Contacts of the strand formed by residues 273 - 281 (chain B) in PDB entry 3IEU
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 VAL 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B TYR* 3.5 13.7 - - + +
231B ILE* 3.9 22.9 - - + -
262B ARG* 3.3 33.1 + - + +
265B MET* 4.1 18.6 - - + +
266B GLN* 2.9 47.5 + - + +
269B PHE* 4.5 9.0 - - + -
271B ALA 3.8 2.0 - - - +
272B PRO* 1.3 81.8 - - - +
274B HIS* 1.3 67.5 + - - +
275B LEU* 4.2 3.1 - - + +
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Residues in contact with HIS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TYR 2.9 15.8 + - - +
230B ASP* 3.4 18.5 + - + +
231B ILE 2.9 27.4 + - - +
262B ARG* 4.9 1.3 - - - +
273B VAL* 1.3 71.3 - - - +
275B LEU* 1.3 62.8 + - - +
276B GLU* 3.1 43.1 - - + +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 5.0 1.8 - - + -
231B ILE* 3.5 34.8 - - + +
233B GLY* 4.5 2.0 - - - +
258B GLY* 3.7 13.4 - - - +
261B ALA* 3.8 5.8 - - + -
262B ARG* 3.6 36.3 - - + +
265B MET* 3.4 32.8 - - + -
273B VAL* 3.8 6.4 + - + -
274B HIS* 1.3 78.3 + - - +
276B GLU* 1.3 63.1 + - - +
277B LEU* 3.5 31.7 + - + -
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Residues in contact with GLU 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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230B ASP* 5.1 0.9 - - - +
231B ILE 3.0 7.5 + - - -
232B ASN* 3.4 31.6 + - - +
233B GLY 2.6 34.2 + - - +
274B HIS* 3.1 33.2 - - + +
275B LEU* 1.3 73.9 - - - +
277B LEU* 1.3 60.6 + - - +
278B TRP* 3.8 21.1 + - - +
296B GLY 5.2 6.6 - - - +
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Residues in contact with LEU 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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198B ILE* 4.2 15.0 - - + -
233B GLY* 3.3 13.7 - - - +
235B ILE* 4.3 13.7 - - + -
254B ILE* 3.9 33.6 - - + +
257B ILE* 3.9 12.1 - - + +
258B GLY* 3.6 33.0 - - - +
261B ALA* 5.3 0.4 - - + -
275B LEU* 3.5 33.5 + - + -
276B GLU* 1.3 82.9 - - - +
278B TRP* 1.3 65.8 + - - +
279B VAL* 4.3 0.5 + - - +
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Residues in contact with TRP 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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219B GLU* 4.7 3.8 - - - -
232B ASN* 4.8 6.7 - - - +
233B GLY 2.9 15.5 + - - +
234B LEU* 3.5 13.2 - - + +
235B ILE* 2.7 35.0 + - - +
276B GLU* 3.8 26.9 + - + +
277B LEU* 1.3 82.9 - - - +
279B VAL* 1.3 60.0 + - - +
280B LYS 4.0 0.2 - - - -
285B TRP* 4.2 11.4 - + + -
289B GLU* 4.7 4.3 - - + -
292B LEU* 3.8 28.5 - - + -
293B ARG* 3.1 74.4 - - + +
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Residues in contact with VAL 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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235B ILE* 3.3 16.2 - - + +
237B VAL* 4.6 5.6 - - + -
243B LYS* 3.5 49.9 - - + +
246B VAL* 3.8 31.2 - - + -
247B ILE* 4.3 14.5 - - + +
254B ILE* 4.1 23.6 - - + -
277B LEU 5.2 0.2 - - - +
278B TRP* 1.3 76.8 - - - +
280B LYS* 1.3 60.3 + - - +
285B TRP* 4.2 7.8 - - - -
289B GLU* 4.7 4.0 - - - +
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Residues in contact with LYS 280 (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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38B ARG* 4.6 16.0 - - - +
234B LEU* 4.0 13.9 - - + +
235B ILE 2.8 7.1 + - - -
236B LEU* 3.3 24.9 - - + +
237B VAL* 3.0 26.6 + - - +
243B LYS* 4.7 1.1 - - - -
278B TRP 3.9 0.2 + - - -
279B VAL* 1.3 73.0 - - - +
281B VAL* 1.3 76.5 + - - +
282B LYS 4.2 8.0 + - - -
284B GLY 4.7 2.0 - - - +
285B TRP* 3.4 59.7 - - + +
289B GLU* 5.3 1.1 - - - -
303B SO4 5.1 3.6 + - - -
307B SO4 3.5 32.8 + - - -
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Residues in contact with VAL 281 (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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237B VAL* 3.4 7.0 - - + +
238B GLU 3.2 27.1 - - - +
239B ARG* 3.5 18.6 - - - +
240B GLU* 3.7 11.7 - - + +
243B LYS* 3.1 48.2 - - + +
280B LYS* 1.3 80.2 - - - +
282B LYS* 1.3 67.0 + - - +
283B SER* 3.1 9.4 + - - +
284B GLY 3.0 26.2 + - - +
285B TRP 5.8 0.2 - - - +
289B GLU* 5.4 1.0 + - - -
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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