Contacts of the strand formed by residues 214 - 223 (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 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS 3.5 3.0 + - - +
33B ILE* 3.3 30.2 - - + -
34B SER* 2.9 22.5 + - - -
202B LEU* 4.2 9.2 - - + -
206B LEU* 5.7 3.8 - - + -
210B LEU* 4.9 4.9 - - + -
211B PRO* 3.8 41.3 - - + +
212B TYR 3.2 0.6 - - - +
213B SER* 1.3 77.9 - - - +
215B THR* 1.3 67.0 + - - +
235B ILE* 4.1 21.3 - - + -
236B LEU 3.4 11.7 - - - +
237B VAL* 4.6 10.8 - - + -
246B VAL* 6.1 2.2 - - + -
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Residues in contact with THR 215 (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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26B ASN* 5.1 1.3 - - - +
34B SER* 3.3 25.8 - - - -
36B THR* 4.5 19.8 - - + +
213B SER* 4.5 2.0 - - - +
214B VAL* 1.3 81.0 - - - +
216B VAL* 1.3 64.3 + - - +
234B LEU 3.9 0.5 - - - +
235B ILE* 3.7 1.9 - - - -
236B LEU* 2.8 58.8 + - - +
282B LYS* 4.0 20.3 - - - +
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Residues in contact with VAL 216 (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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33B ILE* 3.9 13.7 - - + -
34B SER 2.8 10.3 + - - +
35B ILE* 3.4 9.7 - - + +
36B THR* 3.0 24.9 + - - +
195B SER* 4.0 20.6 - - - +
198B ILE* 3.9 36.6 - - + -
199B ARG* 4.1 8.5 - - + +
202B LEU* 3.9 27.4 - - + -
215B THR* 1.3 78.1 - - - +
217B GLU* 1.3 70.1 + - - +
234B LEU 3.8 6.3 - - - +
235B ILE* 4.8 2.5 - - + -
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Residues in contact with GLU 217 (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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36B THR* 3.1 33.8 + - - +
37B SER* 4.4 3.4 - - - +
38B ARG* 2.7 47.5 + - - +
195B SER* 5.1 0.9 - - - -
216B VAL* 1.3 82.7 - - - +
218B ILE* 1.3 69.8 + - - +
219B GLU* 3.5 14.6 + - + +
233B GLY* 3.9 1.4 - - - -
234B LEU* 2.9 51.6 + - + +
236B LEU* 4.1 16.0 - - + +
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Residues in contact with ILE 218 (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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36B THR 4.3 2.8 + - - -
37B SER* 5.9 1.8 - - - +
38B ARG 5.9 0.9 + - - -
191B ARG* 3.1 49.5 + - + +
194B ALA* 3.5 24.9 - - + -
195B SER* 3.3 26.4 + - - +
198B ILE* 4.0 19.7 - - + -
217B GLU* 1.3 80.4 - - - +
219B GLU* 1.3 56.2 + - - +
220B ARG 3.7 24.7 - - - +
221B PHE* 4.3 6.3 - - + -
231B ILE* 3.9 17.3 - - + -
232B ASN 3.7 5.8 - - - +
233B GLY* 4.7 0.7 - - - -
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Residues in contact with GLU 219 (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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191B ARG* 4.5 3.9 + - - -
217B GLU* 3.5 11.4 + - - +
218B ILE* 1.3 71.9 - - - +
220B ARG* 1.3 61.5 + - + +
232B ASN* 3.1 25.3 + - + +
233B GLY 5.1 0.2 - - - +
234B LEU* 3.1 44.2 - - + +
278B TRP* 4.7 2.3 - - - -
285B TRP* 5.1 0.2 - - - -
293B ARG* 3.1 39.1 + - - -
303B SO4 4.8 4.0 + - - -
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Residues in contact with ARG 220 (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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191B ARG* 4.8 2.0 - - - +
218B ILE* 3.3 8.3 + - - +
219B GLU* 1.3 82.2 - - + +
221B PHE* 1.3 62.2 + - - +
222B VAL* 3.2 30.1 - - + +
230B ASP* 3.9 30.3 + - - +
231B ILE* 3.3 5.5 - - - -
232B ASN* 2.9 56.8 + - + +
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Residues in contact with PHE 221 (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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190B GLN* 3.8 35.2 - - + -
191B ARG* 3.6 47.6 + - + +
194B ALA* 4.4 3.4 - - + -
218B ILE* 4.3 9.9 - - + -
220B ARG* 1.3 74.9 - - - +
222B VAL* 1.3 68.6 + - - +
229B TYR* 3.9 30.7 - + - -
230B ASP 3.8 2.0 - - - -
231B ILE* 3.7 29.4 - - + -
269B PHE* 3.8 25.1 - + - -
305B SO4 4.5 11.4 - - - -
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Residues in contact with VAL 222 (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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220B ARG* 3.2 42.4 - - + +
221B PHE* 1.3 83.4 - - - +
223B SER* 1.3 69.0 + - - +
224B ASN* 4.5 2.2 - - + +
229B TYR* 3.3 12.8 - - - +
230B ASP* 2.8 56.2 + - + +
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Residues in contact with SER 223 (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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222B VAL* 1.3 81.2 - - - +
224B ASN* 1.3 66.0 + - - +
227B GLY* 5.4 3.1 - - - -
228B GLY 3.1 13.7 - - - -
229B TYR* 3.7 18.6 - - - -
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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