Contacts of the strand formed by residues 241 - 251 (chain D) in PDB entry 3HN3
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 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D VAL* 3.2 9.0 - - - +
238D GLU* 2.6 50.4 + - - -
240D ASP* 1.3 76.0 + - - +
242D GLY* 1.3 62.5 + - - +
243D LEU* 4.3 1.7 - - - +
281D LYS* 3.1 43.5 - - - +
282D VAL 3.5 8.4 + - - -
283D PRO* 4.6 2.4 - - - -
284D GLY 4.7 1.6 - - - +
285D VAL* 3.7 2.9 - - - -
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Residues in contact with GLY 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER 3.8 4.7 - - - -
237D VAL* 4.8 0.2 - - - -
241D SER* 1.3 76.0 + - - +
243D LEU* 1.3 61.6 + - - +
244D VAL 4.2 0.2 - - - -
280D LEU 3.7 0.5 - - - +
281D LYS* 3.4 4.3 - - - -
282D VAL* 2.7 44.6 + - - +
285D VAL* 3.4 26.4 - - - +
326D ILE* 4.2 6.3 - - - -
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D THR 3.8 0.5 - - - +
235D THR* 3.2 8.0 - - - -
236D SER* 2.9 55.8 + - - +
238D GLU* 3.2 39.7 - - + +
241D SER* 4.3 3.6 - - - +
242D GLY* 1.3 80.2 - - - +
244D VAL* 1.3 62.3 + - - +
245D ASN* 3.9 3.1 + - - +
279D GLN* 3.4 34.5 - - + +
280D LEU 3.4 5.6 - - - +
281D LYS* 4.1 22.9 - - + -
326D ILE* 4.6 0.8 - - - +
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D VAL* 3.8 28.9 - - + -
234D THR 3.8 2.2 - - - -
235D THR* 4.5 1.3 - - + -
243D LEU* 1.3 73.7 - - - +
245D ASN* 1.3 64.3 + - - +
246D TYR* 3.7 3.2 + - + -
262D LEU* 3.8 25.8 - - + -
279D GLN* 3.5 0.9 - - - -
280D LEU* 2.8 49.5 + - + +
282D VAL* 4.1 5.8 - - + -
303D LEU* 5.1 4.5 - - + -
324D VAL* 4.2 12.3 - - + -
326D ILE* 3.6 33.9 - - + -
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Residues in contact with ASN 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D THR 3.7 0.7 - - - +
233D VAL* 3.2 8.5 - - - +
234D THR* 2.9 47.7 + - - +
236D SER* 5.4 1.2 + - - -
243D LEU* 4.6 4.2 - - - +
244D VAL* 1.3 73.7 + - - +
246D TYR* 1.3 58.6 + - - +
247D GLN* 5.7 6.5 - - - +
278D GLY 3.5 7.3 + - - +
279D GLN* 2.7 41.6 + - - +
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Residues in contact with TYR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ILE* 5.4 0.4 - - + -
232D THR 3.3 6.3 - - - +
233D VAL* 4.4 2.9 - - + -
244D VAL* 4.0 4.3 - - + -
245D ASN* 1.3 74.1 - - - +
247D GLN* 1.3 69.2 + - - +
248D ILE* 3.9 19.7 - - + -
260D VAL* 4.1 20.0 - - + -
273D GLY* 3.7 4.9 - - - -
274D THR 2.9 31.2 + - - -
275D GLY 3.8 14.4 - - - -
277D GLN* 3.2 12.9 - - - +
278D GLY* 3.0 65.8 + - - +
279D GLN 4.0 0.2 - - - -
280D LEU* 3.7 37.2 - - + +
303D LEU* 4.2 21.5 - - + -
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Residues in contact with GLN 247 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D ASP 4.0 0.3 - - - +
231D ILE* 3.4 4.3 - - - +
232D THR* 2.9 58.7 + - - +
245D ASN* 6.0 6.9 - - + +
246D TYR* 1.3 81.2 - - - +
248D ILE* 1.3 62.9 + - - +
276D THR 3.3 5.8 - - - +
277D GLN* 3.9 26.3 + - + +
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Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ILE* 4.1 20.2 - - + -
230D ASP 3.5 8.7 - - - +
231D ILE* 4.6 12.6 - - + -
246D TYR* 3.9 15.7 - - + -
247D GLN* 1.3 80.5 - - - +
249D SER* 1.3 67.1 + - - +
250D VAL* 4.5 1.8 - - + -
258D LEU* 3.9 25.6 - - + -
260D VAL* 3.5 32.5 - - + -
275D GLY 4.2 8.3 - - - +
276D THR* 2.6 36.3 + - - +
303D LEU* 5.6 0.4 - - + -
305D VAL* 3.7 17.3 - - + -
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Residues in contact with SER 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ILE* 3.8 2.3 - - - -
229D ASP* 2.8 41.9 + - - +
230D ASP* 2.9 30.1 + - - +
248D ILE* 1.3 75.8 - - - +
250D VAL* 1.3 61.8 + - - +
251D LYS* 5.1 2.6 - - - +
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Residues in contact with VAL 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D THR* 3.7 26.0 - - + -
227D TYR 3.5 11.2 - - - +
228D ILE* 4.9 2.0 - - - -
248D ILE* 4.3 3.3 + - + +
249D SER* 1.3 81.1 + - - +
251D LYS* 1.3 68.8 + - - +
253D SER 4.2 2.0 - - - +
256D PHE* 3.8 45.8 - - + -
258D LEU* 4.2 16.6 - - + -
276D THR* 5.3 1.7 - - + +
307D LEU* 3.8 21.1 - - + -
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Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLY* 5.6 4.0 - - - -
226D THR* 3.2 6.4 - - - +
227D TYR* 3.0 67.3 + - + +
229D ASP* 3.7 26.9 - - + +
249D SER* 4.4 3.5 + - - +
250D VAL* 1.3 78.4 - - - +
252D GLY* 1.3 60.7 + - - +
253D SER 4.9 0.2 - - - -
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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