Contacts of the strand formed by residues 388 - 393 (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 VAL 388 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.5 10.1 - - + -
48B TRP* 4.1 3.1 - - + -
85B ILE* 4.5 8.7 - - + -
381B TRP* 3.9 1.7 - - - -
382B ASN* 2.8 48.7 + - + +
385B GLU* 3.2 28.0 + - + +
386B PRO 3.1 1.6 - - - -
387B TRP* 1.3 78.2 - - - +
389B ILE* 1.3 63.7 + - - +
400B ILE* 4.0 25.4 - - + -
401B TRP 3.4 4.3 - - - +
402B GLN* 3.7 32.5 - - + +
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 4.4 3.8 - - - -
341B LEU* 4.4 11.4 - - + -
343B VAL* 5.0 1.8 - - + -
379B PHE* 4.1 18.2 - - + -
380B SER 3.5 10.5 - - - +
381B TRP* 3.6 52.7 - - + +
387B TRP 4.5 3.4 - - - +
388B VAL* 1.3 77.5 - - - +
390B CYS* 1.3 75.7 + - - +
399B GLN 3.6 0.7 - - - +
400B ILE* 3.3 4.5 - - - +
401B TRP* 2.8 74.9 + - + +
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Residues in contact with CYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.9 15.9 - - + +
48B TRP* 3.5 27.5 - - + +
65B LEU* 4.4 7.0 - - + -
379B PHE* 3.0 2.9 - - - -
380B SER* 2.7 37.0 + - - -
389B ILE* 1.3 77.8 - - - +
391B SER* 1.3 64.8 + - - +
398B MSE 3.3 33.4 - - - -
399B GLN 3.1 10.8 - - - +
400B ILE* 4.0 9.6 - - + -
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Residues in contact with SER 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.7 0.2 - - - -
341B LEU* 4.1 12.8 - - - -
369B HIS* 4.0 0.7 + - - -
372B HIS* 2.7 30.9 + - - -
376B ILE* 4.3 4.9 - - - -
378B ASP 3.5 6.3 - - - -
379B PHE* 3.7 15.3 - - - -
389B ILE 4.2 0.2 - - - -
390B CYS* 1.3 75.4 - - - +
392B VAL* 1.3 65.2 + - - +
398B MSE 3.4 2.6 - - - +
399B GLN 2.9 29.2 + - - -
401B TRP* 3.1 20.7 + - - -
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.8 1.3 - - + -
43B SER* 3.4 28.5 - - - +
45B THR 4.3 4.5 - - - +
46B VAL* 3.4 38.1 - - + -
67B LEU* 4.2 7.4 - - + -
372B HIS* 4.1 1.8 - - - -
376B ILE* 3.5 5.4 - - - +
377B SER* 2.8 24.8 + - - -
378B ASP* 3.0 23.4 + - + +
391B SER* 1.3 78.5 - - - +
393B SER* 1.3 60.4 + - - +
397B ILE 3.4 5.4 - - - +
398B MSE 3.6 22.2 - - + -
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Residues in contact with SER 393 (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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42B PRO* 4.1 5.7 - - - +
43B SER 4.5 5.4 + - - +
372B HIS* 2.9 29.4 + - - +
374B ALA 3.6 13.5 - - - -
375B LYS 3.1 14.6 - - - -
376B ILE* 4.1 0.7 - - - +
377B SER* 4.4 3.4 - - - -
392B VAL* 1.3 74.9 - - - +
394B GLU* 1.3 61.3 + - - +
395B ASP* 2.4 33.8 + - - -
396B ASN* 3.3 11.3 + - - -
397B ILE* 3.0 14.2 + - - +
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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
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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