Contacts of the strand formed by residues 343 - 347 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C ASN* 5.4 0.5 - - - +
61C ARG* 4.7 4.2 + - - -
82C GLY* 5.6 5.8 - - - -
85C HIS* 3.4 28.7 + - + +
86C GLU* 2.8 28.5 - - - +
163C LEU* 4.4 11.4 - - - +
339C ALA* 3.3 2.8 - - - -
340C VAL* 2.7 46.2 + - + +
341C ASP 3.2 4.1 + - - +
342C GLY* 1.3 70.6 - - - +
344C LEU* 1.3 76.7 + - - +
345C MET* 3.5 6.9 + - - +
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C LEU* 3.8 39.9 - - + -
337C VAL* 3.6 30.5 - - + -
338C PHE 3.5 4.5 - - - +
339C ALA* 4.8 1.1 - - - +
342C GLY 3.6 3.4 + - - -
343C GLU* 1.3 86.3 - - - +
345C MET* 1.3 73.3 + - - +
346C VAL* 4.2 13.7 - - + +
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Residues in contact with MET 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LEU* 6.0 0.2 - - - -
157C THR* 3.6 22.9 - - + -
161C LEU* 5.3 5.2 - - + -
163C LEU* 4.1 18.2 - - + -
169C LEU* 5.9 0.4 - - - -
337C VAL* 3.5 2.4 - - - -
338C PHE* 2.5 56.3 + - + +
340C VAL* 3.6 31.9 - - + -
343C GLU* 4.5 8.7 - - - +
344C LEU* 1.3 79.6 - - - +
346C VAL* 1.3 71.6 + - - +
347C SER* 3.5 32.3 - - - +
350C VAL* 4.4 6.1 - - + -
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Residues in contact with VAL 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C LYS* 3.6 39.1 - - + +
336C GLY 3.6 3.6 - - - +
337C VAL* 4.2 13.5 - - + -
344C LEU* 4.2 19.5 - - + +
345C MET* 1.3 84.0 - - - +
347C SER* 1.3 64.6 + - - +
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Residues in contact with SER 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C THR* 3.5 13.2 - - - -
158C ALA* 3.8 4.7 + - - +
159C SER* 4.7 3.0 + - - -
331C PRO* 4.7 0.3 - - - +
335C LYS* 3.9 11.4 - - - +
336C GLY 3.0 28.0 + - - +
338C PHE* 3.3 12.8 - - - -
345C MET* 3.5 20.9 - - - -
346C VAL* 1.3 76.2 - - - +
348C GLU* 1.3 66.6 + - - +
349C ALA 3.2 17.0 + - - -
350C VAL* 4.0 13.7 - - - -
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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