Contacts of the strand formed by residues 278 - 283 (chain E) in PDB entry 3V56
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 PHE 278 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.8 24.2 - + - -
247D SER* 3.8 11.2 - - - -
248D ALA 3.1 28.5 - - - -
249D GLY* 4.5 0.2 - - - -
148E GLN* 4.9 4.5 - - + -
149E LEU 3.3 14.6 - - - +
150E ILE* 4.0 13.0 - - + -
168E TRP* 3.6 6.8 - - - -
196E TYR* 4.2 22.4 - + - -
197E GLY* 3.4 0.5 - - - -
198E GLN* 2.9 70.5 + - + +
246E TYR* 4.3 3.4 - + - -
261E LEU* 4.3 0.9 - - - +
274E GLY 3.9 10.8 - - - -
275E ASP 3.7 12.8 - - - -
276E VAL 4.0 0.4 - - - -
277E THR* 1.3 80.6 - - - +
279E PHE* 1.3 64.6 + - - +
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Residues in contact with PHE 279 (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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148E GLN* 3.6 0.6 - - - -
149E LEU* 2.7 48.8 + - + +
168E TRP* 3.7 36.3 - + + -
184E LYS* 5.4 1.3 - - - -
185E ILE* 3.8 23.3 - - + +
195E ILE* 4.1 9.2 - - + -
196E TYR* 3.3 22.7 - - - -
197E GLY* 4.2 0.4 - - - -
212E ILE* 4.1 25.4 - - + -
259E LEU* 3.8 24.7 - - + -
260E GLN* 3.8 23.3 - - - -
261E LEU* 3.8 26.9 - - + -
278E PHE* 1.3 77.0 - - - +
280E GLY* 1.3 54.9 + - - +
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Residues in contact with GLY 280 (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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147E LEU 3.2 12.6 - - - -
148E GLN* 4.1 0.4 - - - -
185E ILE* 4.0 7.4 - - - -
195E ILE* 3.6 5.7 - - - +
196E TYR* 2.9 56.4 + - - +
279E PHE* 1.3 76.1 - - - +
281E ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 281 (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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250D ILE* 4.4 1.0 - - - +
146E CYS* 3.3 4.9 - - - +
147E LEU 3.0 30.4 + - - +
178E LEU* 3.4 26.9 - - + +
185E ILE* 4.3 6.5 - - + +
193E PHE* 4.9 4.3 - - + -
194E PHE 3.3 10.5 - - - +
195E ILE* 4.2 15.7 - - + -
196E TYR* 3.7 2.8 - - - -
259E LEU* 4.4 11.0 - - + -
280E GLY* 1.3 75.1 - - - +
282E LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 282 (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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194D PHE* 5.3 5.8 - - + -
250D ILE* 3.9 16.6 - - + -
282D LEU* 6.5 0.4 - - + -
284D LEU* 3.6 43.5 - - + -
144E GLN* 3.7 34.5 - - + +
145E ASP 3.6 8.1 - - - +
146E CYS* 4.1 3.4 - - + -
193E PHE* 3.3 5.9 - - - -
194E PHE* 2.8 63.6 + - + +
196E TYR* 5.0 0.2 - - + -
281E ALA* 1.3 75.6 - - - +
283E LYS* 1.3 63.0 + - - +
284E LEU* 3.5 5.1 + - + -
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Residues in contact with LYS 283 (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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144E GLN* 3.3 27.8 + - - +
145E ASP* 2.8 30.9 + - + +
177E ALA* 3.8 6.3 - - + +
178E LEU* 4.6 0.4 - - - +
189E GLU* 2.7 38.5 + - - +
190E THR 4.0 18.4 + - - -
191E GLY* 4.4 4.9 - - - -
192E TYR 4.0 3.6 - - - +
193E PHE* 3.5 37.7 - - + -
282E LEU* 1.3 71.8 - - - +
284E LEU* 1.3 74.8 + - - +
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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