Contacts of the strand formed by residues 301 - 311 (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 TYR 301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262D LEU* 3.9 21.8 - - + -
263D LEU 3.2 22.4 - - - +
264D ASP* 3.5 20.6 - - + +
270D VAL* 4.0 21.5 - - + -
282D VAL* 3.8 12.3 - - + +
284D GLY 4.7 1.0 + - - -
285D VAL* 3.7 6.5 - - + +
286D SER* 2.9 44.5 + - - -
299D TYR* 3.3 25.7 + + - -
300D LEU* 1.3 77.6 - - - +
302D SER* 1.3 60.6 + - - +
323D PRO* 3.6 4.7 - - - +
324D VAL* 2.8 36.5 + - + +
326D ILE* 3.9 24.0 - - + -
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Residues in contact with SER 302 (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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261D ARG 3.5 1.7 - - - +
262D LEU* 3.4 6.9 - - - -
263D LEU* 2.8 64.3 + - - +
264D ASP 5.1 0.7 + - - -
267D ASN* 4.0 7.6 + - - -
301D TYR* 1.3 76.5 - - - +
303D LEU* 1.3 60.6 + - - +
304D GLU 3.5 0.7 + - - -
321D THR* 3.7 19.9 - - - +
322D LEU 3.6 5.4 - - - -
323D PRO* 4.7 3.8 - - - -
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Residues in contact with LEU 303 (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* 4.3 9.0 - - + -
233D VAL* 3.9 27.4 - - + -
244D VAL* 5.1 4.0 - - + -
246D TYR* 4.2 14.1 - - + -
248D ILE* 5.6 0.9 - - + -
260D VAL* 3.0 35.4 - - + -
261D ARG 3.4 6.5 - - - +
262D LEU* 4.1 9.1 - - + +
280D LEU* 3.9 18.8 - - + -
302D SER* 1.3 70.4 - - - +
304D GLU* 1.3 59.3 + - - +
305D VAL* 3.6 17.1 + - + +
320D TYR 3.6 0.7 - - - +
321D THR* 3.3 4.2 - - - -
322D LEU* 2.7 45.7 + - + +
324D VAL* 4.0 10.3 - - + +
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Residues in contact with GLU 304 (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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259D GLU 3.8 0.9 - - - +
260D VAL* 3.4 4.7 - - - +
261D ARG* 2.8 89.8 + - + +
263D LEU* 3.9 23.1 - - + +
302D SER 3.5 1.6 + - - -
303D LEU* 1.3 70.5 - - - +
305D VAL* 1.3 67.3 + - - +
306D GLN* 4.9 7.5 - - + +
319D PHE* 5.1 16.2 - - + -
320D TYR 3.9 3.1 - - - +
321D THR* 4.1 15.2 + - - +
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Residues in contact with VAL 305 (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* 3.4 25.3 - - + +
231D ILE* 3.8 22.0 - - + -
248D ILE* 3.7 31.0 - - + -
258D LEU* 3.8 14.1 - - + -
259D GLU 3.8 2.5 - - - -
260D VAL* 4.4 4.3 - - + -
303D LEU* 4.1 23.3 - - + +
304D GLU* 1.3 76.7 - - - +
306D GLN* 1.3 61.9 + - - +
319D PHE* 3.3 8.0 - - - +
320D TYR 2.8 39.8 + - - +
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Residues in contact with GLN 306 (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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257D LYS 3.8 0.5 - - - +
258D LEU* 3.5 6.3 - - - -
259D GLU* 2.9 70.0 + - + +
261D ARG* 4.7 12.0 + - - -
304D GLU* 4.1 6.3 + - + +
305D VAL* 1.3 74.4 - - - +
307D LEU* 1.3 66.5 + - - +
308D THR* 4.0 13.1 + - - +
317D SER* 5.0 5.6 + - - -
318D ASP 3.4 4.0 - - - +
319D PHE* 3.3 42.4 - - + -
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Residues in contact with LEU 307 (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* 3.9 13.7 - - + +
227D TYR* 3.8 35.7 - - - +
228D ILE* 4.1 7.4 - - + +
250D VAL* 3.8 16.2 - - + -
256D PHE* 3.5 44.6 - - + -
257D LYS 3.5 7.2 - - - +
258D LEU* 3.9 16.2 - - + -
305D VAL 4.2 0.6 - - - -
306D GLN* 1.3 73.1 - - - +
308D THR* 1.3 63.3 + - - +
309D ALA* 4.4 3.1 - - + -
316D VAL* 5.5 1.1 - - + +
317D SER* 3.2 7.8 - - - -
318D ASP* 2.8 45.0 + - + +
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Residues in contact with THR 308 (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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256D PHE* 3.1 3.1 - - - +
257D LYS* 2.7 71.9 + - + +
259D GLU* 4.4 2.9 + - - -
306D GLN* 4.0 15.6 + - - +
307D LEU* 1.3 74.7 + - - +
309D ALA* 1.3 64.5 + - - +
310D GLN* 6.3 0.9 - - - +
315D PRO* 5.5 6.5 - - + -
316D VAL 3.5 7.6 - - - +
317D SER* 4.7 7.1 + - - +
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Residues in contact with ALA 309 (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 28.3 - - + -
253D SER* 4.9 0.4 - - - -
255D LEU 3.5 6.5 - - - +
256D PHE* 3.7 16.4 - - + +
307D LEU* 4.1 5.6 - - + -
308D THR* 1.3 76.1 - - - +
310D GLN* 1.3 63.8 + - - +
311D THR* 4.1 1.8 - - + -
315D PRO* 3.3 6.4 - - - +
316D VAL* 2.9 44.8 + - + -
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Residues in contact with GLN 310 (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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253D SER* 2.7 29.6 + - - -
255D LEU* 2.9 39.5 + - + +
308D THR* 6.3 0.8 - - - +
309D ALA* 1.3 73.2 + - - +
311D THR* 1.3 66.8 + - - +
314D GLY* 4.2 3.2 - - - -
315D PRO* 3.6 35.9 - - - +
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Residues in contact with THR 311 (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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116D ARG* 5.8 0.3 - - - +
225D THR* 4.6 12.0 + - - +
226D THR* 3.8 21.1 - - - +
253D SER* 4.8 3.4 - - - -
309D ALA 4.3 1.3 - - - +
310D GLN* 1.3 81.4 + - - +
312D SER* 1.3 65.4 + - - +
313D LEU* 3.1 13.3 + - - +
314D GLY* 2.4 36.5 + - - +
316D VAL* 3.4 41.3 - - + +
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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