Contacts of the helix formed by residues 332 - 337 (chain B) in PDB entry 3F4V
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 SER 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP* 3.5 21.5 + - - -
204B SER* 3.4 14.8 - - - -
205B ALA* 3.9 3.4 - - - +
331B THR* 1.3 86.1 + - - +
333B TYR* 1.3 65.2 + - - +
334B SER* 3.4 6.8 + - - -
335B ALA* 3.0 25.5 + - - +
336B ASP* 2.9 29.5 + - - +
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG* 3.2 31.7 + - + +
182B LEU* 3.9 23.8 - - + -
186B ASP* 3.5 13.6 + - - +
204B SER 3.1 8.5 + - - -
205B ALA* 4.4 1.2 - - - +
208B PRO* 3.9 19.5 - - + -
209B TYR* 3.4 36.3 - + + +
266B PHE* 2.7 31.5 + + - -
270B TRP* 3.3 39.2 - + - -
332B SER* 1.3 71.9 - - - +
334B SER* 1.3 66.6 + - - +
336B ASP* 3.2 11.4 + - - +
337B TRP* 3.0 41.8 - + - -
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.3 19.9 - - - +
186B ASP* 2.9 26.4 + - - -
187B GLN* 4.6 6.9 + - - +
332B SER* 3.1 6.0 - - - -
333B TYR* 1.3 79.6 - - - +
335B ALA* 1.3 60.9 + - - +
336B ASP 3.4 0.2 + - - -
337B TRP* 3.5 26.0 + - - +
338B GLN 4.7 0.3 + - - -
339B VAL* 5.7 0.3 - - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLN* 4.0 14.7 - - - +
331B THR* 3.4 26.7 - - - +
332B SER* 3.0 15.0 + - - +
334B SER* 1.3 72.0 - - - +
336B ASP* 1.3 65.8 + - - +
337B TRP 3.1 3.6 + - - -
338B GLN* 3.2 19.8 + - - +
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Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TYR* 2.6 26.8 + - - +
266B PHE* 3.7 19.8 - - + -
287B LEU* 3.7 18.0 - - + +
288B VAL* 4.0 4.6 - - + +
291B ARG* 2.8 42.5 + - - -
328B GLN* 5.6 0.7 - - - -
330B PRO* 4.7 7.8 - - - +
331B THR 4.9 0.3 + - - -
332B SER 2.9 20.7 + - - +
333B TYR 3.2 11.1 + - - +
335B ALA* 1.3 78.1 - - - +
337B TRP* 1.3 60.6 + - - +
338B GLN* 3.2 6.8 + - - +
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Residues in contact with TRP 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG* 3.8 15.3 - - - -
247B TYR* 3.4 30.5 - + - -
262B ARG* 2.9 30.4 + - - +
263B ALA* 3.7 33.4 - - + -
266B PHE* 3.4 42.1 - + + +
267B HIS* 4.1 7.9 - - + -
320B MET* 5.5 1.8 - - + -
333B TYR* 3.0 62.6 + + - -
334B SER* 3.5 14.9 + - - +
335B ALA 3.1 0.8 - - - -
336B ASP* 1.3 77.7 - - - +
338B GLN* 1.3 61.5 + - - +
339B VAL* 3.4 26.2 + - + +
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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
------------------------------------------------------------
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