Contacts of the helix formed by residues 291 - 297 (chain B) in PDB entry 3F78
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 THR 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B ILE* 3.6 14.5 - - - +
262B GLY* 5.1 0.4 - - - -
289B LEU* 3.3 4.5 - - - +
290B ASP* 1.3 104.0 + - + +
292B PHE* 1.3 62.8 + - - +
293B GLU* 3.4 25.4 + - - +
294B LYS* 3.2 33.4 + - - +
295B LEU 4.3 0.7 + - - -
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Residues in contact with PHE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 3.5 32.5 - - + -
146B GLU* 3.3 49.4 - - + -
149B LYS* 3.6 28.3 - - + +
150B ILE* 4.2 12.8 - - + -
238B THR 5.8 0.4 - - - -
239B ASP* 4.1 11.7 - - + -
261B ILE* 3.7 46.4 - - + -
262B GLY* 4.9 4.5 - - - -
291B THR* 1.3 70.4 - - - +
293B GLU* 1.3 68.3 + - - +
294B LYS 3.1 2.2 - - - -
295B LEU* 3.2 28.4 + - + +
296B LYS* 5.7 0.5 - - - +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ASP* 5.0 1.9 - - - +
149B LYS* 3.6 28.1 + - - +
291B THR* 3.2 22.4 - - - +
292B PHE* 1.3 77.4 + - - +
294B LYS* 1.3 59.8 + - + +
295B LEU 3.3 1.0 + - - -
296B LYS* 3.5 24.3 + - - +
297B ASP* 4.8 1.7 - - - +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 3.9 27.7 - - + +
290B ASP* 2.6 44.5 + - - +
291B THR* 3.2 19.7 + - - +
292B PHE 3.1 1.8 - - - -
293B GLU* 1.3 74.1 - - + +
295B LEU* 1.3 63.4 + - - +
296B LYS 3.1 2.9 - - - -
297B ASP* 3.0 38.6 + - + +
298B LEU* 3.9 2.4 + - - +
271C GLN* 4.9 10.0 - - - +
288C ILE* 6.4 2.5 - - - -
290C ASP* 5.8 9.2 - - + -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 3.8 29.2 - - + +
150B ILE* 4.1 10.1 - - + +
153B PHE* 3.5 54.9 - - + -
237B ILE* 4.8 3.4 - - + -
259B ILE* 4.3 10.8 - - + -
261B ILE* 3.9 32.5 - - + -
289B LEU* 3.9 14.8 - - + +
292B PHE* 3.2 23.8 + - + +
294B LYS* 1.3 76.8 - - - +
296B LYS* 1.3 62.2 + - + +
298B LEU* 3.2 18.9 + - + +
299B PHE* 4.3 1.4 + - - -
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ASP* 5.2 8.9 - - - +
156B ASP* 3.2 24.0 + - - -
292B PHE 5.7 0.4 - - - +
293B GLU* 3.6 18.2 - - - +
295B LEU* 1.3 79.2 - - + +
297B ASP* 1.3 65.5 + - - +
299B PHE* 3.0 42.9 + - + +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 6.1 1.1 - - + -
293B GLU 4.8 0.9 - - - +
294B LYS* 3.0 39.1 + - + +
296B LYS* 1.3 84.4 - - - +
298B LEU* 1.3 62.2 + - + +
299B PHE 3.5 0.8 + - - -
300B THR* 4.7 5.5 + - - -
301B GLU* 5.1 3.3 + - - +
287C LYS* 6.0 0.3 + - - -
294C LYS* 5.2 16.9 + - - +
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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