Contacts of the strand formed by residues 223 - 231 (chain A) in PDB entry 5F85
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 ARG 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLN 3.7 2.9 + - - +
222A LYS* 1.3 71.9 - - - +
224A SER* 1.3 59.0 + - - +
225A LEU* 3.1 15.3 + - + +
283A LYS* 2.9 55.3 + - + +
284A TYR* 3.1 43.2 + - + -
285A LYS* 2.8 32.2 + - - +
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Residues in contact with SER 224 (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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222A LYS 3.6 1.2 + - - -
223A ARG* 1.3 69.0 - - - +
225A LEU* 1.3 69.9 + - - +
249A GLU 4.9 0.9 - - - +
250A LEU 4.8 0.9 - - - +
285A LYS* 3.2 29.8 - - - +
286A TYR* 3.8 18.8 + - - -
350A LYS* 4.2 24.2 + - - +
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Residues in contact with LEU 225 (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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223A ARG* 3.1 10.2 + - + +
224A SER* 1.3 88.5 - - - +
226A GLY* 1.3 64.6 + - - +
227A PHE 3.6 0.5 + - - -
248A PRO 3.2 26.5 - - - +
249A GLU* 3.4 24.2 - - - +
250A LEU 3.6 7.0 - - - +
252A GLU* 4.2 21.8 - - + +
284A TYR* 3.9 26.1 - - + +
286A TYR* 3.5 26.6 + - - +
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Residues in contact with GLY 226 (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 LEU* 1.3 73.2 - - - +
227A PHE* 1.3 58.1 + - - +
250A LEU 3.0 15.0 + - - -
251A VAL* 3.5 9.2 - - - +
252A GLU* 2.7 33.4 + - - +
286A TYR* 3.3 14.1 - - - -
288A PHE* 3.8 19.1 - - - -
346A LEU* 4.4 4.8 - - - +
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Residues in contact with PHE 227 (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 GLY* 1.3 75.3 - - - +
228A PHE* 1.3 60.8 + - - +
229A ARG* 3.8 33.9 - - + -
252A GLU* 3.3 34.1 - - + -
253A ALA* 5.2 0.7 - - - -
276A VAL* 4.0 21.1 - - + -
281A HIS* 3.6 45.8 - + - -
284A TYR* 3.5 53.6 - + + -
286A TYR 2.8 10.7 + - - -
287A LEU* 3.8 12.4 - - + +
288A PHE* 3.1 28.8 + - - +
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Residues in contact with PHE 228 (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 PHE* 1.3 82.5 - - - +
229A ARG* 1.3 64.4 + - - +
230A GLY* 3.5 22.4 - - - -
237A ARG* 3.5 34.8 - - + -
240A LEU* 3.7 19.7 - - + -
241A ILE* 4.0 25.6 - - + -
252A GLU 3.1 9.2 + - - +
253A ALA* 3.1 23.2 - - + +
254A GLN 3.4 5.3 + - - -
255A TYR* 4.8 1.3 - + - -
281A HIS* 5.6 1.3 - - - -
288A PHE* 3.3 22.4 - - + -
290A PHE* 3.6 28.7 - + - -
298A ARG* 3.5 31.6 - - - -
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Residues in contact with ARG 229 (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 PHE* 3.8 27.4 - - + -
228A PHE* 1.3 78.9 + - - +
230A GLY* 1.3 58.2 + - - +
252A GLU* 2.9 26.3 + - - +
254A GLN* 3.6 28.3 + - - +
256A THR* 3.8 6.5 - - + -
273A ALA* 3.7 18.3 - - - +
274A ASP 2.9 34.2 + - - +
276A VAL* 3.7 16.9 - - + +
281A HIS* 4.4 6.2 + - - +
298A ARG* 3.0 17.6 + - - -
501A UDP 3.3 32.2 + - + +
504A SO4 3.0 44.5 + - - -
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Residues in contact with GLY 230 (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 PHE* 3.5 12.8 - - - -
229A ARG* 1.3 76.7 - - - +
231A SER* 1.3 61.2 + - - -
254A GLN 3.5 2.9 + - - +
255A TYR* 3.2 13.2 - - - -
256A THR* 2.8 27.7 + - - -
298A ARG* 3.2 17.3 - - - -
501A UDP 3.3 6.3 - - - -
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Residues in contact with SER 231 (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 GLY* 1.3 72.7 - - - -
232A ARG* 1.3 59.3 + - - +
233A THR* 2.9 10.3 + - - +
237A ARG* 2.9 26.5 + - - -
255A TYR* 3.7 3.8 - - - -
256A THR* 3.1 27.0 + - - -
257A LYS 4.3 0.2 - - - -
258A ASN* 2.9 37.9 + - - +
501A UDP 2.7 29.5 + - - -
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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