Contacts of the strand formed by residues 241 - 251 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237E VAL* 3.2 10.4 - - - +
238E GLU* 2.8 43.2 + - - -
239E GLN* 5.4 2.1 + - - +
240E ASP* 1.3 85.9 + - - +
242E GLY* 1.3 60.3 + - - +
281E LYS* 4.3 19.6 - - - +
282E VAL 3.3 8.7 - - - -
283E PRO* 3.9 14.0 - - - +
285E VAL* 3.7 4.5 - - - -
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Residues in contact with GLY 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E SER 3.7 6.1 - - - -
237E VAL* 4.7 0.2 - - - -
241E SER* 1.3 73.5 - - - +
243E LEU* 1.3 64.8 + - - +
280E LEU 3.6 0.3 - - - +
281E LYS* 3.4 5.5 - - - +
282E VAL* 2.8 43.3 + - - +
285E VAL* 3.6 18.0 - - - +
326E ILE* 4.1 11.4 - - - -
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Residues in contact with LEU 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E THR 3.9 0.3 - - - +
235E THR* 3.2 9.2 - - - -
236E SER* 2.9 52.6 + - - +
237E VAL 4.9 1.1 - - - +
238E GLU* 4.1 43.3 - - + +
242E GLY* 1.3 81.7 - - - +
244E VAL* 1.3 61.4 + - - +
245E ASN* 4.0 3.0 + - - +
279E GLN* 4.1 35.4 - - - +
280E LEU 3.4 2.2 - - - +
281E LYS* 4.2 21.1 - - + -
326E ILE* 4.7 0.4 - - - +
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Residues in contact with VAL 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E VAL* 3.7 28.3 - - + -
234E THR 3.8 2.2 - - - -
235E THR* 4.2 3.6 - - + -
243E LEU* 1.3 74.4 - - - +
245E ASN* 1.3 64.0 + - - +
246E TYR* 3.8 4.5 + - + +
262E LEU* 3.8 18.4 - - + -
279E GLN* 3.3 2.8 - - - +
280E LEU* 2.8 56.0 + - + +
282E VAL* 4.4 4.5 - - + -
303E LEU* 4.8 8.5 - - + -
324E VAL* 4.4 8.7 - - + -
326E ILE* 3.8 32.3 - - + -
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Residues in contact with ASN 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E THR 3.6 0.7 - - - +
233E VAL* 3.2 9.2 - - - +
234E THR* 2.8 56.2 + - - +
235E THR* 4.6 0.9 + - - -
236E SER* 4.7 8.5 + - - -
243E LEU 4.4 4.7 - - - +
244E VAL* 1.3 72.4 - - - +
246E TYR* 1.3 60.3 + - - +
247E GLN* 5.7 3.6 - - + +
278E GLY 3.5 5.8 + - - +
279E GLN* 2.8 37.7 + - - +
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Residues in contact with TYR 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E ILE* 5.3 0.4 - - + -
232E THR 3.4 4.9 - - - +
233E VAL* 4.4 2.7 - - + -
244E VAL* 4.0 4.3 - - + -
245E ASN* 1.3 73.4 - - - +
247E GLN* 1.3 67.6 + - - +
248E ILE* 4.0 20.0 - - + -
260E VAL* 3.9 18.4 - - + -
273E GLY* 3.6 4.3 - - - -
274E THR 2.7 37.5 + - - -
275E GLY 3.7 9.6 - - - -
277E GLN* 3.2 21.2 - - - +
278E GLY* 2.9 55.7 + - - +
279E GLN 3.8 1.1 + - - -
280E LEU* 3.7 38.0 - - + +
303E LEU* 4.2 21.5 - - + -
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Residues in contact with GLN 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E ILE* 3.3 5.2 - - - +
232E THR* 2.8 56.5 + - - +
234E THR* 6.4 0.2 - - - +
245E ASN* 5.7 3.8 - - + +
246E TYR* 1.3 80.2 - - - +
248E ILE* 1.3 63.4 + - - +
276E THR 3.3 7.4 - - - +
277E GLN* 4.5 14.0 - - + +
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Residues in contact with ILE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ILE* 4.2 15.5 - - + -
230E ASP 3.4 9.4 - - - +
231E ILE* 4.4 13.2 - - + -
246E TYR* 4.0 15.9 - - + -
247E GLN* 1.3 79.2 - - - +
249E SER* 1.3 71.3 + - - +
250E VAL* 4.3 1.6 - - + -
258E LEU* 4.0 25.1 - - + -
260E VAL* 3.7 23.8 - - + -
275E GLY 4.3 6.3 - - - +
276E THR* 2.8 34.9 + - - +
303E LEU* 5.5 0.2 - - + -
305E VAL* 3.7 28.3 - - + -
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Residues in contact with SER 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ILE* 3.7 2.1 - - - -
229E ASP* 2.8 38.0 + - - +
230E ASP* 2.9 26.8 + - - +
248E ILE* 1.3 75.3 - - - +
250E VAL* 1.3 59.7 + - - +
251E LYS* 4.1 19.8 - - - -
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Residues in contact with VAL 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E THR* 3.7 25.4 - - + -
227E TYR 3.3 13.9 - - - +
228E ILE* 4.7 2.9 - - - -
248E ILE* 4.4 3.8 - - + +
249E SER* 1.3 78.4 + - - +
251E LYS* 1.3 73.3 + - - +
253E SER 4.3 4.7 - - - +
256E PHE* 3.8 35.5 - - + -
258E LEU* 4.0 17.7 - - + -
276E THR* 5.9 0.8 - - - +
307E LEU* 3.7 31.2 - - + -
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Residues in contact with LYS 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E THR* 3.1 6.3 - - - +
227E TYR* 2.9 60.1 + - + +
229E ASP* 3.8 24.6 - - + +
249E SER* 4.1 14.6 - - - -
250E VAL* 1.3 79.6 + - - +
252E GLY* 1.3 60.4 + - - +
253E SER 3.6 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