Contacts of the strand formed by residues 301 - 311 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU* 3.6 28.9 - - + -
263A LEU 3.2 18.4 - - - +
264A ASP* 3.6 19.7 - - + +
270A VAL* 4.0 14.1 - - + -
282A VAL* 3.9 12.7 - - + +
284A GLY 5.0 0.5 + - - -
285A VAL* 3.7 6.6 - - + +
286A SER* 2.9 48.6 + - - -
299A TYR* 3.4 21.6 + + - -
300A LEU* 1.3 77.4 - - - +
302A SER* 1.3 58.1 + - - +
323A PRO* 3.4 4.9 - - - +
324A VAL* 2.7 42.0 + - + +
326A ILE* 3.9 22.7 - - + -
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG 3.4 2.1 - - - +
262A LEU* 3.3 7.2 - - - -
263A LEU* 2.7 62.6 + - - +
264A ASP 4.8 2.3 + - - -
267A ASN* 5.0 4.5 + - - -
301A TYR* 1.3 75.6 - - - +
303A LEU* 1.3 59.0 + - - +
304A GLU* 3.8 1.3 + - - +
321A THR* 3.6 23.9 - - - +
322A LEU 3.6 5.6 - - - -
323A PRO* 4.4 2.7 - - - -
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ILE* 4.1 12.3 - - + -
233A VAL* 3.8 24.7 - - + -
244A VAL* 4.6 10.3 - - + -
246A TYR* 4.4 10.5 - - + -
248A ILE* 5.6 0.4 - - + -
260A VAL* 3.3 29.4 - - + -
261A ARG 3.5 2.0 - - - +
262A LEU* 4.0 11.3 - - + +
280A LEU* 3.8 19.5 - - + -
302A SER* 1.3 69.8 - - - +
304A GLU* 1.3 59.0 + - - +
305A VAL* 3.7 19.2 + - + +
320A TYR 3.7 1.7 - - - +
321A THR* 3.2 4.5 - - - -
322A LEU* 2.8 46.8 + - + +
324A VAL* 3.9 11.0 - - + +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLU 3.8 0.7 - - - +
260A VAL* 3.5 3.5 - - - -
261A ARG* 2.7 75.1 + - + +
263A LEU* 4.0 26.3 - - + +
302A SER* 3.8 1.5 + - - +
303A LEU* 1.3 71.3 - - - +
305A VAL* 1.3 61.9 + - - +
306A GLN 3.9 0.3 + - - -
319A PHE* 4.3 19.1 - - + -
320A TYR 3.8 3.6 - - - +
321A THR* 3.9 20.9 + - + +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ILE* 3.6 18.2 - - + +
231A ILE* 4.1 17.0 - - + -
248A ILE* 3.7 23.6 - - + -
258A LEU* 3.5 28.5 - - + -
259A GLU 3.6 5.4 - - - +
260A VAL* 4.5 2.7 - - + +
303A LEU* 4.0 28.0 - - + +
304A GLU* 1.3 75.3 - - - +
306A GLN* 1.3 61.5 + - - +
318A ASP 3.6 1.2 - - - +
319A PHE* 3.4 7.3 - - - -
320A TYR 2.8 38.8 + - - +
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LYS 4.0 0.5 - - - +
258A LEU* 3.6 4.8 - - - -
259A GLU* 2.9 59.5 + - + +
261A ARG* 3.1 31.3 + - - +
304A GLU 3.9 1.0 + - - -
305A VAL* 1.3 71.3 - - - +
307A LEU* 1.3 69.3 + - - +
308A THR* 4.3 12.4 - - + +
317A SER* 5.0 4.9 + - - -
318A ASP 3.4 3.8 - - - +
319A PHE* 3.5 38.2 - - + -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 4.0 13.5 - - + +
227A TYR* 3.8 24.9 - - - -
228A ILE* 4.0 7.8 - - + +
250A VAL* 3.5 25.8 - - + -
256A PHE* 3.5 39.3 - - + -
257A LYS 3.7 9.2 - - - +
258A LEU* 3.8 17.5 - - + +
305A VAL 4.1 0.8 - - - -
306A GLN* 1.3 73.9 - - - +
308A THR* 1.3 68.2 + - - +
309A ALA* 4.4 2.7 - - + -
316A VAL* 5.6 0.7 - - + +
317A SER* 3.1 8.7 - - - -
318A ASP* 2.7 43.9 + - + +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PHE* 3.3 3.5 - - - +
257A LYS* 2.8 67.6 + - - +
259A GLU* 4.6 6.2 + - - +
306A GLN* 4.3 20.2 - - + +
307A LEU* 1.3 77.2 - - - +
309A ALA* 1.3 60.5 + - - +
310A GLN* 4.0 8.8 + - - +
316A VAL 3.5 5.2 - - - -
317A SER* 4.4 9.4 - - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 3.4 38.4 - - + +
255A LEU 3.7 4.9 - - - +
256A PHE* 3.8 11.4 - - + -
307A LEU* 4.2 6.0 - - + -
308A THR* 1.3 75.0 - - - +
310A GLN* 1.3 67.7 + - - +
311A THR* 4.0 1.4 + - + -
315A PRO* 3.1 4.5 - - - +
316A VAL* 2.8 40.8 + - + +
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A SER* 2.7 30.0 + - - -
255A LEU* 3.3 26.8 + - + +
256A PHE* 4.2 1.6 - - - -
308A THR* 4.0 8.1 + - - +
309A ALA* 1.3 83.7 - - - +
311A THR* 1.3 59.8 + - - +
314A GLY 5.5 0.2 - - - -
315A PRO* 4.2 20.9 - - + +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ARG* 5.8 0.2 - - - +
225A THR* 4.4 12.9 + - - +
226A THR* 3.5 32.1 - - - +
253A SER* 4.7 2.7 - - - -
309A ALA 4.2 0.9 - - - +
310A GLN* 1.3 80.0 - - - +
312A SER* 1.3 63.8 + - - +
313A LEU* 3.2 13.7 + - - +
314A GLY* 2.5 36.3 + - - +
316A VAL* 3.9 25.6 - - + +
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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