Contacts of the strand formed by residues 241 - 251 (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 SER 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A VAL* 3.5 6.6 - - - +
238A GLU* 2.8 39.3 + - - -
239A GLN 3.5 0.2 - - - -
240A ASP* 1.3 80.6 - - - +
242A GLY* 1.3 59.8 - - - +
243A LEU* 5.6 0.4 - - - -
281A LYS* 4.0 32.9 + - - +
282A VAL 3.3 11.3 + - - -
283A PRO* 3.8 12.1 - - - +
284A GLY 4.3 0.3 + - - -
285A VAL* 3.8 3.8 - - - -
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Residues in contact with GLY 242 (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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236A SER 3.7 5.6 - - - -
237A VAL* 4.7 0.4 - - - -
241A SER* 1.3 75.4 - - - +
243A LEU* 1.3 64.0 + - - +
244A VAL 4.2 0.2 - - - -
280A LEU 3.6 0.2 - - - +
281A LYS* 3.4 4.3 - - - +
282A VAL* 2.7 45.5 + - - -
285A VAL* 3.6 23.8 - - - +
326A ILE* 4.2 7.2 - - - -
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 3.3 9.2 - - - -
236A SER* 2.8 53.7 + - - +
238A GLU* 3.6 43.5 - - + +
241A SER* 4.9 0.9 - - - +
242A GLY* 1.3 75.5 - - - -
244A VAL* 1.3 61.5 + - - +
245A ASN* 3.9 2.5 + - - +
279A GLN* 3.7 40.2 - - + +
280A LEU 3.5 1.1 - - - -
281A LYS* 3.7 35.9 - - + -
326A ILE* 4.9 1.1 - - - +
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Residues in contact with VAL 244 (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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233A VAL* 3.8 31.4 - - + -
234A THR 3.8 2.2 - - - +
235A THR* 4.5 2.9 - - + -
243A LEU* 1.3 76.9 - - - +
245A ASN* 1.3 65.1 + - - +
246A TYR* 3.7 6.1 + - + +
262A LEU* 4.1 17.3 - - + -
279A GLN* 3.2 1.7 - - - -
280A LEU* 2.8 49.1 + - + +
282A VAL* 4.2 3.1 - - + -
303A LEU* 4.6 16.4 - - + -
324A VAL* 4.3 9.4 - - + -
326A ILE* 3.9 30.3 - - + -
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Residues in contact with ASN 245 (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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232A THR 3.6 1.6 - - - +
233A VAL* 3.3 5.8 - - - -
234A THR* 2.9 49.8 + - - +
235A THR* 5.0 0.4 - - - +
236A SER* 4.4 6.5 + - - -
243A LEU* 3.9 11.9 + - - +
244A VAL* 1.3 75.0 - - - +
246A TYR* 1.3 59.3 + - - +
247A GLN* 5.2 3.8 - - - +
278A GLY 3.4 6.2 - - - +
279A GLN* 3.1 39.3 + - - +
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Residues in contact with TYR 246 (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* 5.4 0.4 - - + -
232A THR 3.5 4.9 - - - +
233A VAL* 4.4 3.8 - - + -
244A VAL* 4.0 9.2 - - + +
245A ASN* 1.3 72.7 - - - +
247A GLN* 1.3 69.4 + - - +
248A ILE* 3.9 18.6 - - + -
260A VAL* 3.9 18.4 - - + -
273A GLY* 3.8 4.9 - - - -
274A THR 2.8 36.4 + - - -
275A GLY 3.8 9.2 - - - -
277A GLN* 3.2 21.8 - - - +
278A GLY* 2.9 54.8 + - - +
279A GLN 3.8 0.8 + - - -
280A LEU* 3.6 32.7 - - + +
303A LEU* 4.4 22.2 - - + -
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Residues in contact with GLN 247 (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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230A ASP 4.6 0.2 - - - -
231A ILE* 3.3 4.7 - - - +
232A THR* 2.9 56.7 + - - +
245A ASN* 5.2 3.2 - - - +
246A TYR* 1.3 81.1 - - - +
248A ILE* 1.3 63.4 + - - +
249A SER 4.5 0.2 + - - -
276A THR 3.2 7.6 - - - +
277A GLN* 4.5 13.4 + - + +
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Residues in contact with ILE 248 (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* 4.0 20.0 - - + -
230A ASP 3.5 9.4 - - - +
231A ILE* 4.7 8.3 - - + -
246A TYR* 3.9 15.9 - - + -
247A GLN* 1.3 80.5 - - - +
249A SER* 1.3 67.3 + - - +
250A VAL* 4.3 2.0 + - + -
258A LEU* 3.9 26.0 - - + -
260A VAL* 3.5 32.1 - - + -
275A GLY 4.0 8.7 - - - +
276A THR* 2.7 33.3 + - - +
305A VAL* 3.7 22.2 - - + -
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Residues in contact with SER 249 (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 3.1 - - - -
229A ASP* 2.7 35.4 + - - +
230A ASP* 2.8 43.2 + - - +
248A ILE* 1.3 74.2 - - - +
250A VAL* 1.3 57.8 + - - +
251A LYS* 6.1 1.1 - - - -
276A THR* 5.9 0.2 - - - -
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Residues in contact with VAL 250 (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* 3.8 16.6 - - + -
227A TYR 3.3 13.0 - - - +
228A ILE* 4.8 2.0 - - - -
248A ILE* 4.3 5.1 + - + +
249A SER* 1.3 78.6 - - - +
251A LYS* 1.3 68.0 + - - +
253A SER 4.8 2.6 - - - +
256A PHE* 3.7 45.2 - - + -
258A LEU* 4.0 14.1 - - + -
276A THR* 6.0 0.4 - - - +
307A LEU* 3.5 34.1 - - + -
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Residues in contact with LYS 251 (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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24A GLN* 3.6 21.8 + - - -
25A GLY* 3.9 14.2 - - - -
226A THR* 3.3 5.4 - - - +
227A TYR* 3.0 66.0 + - + +
229A ASP* 3.6 28.9 + - + +
249A SER* 4.3 1.3 - - - +
250A VAL* 1.3 78.0 - - - +
252A GLY* 1.3 60.6 + - - +
253A SER 4.1 0.9 - - - -
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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