Contacts of the strand formed by residues 343 - 347 (chain F) in PDB entry 3VZC
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 GLU 343 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57F ARG* 5.6 5.7 - - - +
82F GLY* 3.6 35.1 - - - +
85F HIS* 4.5 12.8 - - + +
86F GLU* 3.3 23.2 - - - +
339F ALA* 3.5 1.7 - - - -
340F VAL* 2.8 42.5 + - + +
341F ASP 4.3 1.1 - - - +
342F GLY* 1.3 77.3 - - - +
344F LEU* 1.3 65.6 + - - +
345F MET* 4.7 0.2 - - - +
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Residues in contact with LEU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F LEU* 3.8 35.9 - - + -
337F VAL* 3.8 28.0 - - + -
338F PHE 3.6 5.8 - - - +
339F ALA* 4.9 1.1 - - - +
342F GLY 3.6 3.4 + - - +
343F GLU* 1.3 75.6 - - - +
345F MET* 1.3 78.9 + - - +
346F VAL* 4.4 6.7 - - + -
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Residues in contact with MET 345 (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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155F LEU* 6.3 0.4 - - - -
157F THR* 4.1 13.0 - - + -
161F LEU* 5.2 7.6 - - + -
163F LEU* 4.3 25.8 - - - -
169F LEU* 5.9 0.4 - - + -
337F VAL* 3.5 0.3 - - - -
338F PHE* 2.8 65.6 + - + +
340F VAL* 4.3 23.8 - - + -
343F GLU 4.7 0.2 - - - +
344F LEU* 1.3 80.8 - - - +
346F VAL* 1.3 71.9 + - - +
347F SER* 3.8 24.5 - - - -
350F VAL* 4.2 4.7 - - + -
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Residues in contact with VAL 346 (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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159F SER* 5.3 0.3 + - - -
335F LYS* 4.1 26.6 - - + +
336F GLY 3.1 14.1 - - - +
337F VAL* 3.8 19.7 - - + -
344F LEU* 4.4 7.4 - - + -
345F MET* 1.3 88.0 - - - +
347F SER* 1.3 66.7 + - - +
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Residues in contact with SER 347 (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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157F THR* 3.6 15.5 - - - -
159F SER* 2.9 28.7 + - - -
335F LYS* 4.7 7.0 - - - +
336F GLY* 2.8 32.2 + - - +
338F PHE* 3.6 10.7 - - - -
345F MET* 3.8 18.4 - - - -
346F VAL* 1.3 78.3 - - - +
348F GLU* 1.3 71.3 + - - +
349F ALA 4.1 3.3 + - - -
350F VAL* 4.4 4.0 - - - -
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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