Contacts of the strand formed by residues 331 - 336 (chain B) in PDB entry 3CFV
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 ILE 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B TRP* 3.4 10.5 - - - -
325B SER* 3.0 36.3 + - - -
328B ASN* 3.1 26.9 + - + +
329B GLU 3.3 0.6 - - - -
330B THR* 1.3 82.2 - - - +
332B LEU* 1.3 63.8 + - - +
343B VAL* 3.7 23.6 - - + -
344B TRP 3.3 4.9 - - - +
345B ASP* 3.6 32.3 - - + +
366B LEU* 4.5 3.6 - - + -
381B TRP* 3.8 19.5 - - + -
387B TRP* 3.8 25.6 - - + -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA* 3.9 20.4 - - + -
297B VAL* 4.1 16.6 - - + -
312B PHE* 4.3 17.3 - - + -
322B VAL* 3.5 21.1 - - + -
323B HIS 3.3 20.2 - - - +
324B TRP* 3.8 34.1 - - + +
330B THR 4.1 0.6 + - - +
331B ILE* 1.3 74.1 - - - +
333B ALA* 1.3 69.9 + - - +
343B VAL* 3.3 4.0 - - - +
344B TRP* 2.5 58.8 + - + +
346B LEU* 5.4 3.1 - - + -
381B TRP* 4.6 3.1 - - - -
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.3 6.8 - - - +
323B HIS 2.9 32.8 + - - -
332B LEU* 1.3 76.5 - - - +
334B SER* 1.3 60.9 + - - +
341B LEU* 4.1 11.9 - - + -
342B ASN 3.1 9.6 - - - +
343B VAL* 4.4 2.7 - - + -
344B TRP* 4.6 1.1 - - - -
379B PHE* 3.4 23.1 - - + -
381B TRP* 3.6 24.9 - - + +
389B ILE* 4.6 0.4 - - + -
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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
----------------------------------------------------------
297B VAL* 3.9 20.4 - - - +
315B HIS* 2.7 32.0 + - - -
319B ILE* 4.3 5.4 - - - -
321B GLN 3.2 11.4 - - - -
322B VAL* 4.3 5.4 - - - -
333B ALA* 1.3 75.4 - - - +
335B SER* 1.3 60.7 + - - +
341B LEU* 3.4 2.5 - - - +
342B ASN 2.8 32.8 + - - -
344B TRP* 3.0 18.9 + - - -
379B PHE* 4.2 2.9 - - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B HIS* 4.0 4.5 - - - -
319B ILE* 3.5 6.5 - - - +
320B PHE 3.0 19.8 + - - -
321B GLN* 2.9 21.1 + - - +
334B SER* 1.3 75.0 - - - +
336B GLY* 1.3 60.9 + - - +
340B ARG 3.4 10.8 - - - -
341B LEU* 4.2 4.3 - - - -
376B ILE* 3.7 32.6 + - - +
378B ASP 4.9 0.2 - - - -
379B PHE* 3.3 24.7 - - - -
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Residues in contact with GLY 336 (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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315B HIS* 5.2 0.4 - - - -
318B GLU 3.2 13.5 - - - -
319B ILE* 4.1 0.2 - - - -
320B PHE* 4.0 8.3 - - - -
335B SER* 1.3 78.6 - - - +
337B THR* 1.3 63.2 - - - -
338B ASP* 3.3 7.9 + - - -
339B ARG* 3.4 6.8 + - - -
340B ARG 3.6 7.5 + - - -
375B LYS* 4.2 6.1 - - - -
376B ILE* 3.3 27.7 + - - +
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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
------------------------------------------------------------
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