Contacts of the strand formed by residues 301 - 311 (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 TYR 301 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.7 27.8 - - + -
263E LEU 3.2 20.0 - - - +
264E ASP* 3.6 20.6 - - + +
270E VAL* 3.9 19.7 - - + -
282E VAL* 3.6 14.5 - - + +
284E GLY 4.8 1.0 + - - -
285E VAL* 3.4 6.2 - - - +
286E SER* 3.0 46.3 + - - -
299E TYR* 3.5 17.3 + + - -
300E LEU* 1.3 78.8 - - - +
302E SER* 1.3 61.4 + - - +
323E PRO* 3.5 4.9 - - - +
324E VAL* 2.7 37.2 + - + +
326E ILE* 3.7 24.0 - - + -
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Residues in contact with SER 302 (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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261E ARG 3.5 1.6 - - - +
262E LEU* 3.3 7.1 - - - -
263E LEU* 2.7 67.2 + - - +
264E ASP 4.9 2.2 + - - -
267E ASN* 5.7 0.7 - - - +
301E TYR* 1.3 75.2 - - - +
303E LEU* 1.3 60.1 + - - +
304E GLU 3.6 1.4 + - - -
321E THR* 3.6 20.6 - - - +
322E LEU 3.6 3.6 - - - -
323E PRO* 4.8 4.5 - - - -
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Residues in contact with LEU 303 (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* 4.2 9.9 - - + -
233E VAL* 3.8 26.9 - - + -
244E VAL* 4.8 5.8 - - + -
246E TYR* 4.2 11.4 - - + -
248E ILE* 5.5 0.4 - - + -
260E VAL* 3.1 35.2 - - + -
261E ARG 3.4 4.5 - - - +
262E LEU* 4.0 7.8 - - + +
280E LEU* 3.7 22.0 - - + -
302E SER* 1.3 69.0 - - - +
304E GLU* 1.3 60.3 + - - +
305E VAL* 3.6 17.4 + - + +
320E TYR 3.6 1.0 - - - +
321E THR* 3.3 3.9 - - - -
322E LEU* 2.8 41.5 + - + +
324E VAL* 3.9 11.4 - - + +
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Residues in contact with GLU 304 (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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259E GLU 3.8 0.7 - - - +
260E VAL* 3.4 5.1 - - - +
261E ARG* 2.8 73.9 + - + +
263E LEU* 3.6 29.7 - - + +
302E SER 3.6 1.4 + - - -
303E LEU* 1.3 70.8 - - - +
305E VAL* 1.3 62.0 + - - +
306E GLN 4.1 0.2 + - - -
319E PHE* 4.4 20.4 - - + -
320E TYR 4.9 0.2 - - - +
321E THR* 3.8 21.0 + - + +
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Residues in contact with VAL 305 (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* 3.6 22.4 - - + +
231E ILE* 4.0 17.7 - - + -
248E ILE* 3.7 35.4 - - + -
258E LEU* 3.7 15.0 - - + -
259E GLU 3.6 5.2 - - - +
260E VAL* 4.4 2.2 - - + -
303E LEU* 4.0 22.0 - - + +
304E GLU* 1.3 77.2 - - - +
306E GLN* 1.3 61.1 + - - +
318E ASP 3.6 1.0 - - - +
319E PHE* 3.3 8.7 - - - +
320E TYR 2.8 38.6 + - - +
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Residues in contact with GLN 306 (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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257E LYS 3.8 1.0 - - - +
258E LEU* 3.5 5.0 - - - -
259E GLU* 2.8 53.7 + - + +
261E ARG* 2.9 36.0 + - - +
304E GLU 4.1 0.2 + - - -
305E VAL* 1.3 73.6 - - - +
307E LEU* 1.3 67.1 + - - +
308E THR* 4.0 9.8 + - - +
317E SER* 4.9 5.6 + - - +
318E ASP 3.4 2.7 - - - -
319E PHE* 3.3 37.6 - - + -
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Residues in contact with LEU 307 (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* 3.9 14.8 - - + +
227E TYR* 3.8 31.9 - - - +
228E ILE* 4.1 5.6 - - + +
250E VAL* 3.7 25.4 - - + -
256E PHE* 3.6 41.5 - - + -
257E LYS 3.6 6.3 - - - +
258E LEU* 3.8 11.4 - - + -
305E VAL 4.1 1.0 - - - -
306E GLN* 1.3 73.8 - - - +
308E THR* 1.3 67.0 + - - +
309E ALA* 4.2 3.6 - - + +
316E VAL* 5.7 0.9 - - + -
317E SER* 3.2 8.3 - - - -
318E ASP* 2.8 44.1 + - + +
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Residues in contact with THR 308 (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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256E PHE* 3.2 3.4 - - - +
257E LYS* 2.8 69.1 + - + +
259E GLU* 4.8 3.8 + - - -
306E GLN* 4.0 12.2 + - - +
307E LEU* 1.3 73.1 + - - +
309E ALA* 1.3 63.2 + - - +
310E GLN* 4.4 17.8 + - - +
315E PRO* 5.5 3.8 - - + -
316E VAL 3.5 7.4 - - - +
317E SER* 4.6 7.9 + - - +
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Residues in contact with ALA 309 (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* 3.6 33.7 - - + +
253E SER* 4.9 0.2 - - - -
255E LEU 3.6 5.4 - - - +
256E PHE* 3.8 9.6 - - + +
307E LEU* 4.1 7.2 - - + -
308E THR* 1.3 74.3 - - - +
310E GLN* 1.3 73.5 + - - +
311E THR* 4.0 0.9 - - + -
315E PRO* 3.1 0.5 - - - +
316E VAL* 2.9 44.5 + - + -
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Residues in contact with GLN 310 (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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253E SER* 2.6 27.9 + - - -
255E LEU* 2.9 39.5 + - + +
256E PHE* 5.0 2.0 - - - +
257E LYS* 6.0 1.6 - - - +
308E THR* 4.4 17.2 + - - +
309E ALA* 1.3 94.2 + - - +
311E THR* 1.3 58.6 + - - +
314E GLY 4.3 2.0 - - - -
315E PRO* 3.4 19.3 - - + +
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Residues in contact with THR 311 (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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116E ARG* 6.0 0.2 - - - +
225E THR* 4.2 15.2 + - - +
226E THR* 3.7 22.0 - - - +
253E SER* 4.6 3.6 - - - -
309E ALA 4.5 0.4 - - - +
310E GLN* 1.3 77.0 - - - +
312E SER* 1.3 59.2 + - - +
313E LEU* 3.1 16.3 + - - +
314E GLY* 2.5 40.7 + - - +
316E VAL* 3.6 34.7 - - + +
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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