Contacts of the strand formed by residues 343 - 347 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ARG* 4.9 2.4 + - - -
82A GLY* 5.8 7.2 - - - -
85A HIS* 3.3 30.4 - - + +
86A GLU* 4.3 11.7 - - - +
163A LEU* 4.9 6.6 - - - +
339A ALA* 3.4 3.9 - - - -
340A VAL* 2.8 42.0 + - + +
341A ASP 3.4 2.5 + - - +
342A GLY* 1.3 76.9 - - - +
344A LEU* 1.3 72.1 + - - +
345A MET* 5.7 2.0 - - + +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.9 38.4 - - + -
337A VAL* 4.1 27.4 - - + -
338A PHE 3.7 4.5 - - - +
339A ALA* 4.9 0.9 - - - +
342A GLY 4.0 1.8 + - - -
343A GLU* 1.3 85.4 - - - +
345A MET* 1.3 68.2 + - - +
346A VAL* 4.4 15.9 - - + -
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Residues in contact with MET 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 5.6 0.9 - - - -
157A THR* 3.9 21.5 - - + -
161A LEU* 5.5 7.6 - - + -
163A LEU* 4.3 17.3 - - + -
169A LEU* 4.8 2.2 - - + -
337A VAL* 3.6 1.4 - - - -
338A PHE* 2.7 58.8 + - + +
340A VAL* 3.6 31.6 - - + -
343A GLU* 5.7 2.7 - - + +
344A LEU* 1.3 79.3 - - - +
346A VAL* 1.3 65.7 + - - +
347A SER* 4.0 13.7 - - - -
350A VAL* 3.6 31.0 - - + -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LYS* 3.7 40.0 + - + +
336A GLY 3.4 9.6 - - - +
337A VAL* 5.2 5.6 - - + -
344A LEU* 4.4 22.9 - - + -
345A MET* 1.3 79.5 - - - +
347A SER* 1.3 66.7 + - - +
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A THR* 3.5 14.9 - - - -
158A ALA* 3.6 5.9 + - - +
159A SER* 4.6 3.1 + - - -
331A PRO* 4.5 0.9 - - - +
335A LYS* 4.1 7.9 - - - +
336A GLY 2.8 36.7 + - - +
338A PHE* 3.6 8.2 - - - -
345A MET* 4.0 20.8 + - - -
346A VAL* 1.3 77.1 - - - +
348A GLU* 1.3 66.6 + - - +
349A ALA 3.3 17.9 + - - -
350A VAL* 4.0 9.0 - - - -
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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