Contacts of the strand formed by residues 428 - 435 (chain F) in PDB entry 3CB4
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 428 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A GLN* 5.3 7.6 - - - +
434A TYR* 3.6 32.3 - - + -
426F ARG 4.3 6.1 - - - +
427F GLY* 1.3 77.9 - - - +
429F GLN* 1.3 67.3 + - - +
430F THR* 3.5 1.8 + - - +
443F TYR* 3.5 4.6 - - - -
444F GLU* 2.7 55.5 + - + +
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Residues in contact with GLN 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A GLN* 3.1 29.8 + - - +
432A MET* 4.0 26.3 - - + +
434A TYR* 3.1 34.6 + - - +
419F ILE* 4.9 2.4 - - - +
428F VAL* 1.3 73.0 - - - +
430F THR* 1.3 63.5 + - - +
431F ASN* 4.0 16.1 + - - +
432F MET* 3.5 20.8 - - - +
441F LEU* 4.2 7.5 - - - +
442F THR 4.0 0.7 - - - +
443F TYR* 3.3 45.8 + - + +
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Residues in contact with THR 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F GLU* 4.6 12.3 - - - +
428F VAL* 3.5 4.2 + - - +
429F GLN* 1.3 74.7 + - - +
431F ASN* 1.3 65.3 + - + +
442F THR* 2.8 31.4 + - + +
444F GLU* 3.4 33.2 + - - +
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Residues in contact with ASN 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429F GLN* 3.7 11.3 - - - +
430F THR* 1.3 86.4 - - + +
432F MET* 1.3 73.0 + - - +
433F VAL* 3.5 24.9 - - - +
440F ALA 5.2 0.2 + - - -
441F LEU* 4.0 1.4 - - - -
442F THR* 3.1 50.2 + - + +
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Residues in contact with MET 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ILE* 6.4 1.6 - - + -
429A GLN* 3.6 41.3 - - + +
443A TYR* 5.0 3.6 - - - +
415F LEU* 3.5 33.9 - - + -
419F ILE* 5.2 4.0 - - + -
429F GLN* 3.5 15.7 - - - +
431F ASN* 1.3 81.4 + - - +
433F VAL* 1.3 66.8 + - - +
434F TYR* 4.2 18.1 - - + +
439F VAL* 3.9 12.1 - - + -
440F ALA 3.4 4.3 - - - +
441F LEU* 3.8 27.6 - - + -
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Residues in contact with VAL 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431F ASN* 3.5 24.7 - - - +
432F MET* 1.3 79.0 - - - +
434F TYR* 1.3 72.4 + - - +
435F HIS* 3.5 28.3 - - + +
439F VAL* 3.6 4.3 - - - +
440F ALA* 2.7 43.9 + - + +
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Residues in contact with TYR 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A VAL* 5.5 2.3 - - - +
427A GLY 4.8 1.2 + - - -
428A VAL* 3.5 27.0 - - + +
429A GLN* 3.1 43.5 + - - +
443A TYR* 5.1 1.6 + - - -
149F ASP* 4.2 1.6 - - - +
412F GLN* 3.3 33.2 - - + -
415F LEU* 4.6 8.8 - - + +
432F MET* 4.2 21.3 - - + +
433F VAL* 1.3 85.4 - - - +
435F HIS* 1.3 71.1 + - - +
436F GLY 4.1 4.0 - - - +
438F GLN 3.8 1.6 - - - -
439F VAL* 3.9 20.6 - - + -
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Residues in contact with HIS 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ASP* 3.1 48.5 + - - +
150F ILE* 3.6 43.6 + - + +
409F LEU* 4.7 4.0 - - - +
433F VAL* 3.5 22.5 + - + +
434F TYR* 1.3 83.8 - - - +
436F GLY* 1.3 64.4 + - - +
437F ASN 3.4 0.3 + - - -
438F GLN* 2.7 33.0 + - + +
440F ALA* 3.7 30.7 + - + +
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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
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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