Contacts of the strand formed by residues 235 - 245 (chain A) in PDB entry 3HFV
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 THR 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A TYR* 5.3 2.1 - - - -
232A PHE* 2.9 31.9 - - - +
233A PRO 3.5 0.8 - - - -
234A PHE* 1.3 86.5 - - + +
236A HIS* 1.3 67.6 + - - +
238A SER* 2.7 29.6 + - - -
255A CYS 4.1 0.2 + - - -
256A GLY* 3.8 18.8 - - - +
257A VAL 3.0 22.4 - - - +
258A MET* 3.9 7.6 - - + -
259A GLU* 3.6 8.3 - - - +
275A ALA* 4.8 2.0 - - + -
416A MTY 4.0 22.4 - - + -
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Residues in contact with HIS 236 (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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187A ARG* 3.3 28.9 - - + +
188A SER 2.7 29.3 + - - -
189A ALA* 3.6 20.0 - - - -
191A LYS 3.2 28.7 + - - -
192A GLN* 2.8 34.8 + - + +
195A HIS* 4.8 1.0 + - - -
231A TYR* 5.9 6.2 - + + -
235A THR* 1.3 78.1 + - - +
237A PRO* 1.3 79.5 + - + +
238A SER* 3.9 0.8 + - - -
257A VAL* 2.6 17.1 + - - +
259A GLU* 3.3 15.3 - - - +
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Residues in contact with PRO 237 (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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189A ALA 4.0 17.3 - - - +
190A HIS* 3.5 27.4 - - - +
191A LYS* 4.2 1.8 - - - -
200A VAL* 3.9 18.8 - - + -
204A GLU* 4.4 6.7 - - - +
236A HIS* 1.3 94.6 + - - +
238A SER* 1.3 61.0 + - - +
239A PHE* 4.0 25.9 - - + -
256A GLY* 3.2 2.6 - - - -
257A VAL* 3.0 31.8 + - + -
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Residues in contact with SER 238 (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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229A ASP* 3.8 2.4 - - - +
230A CYS* 3.2 35.0 + - - +
231A TYR* 4.4 0.5 - - - -
232A PHE* 3.4 24.4 + - - -
235A THR* 2.7 39.1 + - - -
236A HIS* 4.8 1.1 + - - -
237A PRO* 1.3 73.0 - - - +
239A PHE* 1.3 72.4 + - - +
255A CYS 3.2 13.5 - - - -
256A GLY* 4.0 0.7 - - - -
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Residues in contact with PHE 239 (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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204A GLU* 3.6 34.5 - - + -
207A LEU* 4.4 6.7 - - + -
208A LYS* 3.7 30.5 - - - -
227A TRP* 4.3 11.9 - - + -
228A VAL 3.1 11.9 - - - +
229A ASP* 3.4 23.8 - - - -
230A CYS* 3.4 8.9 - - - -
237A PRO* 4.0 29.6 - - + -
238A SER* 1.3 83.8 - - - +
240A GLU* 1.3 64.9 + - - +
254A GLY* 3.6 2.4 - - - -
255A CYS* 2.9 53.3 + - - +
256A GLY* 4.4 6.3 - - - -
257A VAL* 5.4 0.9 - - + -
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Residues in contact with GLU 240 (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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227A TRP* 3.7 2.9 - - - -
228A VAL* 2.8 49.5 + - + +
230A CYS* 3.6 27.5 - - - +
232A PHE* 3.9 20.4 - - + -
239A PHE* 1.3 75.2 - - - +
241A MET* 1.3 59.8 + - - +
242A GLU* 5.2 3.9 - - + +
251A GLU* 4.5 27.4 - - + +
253A LEU* 3.3 15.5 - - - +
254A GLY* 4.5 0.4 - - - -
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Residues in contact with MET 241 (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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211A LEU* 4.9 4.3 - - - +
215A MET* 3.4 37.2 - - + -
225A ILE* 3.5 35.0 - - + -
226A ARG 3.5 7.9 - - - +
227A TRP* 3.6 41.3 - - + -
240A GLU* 1.3 74.8 - - - +
242A GLU* 1.3 63.3 + - - +
243A ILE* 3.6 20.0 - - + -
251A GLU* 3.4 2.9 - - - -
252A VAL* 2.9 31.6 + - + +
253A LEU* 3.3 32.7 + - + +
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Residues in contact with GLU 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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225A ILE* 3.2 8.5 - - - +
226A ARG* 2.5 80.4 + - - -
228A VAL* 3.5 21.9 - - + +
240A GLU* 4.9 4.2 - - + +
241A MET* 1.3 78.2 - - - +
243A ILE* 1.3 64.1 + - - +
249A TRP* 3.4 19.8 - - + +
250A LEU 3.1 5.6 - - - +
251A GLU* 3.7 28.9 + - + +
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Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A MET* 4.5 0.9 - - + -
219A PHE* 3.9 32.1 - - + -
223A LEU* 4.1 15.5 - - + -
224A GLU 3.5 7.2 - - - +
225A ILE* 4.1 7.4 - - + -
241A MET* 3.6 29.8 + - + -
242A GLU* 1.3 74.2 - - - +
244A ASN* 1.3 77.0 + - - +
245A PHE* 3.5 1.4 + - - +
248A GLU 3.3 0.5 - - - +
249A TRP* 3.8 2.5 - - - -
250A LEU* 2.6 37.6 + - - +
252A VAL* 4.1 9.2 - - + -
283A LEU* 4.1 15.3 - - + -
286A ILE* 4.3 24.9 - - + -
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Residues in contact with ASN 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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224A GLU* 3.0 30.7 + - + +
243A ILE* 1.3 79.1 - - - +
245A PHE* 1.3 61.2 + - - +
247A GLY* 3.7 11.7 + - - -
248A GLU 3.2 20.8 + - - +
249A TRP* 2.9 55.7 - - + +
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Residues in contact with PHE 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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243A ILE 4.4 2.5 - - - +
244A ASN* 1.3 76.2 + - - +
246A HIS* 1.3 114.8 + + + +
247A GLY 3.0 1.6 + - - -
248A GLU* 2.8 21.5 + - - +
250A LEU* 3.9 27.8 - - + +
285A MET 4.0 12.6 - - - -
286A ILE* 3.2 52.0 - - + -
289A ASP* 4.0 16.2 - - + -
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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