Contacts of the strand formed by residues 249 - 256 (chain E) in PDB entry 3FFC
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 GLN 249 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E PRO* 3.9 20.0 - - - +
228E VAL 3.7 0.3 - - - +
229E GLN* 3.2 9.0 - - - +
230E PHE* 2.8 40.5 + - + +
245E LYS 4.8 1.4 - - - +
246E PRO* 4.3 1.6 - - - +
247E VAL* 2.8 35.6 + - + +
248E THR* 1.3 76.4 - - - +
250E ILE* 1.3 60.3 + - - +
251E VAL* 3.4 28.8 - - + +
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Residues in contact with ILE 250 (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 ARG* 4.5 1.8 - - - +
227E GLN* 3.6 46.2 - - + +
228E VAL 3.4 4.3 - - - +
229E GLN* 3.4 31.9 - - - +
249E GLN* 1.3 75.0 + - - +
251E VAL* 1.3 62.2 + - - +
252E SER* 3.8 17.8 + - - +
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Residues in contact with VAL 251 (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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138E PRO* 4.8 0.9 - - + -
139E PRO* 3.5 39.7 - - + +
140E GLU* 4.5 1.8 - - - -
141E VAL* 3.3 27.8 - - + +
228E VAL 2.9 29.3 + - - +
249E GLN* 3.4 36.3 - - + +
250E ILE* 1.3 74.3 - - - +
252E SER* 1.3 62.7 + - - +
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Residues in contact with SER 252 (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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141E VAL* 4.1 7.1 - - - +
225E ARG* 3.6 33.1 + - - -
226E CYS 3.1 16.8 - - - -
227E GLN* 3.9 3.1 - - - -
250E ILE* 3.8 11.2 + - - +
251E VAL* 1.3 79.5 - - - +
253E ALA* 1.3 58.5 + - - +
254E GLU* 5.6 1.4 - - - +
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Residues in contact with ALA 253 (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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137D SER* 6.5 0.2 - - - -
141E VAL* 3.4 28.9 - - + +
142E ALA* 3.8 0.7 - - - -
143E VAL* 3.3 32.3 - - + +
225E ARG* 3.5 3.5 - - - +
226E CYS 2.7 37.4 + - - +
252E SER* 1.3 73.6 - - - +
254E GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 254 (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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137D SER* 3.7 12.8 + - - -
143E VAL* 4.2 5.8 - - - +
223E HIS* 2.9 37.6 + - + +
224E PHE 3.3 5.4 - - - +
225E ARG* 4.1 12.9 - - + -
252E SER 5.6 1.1 - - - +
253E ALA* 1.3 77.4 - - - +
255E ALA* 1.3 64.0 + - - +
256E TRP* 5.8 5.8 + - + -
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Residues in contact with ALA 255 (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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137D SER* 4.1 13.0 - - - +
143E VAL* 4.1 18.8 - - + -
145E GLU* 4.2 17.9 - - + +
159E LEU* 4.7 9.0 - - + -
217E TRP* 4.7 0.2 - - + -
223E HIS* 3.8 3.9 - - - -
224E PHE* 2.8 39.1 + - - +
254E GLU* 1.3 77.0 - - - +
256E TRP* 1.3 66.6 + - - +
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Residues in contact with TRP 256 (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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145E GLU* 4.0 7.8 + - - +
217E TRP* 3.3 20.8 - - - -
220E PRO* 3.5 17.9 - - + +
221E ARG* 3.9 19.3 - - - -
222E ASN 3.4 19.1 - - - -
223E HIS* 3.9 43.4 + + + -
254E GLU* 5.7 6.1 + - + -
255E ALA* 1.3 77.4 - - - +
257E GLY* 1.3 68.0 + - - +
258E ARG* 3.7 1.9 + - - +
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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