Contacts of the strand formed by residues 235 - 242 (chain E) in PDB entry 4KYI
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 ASN 235 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E THR 2.8 20.1 + - - +
68E HIS* 3.6 34.1 + - + +
69E VAL* 3.1 21.5 + - - +
222E ARG* 4.2 4.9 + - - +
234E LYS* 1.3 70.3 - - - +
236E LEU* 1.3 64.7 + - - +
237E SER* 3.6 8.6 + - - -
252E SER* 4.9 1.0 - - - -
253E GLU* 3.2 35.2 - - - +
254E ASP* 3.4 28.1 + - - +
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Residues in contact with LEU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E VAL 3.6 12.6 - - - +
76E ALA 4.7 0.2 - - - +
79E ALA* 3.9 28.5 - - + +
80E SER* 3.7 19.7 - - - +
83E ALA* 3.6 16.2 - - + -
215E LEU* 3.8 18.4 - - + +
218E LEU* 4.3 10.0 - - + +
234E LYS 3.4 4.2 + - - -
235E ASN* 1.3 72.0 - - - +
237E SER* 1.3 68.3 + - - +
238E VAL* 3.8 24.0 - - + -
251E TYR 4.1 0.7 - - - +
252E SER 3.7 2.6 - - - -
253E GLU* 3.4 29.0 + - - +
261E ILE* 3.7 29.8 - - + -
265E VAL* 4.9 0.2 - - + -
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Residues in contact with SER 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E HIS* 6.0 1.6 - - - +
69E VAL 3.3 6.9 + - - +
70E SER* 3.1 43.3 + - - -
71E GLY 3.2 2.3 + - - -
235E ASN* 4.3 7.8 + - - -
236E LEU* 1.3 75.4 - - - +
238E VAL* 1.3 64.2 + - - +
239E VAL* 5.4 0.2 - - - -
250E ARG* 4.3 11.8 + - - -
251E TYR 3.2 5.6 - - - -
252E SER* 3.2 27.1 - - - -
297E GLU 5.7 0.5 + - - -
298E ILE* 5.2 5.4 - - - +
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Residues in contact with VAL 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLY 3.2 13.0 - - - +
76E ALA* 4.2 12.1 - - + +
215E LEU* 5.8 0.9 - - + -
236E LEU* 3.8 25.6 - - + -
237E SER* 1.3 77.9 - - - +
239E VAL* 1.3 64.1 + - - +
240E VAL* 4.3 4.3 + - + -
250E ARG* 3.7 2.4 - - - +
251E TYR* 2.9 36.6 + - + +
264E VAL* 3.4 46.2 - - + +
265E VAL* 4.3 18.6 - - + -
268E SER* 4.4 2.7 - - - -
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Residues in contact with VAL 239 (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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70E SER* 4.5 4.9 - - - +
71E GLY 3.3 5.3 + - - -
72E ALA* 3.6 6.8 - - + +
237E SER 5.4 0.2 - - - -
238E VAL* 1.3 80.2 - - - +
240E VAL* 1.3 71.9 + - - +
248E LEU* 4.0 21.8 - - + -
249E GLU 3.4 13.2 - - - +
250E ARG* 3.9 18.4 - - + -
268E SER* 3.0 19.6 + - - -
289E GLY* 3.4 11.5 - - - +
294E ASN* 4.3 9.2 - - - +
296E PRO* 3.7 35.7 - - + -
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Residues in contact with VAL 240 (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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238E VAL* 4.5 1.8 - - + -
239E VAL* 1.3 77.7 - - - +
241E THR* 1.3 65.2 + - - +
248E LEU* 3.5 12.1 - - - +
249E GLU* 3.0 36.3 + - + +
251E TYR* 3.5 35.0 - - + -
264E VAL 3.7 11.7 - - - +
267E TRP* 3.7 8.3 - - + -
268E SER* 3.5 27.8 - - - +
286E ILE* 3.7 15.9 - - + -
287E ALA 3.8 7.0 - - - +
289E GLY* 3.6 7.4 - - - -
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Residues in contact with THR 241 (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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240E VAL* 1.3 78.8 - - - +
242E ASN* 1.3 60.8 + - - +
243E GLN* 3.1 19.0 + - + +
247E GLU 3.8 3.6 - - - +
248E LEU* 3.8 9.7 - - + +
286E ILE* 3.4 2.8 - - - -
287E ALA 3.0 29.6 + - - -
288E ASP 2.5 26.4 + - - -
289E GLY* 3.4 9.2 - - - -
291E ILE* 4.4 8.3 + - + +
291G ILE* 4.2 15.7 - - + -
292G LEU* 3.7 28.2 - - + +
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Residues in contact with ASN 242 (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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240E VAL* 4.0 2.6 + - - +
241E THR* 1.3 68.5 - - - +
243E GLN* 1.3 54.9 + - - +
244E THR* 3.4 10.9 + - - -
245E LYS* 2.8 47.1 + - + +
246E HIS 2.8 30.3 + - - -
247E GLU 2.9 20.5 + - - +
249E GLU* 3.3 34.0 + - + +
280E ASN* 4.5 0.2 - - - +
284E GLU* 2.9 30.0 + - - +
285E TYR 3.6 6.7 - - - -
286E ILE* 4.3 10.9 - - + +
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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