Contacts of the strand formed by residues 286 - 291 (chain E) in PDB entry 4K81
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 286 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E SER* 4.6 2.4 + - - -
282E GLU 3.9 20.7 + - - -
283E PHE* 4.5 7.8 - - - +
284E GLY 3.6 2.3 + - - +
285E ASN* 1.3 77.8 + - - +
287E ASP* 1.3 65.9 + - - +
288E ILE* 4.8 0.6 - - - +
308E PHE* 4.4 13.5 - - - +
309E LYS 3.4 6.5 - - - -
310E PRO* 3.4 25.5 - - - +
311E ASN* 3.7 1.3 - - - -
341E LYS* 2.8 35.4 + - - +
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Residues in contact with ASP 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E GLU* 4.4 0.7 - - - +
162E ARG* 3.8 30.4 + - - +
168E GLU* 5.0 0.7 - - - +
176E ASN* 4.5 9.0 + - - -
286E SER* 1.3 80.6 - - - +
288E ILE* 1.3 62.8 + - - +
289E TYR* 3.4 33.5 + - + +
308E PHE* 3.3 7.6 - - - +
309E LYS* 2.9 35.6 + - - +
311E ASN* 3.5 15.4 - - - +
341E LYS* 3.7 16.3 + - - +
342E TYR* 4.2 1.3 + - - -
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Residues in contact with ILE 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ARG* 3.2 23.2 - - - +
283E PHE* 4.4 5.2 - - + -
287E ASP* 1.3 76.7 - - - +
289E TYR* 1.3 68.0 + - - +
290E VAL* 5.9 0.2 - - - +
306E PHE* 4.5 10.1 - - + -
307E CYS 3.5 3.4 - - - +
308E PHE* 3.6 27.1 - - + -
334E VAL* 4.7 21.6 - - + +
337E ILE* 3.6 33.0 - - + -
338E ARG* 4.3 24.1 - - + +
341E LYS* 3.9 26.5 - - + -
342E TYR* 4.8 4.5 + - + +
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Residues in contact with TYR 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E GLU* 2.7 43.4 + - - -
155E LEU* 3.7 16.6 - - + -
160E VAL* 3.5 29.2 - - + -
161E GLU* 3.5 13.9 - - - +
162E ARG* 3.6 18.8 - - + -
287E ASP* 3.4 34.1 + - + -
288E ILE* 1.3 77.7 - - - +
290E VAL* 1.3 65.2 + - - +
306E PHE* 3.2 8.1 - - - +
307E CYS* 2.9 40.2 + - - -
309E LYS* 3.2 38.7 + - + -
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Residues in contact with VAL 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E VAL* 3.2 5.8 - - - -
161E GLU* 2.8 38.7 + - + +
162E ARG* 6.3 0.2 - - - -
289E TYR* 1.3 77.0 - - - +
291E SER* 1.3 77.5 + - - +
305E GLY 3.8 3.8 - - - -
306E PHE* 4.3 3.8 - - + -
330E ARG* 3.7 26.9 - - + +
334E VAL* 3.9 33.9 - - + -
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Residues in contact with SER 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E GLY 3.5 9.1 + - - -
160E VAL* 4.1 9.7 - - - +
290E VAL* 1.3 87.7 - - - +
292E LEU* 1.3 66.8 + - - +
303E ASN 4.6 6.1 - - - +
305E GLY* 3.1 32.8 + - - -
306E PHE* 4.9 0.5 - - - -
330E ARG* 4.0 11.9 + - - -
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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