Contacts of the strand formed by residues 288 - 293 (chain E) in PDB entry 3T0E
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 288 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E SER* 5.4 0.2 - - - -
184E SER 2.5 16.5 + - - +
185E ILE* 3.2 36.1 - - + +
186E VAL* 2.7 37.6 + - - +
268E GLY 4.0 0.9 - - - -
269E SER* 2.9 35.4 - - - -
286E GLU* 3.9 21.0 + - - +
287E VAL* 1.3 77.1 + - - +
289E LEU* 1.3 57.8 + - - +
308E PRO* 3.8 19.3 - - + +
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Residues in contact with LEU 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E VAL* 3.3 12.8 - - + +
188E LYS* 5.9 0.4 - - + -
194E VAL* 3.3 43.5 - - + -
196E PHE* 4.4 8.7 - - + -
215E TRP* 4.5 12.3 - - + -
259E LEU* 4.4 15.5 - - + -
262E ALA* 5.1 4.5 - - + -
266E TYR* 3.4 28.5 - - + +
267E ALA* 3.6 0.7 - - - -
268E GLY 3.1 34.5 + - - +
287E VAL 4.4 0.4 - - - -
288E ASN* 1.3 76.0 - - - +
290E VAL* 1.3 67.6 + - - +
291E VAL* 3.7 24.2 - - + -
307E GLY* 3.8 2.4 - - - -
308E PRO* 4.7 0.6 - - - +
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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
----------------------------------------------------------
185E ILE* 5.1 2.9 - - + -
186E VAL 3.2 6.1 + - - +
187E TYR* 2.9 43.1 - - + -
188E LYS* 3.1 22.7 + - - +
289E LEU* 1.3 79.5 - - - +
291E VAL* 1.3 62.9 + - - +
305E VAL* 5.1 7.6 - - + -
306E TRP 3.1 16.2 - - - +
307E GLY* 3.7 1.1 - - - -
308E PRO* 3.6 23.8 - - + -
309E THR* 3.5 26.2 - - + +
347E LEU* 5.8 2.2 - - + -
355E LEU* 5.6 2.7 - - + -
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Residues in contact with VAL 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E LYS 3.6 2.9 - - - +
189E LYS 3.0 29.6 - - - +
190E GLU* 4.2 4.7 - - + -
262E ALA* 3.6 21.5 - - + +
263E LEU 3.2 24.0 - - - +
264E PRO* 4.8 1.3 - - + -
267E ALA* 3.7 18.6 - - + -
289E LEU* 3.7 16.4 - - + -
290E VAL* 1.3 80.0 - - - +
292E MET* 1.3 62.2 + - - +
305E VAL* 3.4 5.7 - - - +
306E TRP* 2.9 41.2 + - + -
355E LEU* 5.1 0.2 - - - -
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Residues in contact with MET 292 (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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188E LYS 3.4 5.1 + - - -
189E LYS* 3.8 2.1 - - - +
190E GLU* 3.4 25.5 + - - +
291E VAL* 1.3 78.2 - - - +
293E ARG* 1.3 65.1 + - - +
294E ALA* 4.2 9.3 + - + +
303E CYS* 4.0 11.2 - - - -
304E GLU 3.5 5.8 - - - +
305E VAL* 3.8 13.7 - - + -
306E TRP* 5.8 0.7 - - - -
345E CYS* 3.3 30.7 - - + +
347E LEU* 3.7 16.4 - - + -
355E LEU* 3.3 36.8 - - + +
357E SER* 3.4 39.9 - - - +
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Residues in contact with ARG 293 (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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190E GLU* 2.9 41.5 + - - +
264E PRO* 3.3 20.8 - - - +
292E MET* 1.3 76.3 - - - +
294E ALA* 1.3 60.0 + - - +
295E THR* 3.6 29.1 + - + +
302E THR 4.0 1.4 - - - +
303E CYS* 3.1 30.8 - - - -
304E GLU* 3.2 43.0 + - - +
306E TRP* 3.1 32.1 - - - +
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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