 1.3 62.4 + - - +
278A SER* 2.7 24.9 + - - -
279A MET* 3.5 13.4 + - - +
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Residues in contact with CYS 276 (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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203A PHE* 4.1 10.1 - - - -
272A LEU* 2.9 39.5 + - - +
273A PRO 3.7 2.9 - - - +
275A ALA* 1.3 74.9 - - - +
277A ARG* 1.3 65.6 + - - +
279A MET* 3.1 13.2 + - - -
280A SER 3.3 7.8 + - - -
281A LEU* 3.5 44.0 + - + +
286A ARG* 3.7 24.0 - - - +
289A ALA* 4.0 12.1 - - - -
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Residues in contact with ARG 277 (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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273A PRO* 2.9 37.1 + - - +
274A ASP* 2.5 41.0 + - - +
276A CYS* 1.3 76.3 - - - +
278A SER* 1.3 62.2 + - - +
280A SER* 3.0 19.2 + - - +
281A LEU 5.2 0.2 - - - +
286A ARG* 4.2 16.0 - - - +
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Residues in contact with SER 278 (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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200A HIS* 4.7 4.3 + - - -
274A ASP 2.9 16.7 + - - -
275A ALA* 2.7 21.3 + - - -
276A CYS 3.2 0.4 - - - -
277A ARG* 1.3 75.9 - - - +
279A MET* 1.3 60.1 + - - +
280A SER* 3.4 1.8 + - - -
91B PRO* 3.5 20.6 - - - +
155B ALA* 3.6 23.8 - - - +
158B THR* 5.9 1.8 - - - -
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Residues in contact with MET 279 (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 HIS* 3.6 41.2 + - + +
197A VAL* 4.4 7.0 - - + -
200A HIS* 3.6 31.2 - - + -
203A PHE* 5.5 4.0 - - + -
275A ALA 4.1 8.7 - - - +
276A CYS* 3.1 8.6 + - - +
278A SER* 1.3 86.6 + - - +
280A SER* 1.3 70.1 + - - +
281A LEU* 3.2 26.6 + - + +
91B PRO* 3.8 11.9 - - + -
92B GLU* 3.6 17.8 + - - +
151B PRO* 4.1 22.9 - - + +
152B ALA 4.1 4.5 - - - -
155B ALA* 4.5 2.7 - - + -
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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