Contacts of the helix formed by residues 271 - 279 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B LEU* 4.4 14.5 - - + +
267B ASP* 3.4 29.6 + - - +
268B LEU* 3.0 20.2 + - - +
270B ASP* 1.3 78.0 - - + +
272B LEU* 1.3 64.0 + - - +
273B PRO* 3.4 1.8 - - - -
274B ASP* 3.3 14.8 + - + +
275B ALA* 3.1 21.2 + - + +
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Residues in contact with LEU 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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202B LEU* 4.6 5.4 - - + -
203B PHE* 3.5 28.5 - - + -
206B LEU* 4.8 4.0 - - + -
268B LEU 3.2 5.5 + - - +
269B ARG* 3.2 20.8 + - + +
271B GLN* 1.3 76.2 - - - +
273B PRO* 1.3 80.5 - - + +
275B ALA* 3.2 6.5 + - - +
276B CYS* 3.0 32.9 + - - -
286B ARG* 4.3 4.3 - - - +
289B ALA 4.1 5.2 - - - +
290B GLU* 4.2 23.3 - - + +
293B ALA* 3.4 32.8 - - + -
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Residues in contact with PRO 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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269B ARG 4.0 4.0 - - - +
270B ASP* 3.5 15.7 - - - +
271B GLN 3.6 0.9 - - - -
272B LEU* 1.3 99.2 - - + +
274B ASP* 1.3 62.8 + - - +
276B CYS* 3.2 1.7 + - - +
277B ARG* 3.0 51.5 + - - +
286B ARG* 3.6 26.6 + - - +
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Residues in contact with ASP 274 (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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270B ASP 5.4 1.9 - - - +
271B GLN* 3.3 16.1 + - + +
272B LEU 3.3 0.8 - - - -
273B PRO* 1.3 80.2 - - - +
275B ALA* 1.3 58.1 + - - +
277B ARG* 2.3 38.0 + - - +
278B SER* 3.0 29.1 + - - -
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Residues in contact with ALA 275 (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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200B HIS* 3.9 27.5 + - + +
202B LEU* 4.5 9.6 - - + -
203B PHE* 4.9 5.8 - - + -
271B GLN* 3.1 13.7 + - + +
272B LEU* 3.2 11.6 + - - +
274B ASP* 1.3 78.7 - - - +
276B CYS* 1.3 61.8 + - - +
278B SER* 2.6 25.8 + - - -
279B MET* 3.5 12.8 + - - +
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Residues in contact with CYS 276 (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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197B VAL* 5.5 0.2 - - - -
203B PHE* 4.2 9.0 - - - -
272B LEU* 3.0 30.1 + - - +
273B PRO 3.7 3.1 - - - +
275B ALA* 1.3 72.7 - - - +
277B ARG* 1.3 66.4 + - - +
279B MET* 3.1 13.2 + - - -
280B SER 3.3 8.1 + - - -
281B LEU* 3.4 43.3 + - + +
286B ARG* 3.8 25.4 - - - +
289B ALA* 3.8 20.4 - - - -
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Residues in contact with ARG 277 (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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273B PRO* 3.0 37.4 + - - +
274B ASP* 2.3 43.1 + - - +
276B CYS* 1.3 76.0 - - - +
278B SER* 1.3 57.5 + - - +
280B SER* 2.9 24.4 + - - +
281B LEU 5.2 0.2 - - - +
286B ARG* 4.1 17.5 - - - +
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Residues in contact with SER 278 (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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91A PRO* 3.2 21.1 - - - +
155A ALA* 3.5 25.2 - - - +
157A ARG* 5.9 1.0 + - - -
200B HIS* 4.6 4.0 + - - -
274B ASP 3.0 14.7 + - - -
275B ALA* 2.6 22.9 + - - -
277B ARG* 1.3 76.0 - - - +
279B MET* 1.3 59.5 + - - +
280B SER* 3.4 2.0 + - - -
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Residues in contact with MET 279 (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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91A PRO* 3.8 10.9 - - + -
92A GLU* 4.0 15.9 + - - +
151A PRO* 4.1 16.8 - - + +
152A ALA 4.1 4.0 - - - -
155A ALA* 4.2 11.7 - - + -
196B HIS* 3.3 51.0 + - + +
197B VAL* 4.4 7.9 - - + -
200B HIS* 3.7 27.4 - - + -
203B PHE* 5.6 3.8 - - + -
275B ALA 4.1 7.2 - - - +
276B CYS* 3.1 7.3 + - - +
277B ARG 3.1 0.6 - - - -
278B SER* 1.3 91.4 + - - +
280B SER* 1.3 68.9 + - - +
281B LEU* 3.3 21.9 + - + +
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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