Contacts of the strand formed by residues 301 - 311 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 3.9 28.3 - - + -
263B LEU 3.2 19.1 - - - +
264B ASP* 3.6 21.3 - - + +
270B VAL* 3.9 10.5 - - + -
282B VAL* 3.6 22.8 - - + +
284B GLY 4.7 1.2 + - - -
285B VAL* 3.5 5.5 - - - +
286B SER* 3.0 45.6 + - - -
299B TYR* 3.5 17.1 - + - -
300B LEU* 1.3 78.3 - - - +
302B SER* 1.3 64.1 + - - +
323B PRO* 3.6 3.6 - - - +
324B VAL* 2.8 35.4 + - + +
326B ILE* 3.8 23.8 - - + -
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Residues in contact with SER 302 (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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261B ARG 3.4 1.9 - - - +
262B LEU* 3.4 7.2 - - - -
263B LEU* 2.8 61.4 + - - +
264B ASP 4.8 2.1 + - - -
267B ASN* 5.6 1.6 + - - -
301B TYR* 1.3 76.3 - - - +
303B LEU* 1.3 59.9 + - - +
304B GLU 3.7 0.9 + - - -
321B THR* 3.7 23.4 - - - +
322B LEU 3.6 6.1 - - - -
323B PRO* 4.7 4.0 - - - -
324B VAL 4.5 0.2 - - - +
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Residues in contact with LEU 303 (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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231B ILE* 4.3 14.1 - - + -
233B VAL* 3.6 29.8 - - + -
244B VAL* 5.2 4.9 - - + -
246B TYR* 4.4 14.4 - - + -
248B ILE* 5.6 0.4 - - + -
260B VAL* 4.2 15.0 - - + -
261B ARG 3.5 9.6 - - - +
262B LEU* 4.0 8.4 - - + +
280B LEU* 3.9 25.8 - - + -
302B SER* 1.3 69.5 - - - +
304B GLU* 1.3 59.1 + - - +
305B VAL* 3.7 16.6 + - + +
320B TYR 3.7 0.9 - - - +
321B THR* 3.3 4.3 - - - -
322B LEU* 2.8 44.4 + - + +
324B VAL* 3.9 11.6 - - + +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU 3.9 0.9 - - - +
260B VAL* 3.3 4.2 - - - -
261B ARG* 2.8 83.4 + - + +
263B LEU* 3.7 18.0 - - + +
302B SER 3.7 1.4 + - - -
303B LEU* 1.3 70.7 - - - +
305B VAL* 1.3 65.3 + - - +
306B GLN* 4.0 11.7 + - + +
319B PHE* 4.9 15.2 - - + -
320B TYR 3.8 3.4 - - - +
321B THR* 4.0 20.4 + - + +
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Residues in contact with VAL 305 (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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228B ILE* 3.5 24.3 - - + +
231B ILE* 3.9 22.2 - - + -
248B ILE* 3.8 26.0 - - + -
258B LEU* 3.7 22.4 - - + -
259B GLU 3.6 5.2 - - - +
260B VAL* 4.3 2.5 - - + -
303B LEU* 4.2 20.4 - - + +
304B GLU* 1.3 76.6 - - - +
306B GLN* 1.3 60.4 + - - +
319B PHE* 3.4 6.8 - - - +
320B TYR 2.9 38.8 + - - +
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Residues in contact with GLN 306 (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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257B LYS 3.8 0.9 - - - +
258B LEU* 3.6 5.8 - - - -
259B GLU* 2.8 59.2 + - + +
304B GLU* 4.0 10.3 + - - +
305B VAL* 1.3 73.2 - - - +
307B LEU* 1.3 67.6 + - - +
308B THR* 4.0 10.4 + - - +
317B SER* 4.8 5.9 + - - -
318B ASP 3.4 2.7 - - - -
319B PHE* 3.4 37.9 - - + -
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Residues in contact with LEU 307 (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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226B THR* 3.8 12.6 - - + +
227B TYR* 3.8 40.4 - - - +
228B ILE* 4.0 10.1 - - + +
250B VAL* 3.7 21.5 - - + -
256B PHE* 3.7 33.4 - - + -
257B LYS 3.6 13.9 - - - +
258B LEU* 3.9 6.5 - - + -
305B VAL 4.1 1.0 - - - -
306B GLN* 1.3 74.3 - - - +
308B THR* 1.3 65.8 + - - +
309B ALA* 4.4 2.9 - - + -
316B VAL* 5.4 0.9 - - + +
317B SER* 3.2 8.3 - - - -
318B ASP* 2.7 45.7 + - + +
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Residues in contact with THR 308 (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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256B PHE* 3.3 2.4 - - - -
257B LYS* 2.8 51.2 + - + +
259B GLU* 4.2 14.3 + - - -
306B GLN* 4.3 11.3 + - - -
307B LEU* 1.3 75.4 + - - +
309B ALA* 1.3 63.5 + - - +
310B GLN* 4.9 11.1 - - - +
315B PRO* 5.4 6.3 - - + -
316B VAL 3.5 9.4 - - - +
317B SER* 4.6 6.8 + - - +
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Residues in contact with ALA 309 (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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226B THR* 3.5 37.9 - - + +
253B SER* 4.6 1.6 - - - -
255B LEU 3.5 6.1 - - - +
256B PHE* 3.7 11.4 - - + -
307B LEU* 4.4 5.6 - - + -
308B THR* 1.3 74.9 - - - +
310B GLN* 1.3 66.5 + - - +
311B THR* 3.8 1.0 + - + -
315B PRO* 3.3 6.1 - - - +
316B VAL* 2.9 39.2 + - + +
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Residues in contact with GLN 310 (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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253B SER* 2.5 27.9 + - - -
255B LEU* 2.8 50.6 + - + +
256B PHE* 5.7 0.7 - - - -
257B LYS* 6.1 0.9 - - - -
308B THR* 4.9 11.3 - - - +
309B ALA* 1.3 76.2 - - - +
311B THR* 1.3 60.9 + - - +
314B GLY 5.0 0.2 - - - -
315B PRO* 3.6 30.2 - - - +
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Residues in contact with THR 311 (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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116B ARG* 5.9 0.2 - - - +
225B THR* 4.5 13.0 + - - +
226B THR* 3.7 19.7 - - - +
253B SER* 4.7 2.2 - - - -
309B ALA 4.2 0.4 - - - +
310B GLN* 1.3 78.6 - - - +
312B SER* 1.3 58.4 + - - +
313B LEU* 3.1 16.7 + - - +
314B GLY* 2.6 37.4 + - - +
316B VAL* 3.4 39.7 - - + +
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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