Contacts of the strand formed by residues 341 - 345 (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 LEU 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ALA* 4.1 10.8 - - + -
334B SER 3.4 10.1 - - - +
335B SER* 4.2 5.6 - - - -
340B ARG* 1.3 73.8 - - - +
342B ASN* 1.3 67.0 + - - +
343B VAL* 3.9 16.0 + - + +
367B PHE 3.8 0.9 - - - +
368B ILE* 3.7 0.3 - - - -
369B HIS* 2.7 48.3 + - + +
376B ILE* 3.9 10.0 - - + +
379B PHE* 3.5 41.7 - - + -
389B ILE* 4.4 3.1 - - + -
391B SER* 4.1 11.4 - - - -
401B TRP* 3.8 31.9 - - + -
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Residues in contact with ASN 342 (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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314B SER* 4.0 5.2 - - - -
315B HIS* 3.2 46.0 + - + -
333B ALA* 3.1 5.4 - - - +
334B SER 2.8 33.6 + - - -
340B ARG* 4.0 8.1 - - - +
341B LEU* 1.3 77.8 - - - +
343B VAL* 1.3 62.0 + - - +
344B TRP* 3.7 24.4 + - + -
365B LEU* 4.2 7.0 - - + -
367B PHE 3.4 2.0 - - - -
368B ILE* 3.4 36.1 - - - +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.7 23.8 - - + -
332B LEU 3.3 8.3 - - - +
333B ALA* 4.4 4.9 - - + -
341B LEU* 3.9 18.6 - - + -
342B ASN* 1.3 77.4 - - - +
344B TRP* 1.3 65.6 + - - +
365B LEU* 3.9 2.9 - - - +
366B LEU* 2.9 39.9 + - + +
367B PHE* 2.8 39.4 + - + +
381B TRP* 4.4 9.9 - - + -
387B TRP* 4.3 7.6 - - + -
389B ILE* 5.0 0.2 - - + -
401B TRP* 4.5 7.9 - - + -
403B MSE 5.5 2.5 - - - -
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Residues in contact with TRP 344 (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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297B VAL* 4.5 4.3 - - + +
312B PHE* 3.4 56.5 - + + -
313B GLU 3.6 27.6 - - - -
314B SER* 3.7 13.5 - - - -
315B HIS* 4.2 6.7 - - - -
330B THR 3.5 0.5 - - - +
331B ILE* 3.3 9.8 - - - +
332B LEU* 2.5 64.2 + - + +
333B ALA* 4.4 0.7 - - - -
334B SER* 3.0 26.0 + - - -
342B ASN* 3.7 27.4 + - + -
343B VAL* 1.3 76.1 - - - +
345B ASP* 1.3 60.5 + - - +
346B LEU 4.0 0.7 - - - +
362B PRO* 4.2 6.7 - - + -
364B GLU* 3.2 13.9 - - + +
365B LEU* 3.8 28.0 - - + -
366B LEU* 4.5 1.8 - - - -
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Residues in contact with ASP 345 (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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330B THR* 3.0 26.4 + - - +
331B ILE* 3.6 14.3 - - + +
343B VAL 4.4 0.2 + - - -
344B TRP* 1.3 71.7 - - - +
346B LEU* 1.3 65.2 + - - +
347B SER* 3.1 21.1 + - - -
348B LYS* 3.0 36.7 + - + -
364B GLU* 2.8 27.8 + - - +
366B LEU* 4.1 18.1 - - + +
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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