Contacts of the strand formed by residues 263 - 268 (chain E) in PDB entry 4GOO
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 GLU 263 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 3.5 37.6 - - + +
184E TYR* 2.4 37.3 + - - -
226E SER* 4.0 10.6 + - - +
227E ASN 3.2 19.9 - - - +
228E HIS* 3.5 16.6 + - - -
229E ASP* 4.2 2.5 - - - +
244E VAL* 3.7 4.5 - - - +
245E VAL* 2.9 40.0 + - + +
247E VAL* 6.1 2.9 - - + -
261E VAL 4.8 3.7 - - - +
262E ASP* 1.3 75.7 - - - +
264E LEU* 1.3 64.6 + - - +
265E LEU* 5.7 0.2 - - - -
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Residues in contact with LEU 264 (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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225E ILE 3.8 0.2 - - - +
226E SER* 3.4 5.2 + - - -
227E ASN* 2.6 40.6 + - + +
228E HIS 3.7 9.8 - - - +
229E ASP* 4.0 19.5 - - - +
233E THR* 3.7 27.4 - - - +
234E ARG* 4.3 15.0 - - - +
237E TYR* 4.6 10.1 - - + -
242E LEU* 4.1 30.3 - - + -
243E HIS 3.4 22.4 - - - +
244E VAL* 4.2 11.2 - - + -
263E GLU* 1.3 76.5 - - - +
265E LEU* 1.3 69.4 + - - +
266E ALA 4.2 0.4 - - - +
137F ARG* 6.3 0.4 - - - -
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Residues in contact with LEU 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E LEU* 4.8 9.4 - - + -
20E ASP* 3.7 30.3 - - + +
21E ILE* 4.1 18.4 - - + +
24E HIS* 3.6 31.2 - - + -
179E TYR* 5.3 0.2 - - + -
224E LEU* 4.2 15.0 - - + -
225E ILE 3.4 2.9 - - - +
226E SER* 4.0 21.8 - - - +
241E LYS 3.9 0.3 - - - +
242E LEU* 3.8 2.3 - - - -
243E HIS* 3.1 41.3 + - + +
245E VAL* 4.6 11.9 - - + -
263E GLU 5.7 0.2 - - - -
264E LEU* 1.3 81.6 - - - +
266E ALA* 1.3 61.1 + - - +
267E LEU 3.9 1.3 + - - -
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Residues in contact with ALA 266 (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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224E LEU* 3.3 7.3 - - - +
225E ILE* 2.8 36.9 + - + +
237E TYR* 4.0 25.1 - - + -
240E ALA* 3.8 16.4 - - + -
241E LYS 3.9 3.6 - - - -
242E LEU* 3.8 13.5 - - + -
264E LEU* 4.2 1.3 - - + -
265E LEU* 1.3 73.3 - - - +
267E LEU* 1.3 62.6 + - - +
268E TYR* 3.8 8.3 + - + -
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Residues in contact with LEU 267 (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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24E HIS* 3.4 30.3 - - + +
26E PRO* 3.7 21.5 - - + -
223E VAL 3.9 11.7 - - - +
224E LEU* 4.2 11.4 - - + -
240E ALA* 3.2 4.7 - - - +
241E LYS* 3.1 42.3 + - + +
243E HIS* 4.7 15.5 - - + +
265E LEU 3.9 1.2 + - - -
266E ALA* 1.3 73.2 - - - +
268E TYR* 1.3 59.6 + - - +
269E LYS* 3.6 33.6 + - + +
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Residues in contact with TYR 268 (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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210E ALA* 3.7 11.6 + - - +
213E ALA* 3.9 26.5 - - + -
214E GLU* 3.8 36.7 + - + -
217E VAL* 4.1 22.9 - - + -
222E PRO* 3.5 7.1 - - - +
223E VAL* 2.9 44.4 + - + +
225E ILE* 4.0 15.3 - - + -
236E TRP 3.9 1.2 + - - -
237E TYR* 3.5 30.0 - - - -
239E ARG* 4.3 14.8 - - + -
240E ALA* 3.7 25.6 - - + +
266E ALA* 4.0 9.2 - - + -
267E LEU* 1.3 74.2 - - - +
269E LYS* 1.3 58.5 + - - +
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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