Contacts of the helix formed by residues 340 - 346 (chain B) in PDB entry 3LC4
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 ALA 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 3.6 12.6 - - - +
148B GLN* 4.0 7.4 - - - +
337B ARG* 3.9 11.7 - - - +
338B ILE 3.6 0.8 + - - +
339B PRO* 1.3 73.7 - - - +
341B ILE* 1.3 61.1 + - - +
342B LYS* 3.8 23.6 - - + +
343B ASP* 2.8 39.5 + - - +
448B PHE* 3.9 5.5 - - - -
449B LEU* 3.9 4.5 - - - -
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Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU* 2.8 27.4 + - + +
340B ALA* 1.3 67.0 - - - +
342B LYS* 1.3 65.6 + - + +
343B ASP 3.0 6.4 + - - -
344B ARG* 3.2 24.3 + - + +
345B GLN* 4.7 0.9 + - - +
445B MET* 3.7 43.1 - - + -
448B PHE* 4.4 6.1 - - + -
449B LEU* 3.7 21.8 - - + -
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Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU* 4.3 13.3 + - - -
340B ALA* 3.1 25.8 - - + +
341B ILE* 1.3 84.0 - - + +
343B ASP* 1.3 64.7 + - - +
344B ARG 3.3 0.7 - - - -
345B GLN* 2.8 44.7 - - - +
346B GLU* 4.5 4.3 + - - +
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 4.5 4.6 - - + +
333B ILE* 3.9 8.8 - - + +
337B ARG* 2.5 35.1 + - - -
339B PRO* 3.8 0.9 - - - +
340B ALA* 2.8 38.4 + - - +
341B ILE 3.0 1.2 - - - -
342B LYS* 1.3 84.4 - - - +
344B ARG* 1.3 63.7 + - - +
345B GLN 3.2 0.9 - - - -
346B GLU* 3.0 23.6 + - - +
347B MET* 3.0 40.9 + - + +
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Residues in contact with ARG 344 (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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341B ILE* 3.2 18.1 + - - +
343B ASP* 1.3 78.3 - - - +
345B GLN* 1.3 57.1 + - - +
347B MET* 2.9 27.5 + - - +
348B PRO* 5.2 0.3 - - - +
351B ASP* 3.2 30.7 + - + +
354B VAL* 3.5 29.5 - - - +
355B HIS* 3.8 16.5 - - - -
444B ARG* 3.6 29.3 + - - +
445B MET* 4.6 4.9 - - - +
448B PHE* 3.2 57.9 - - + +
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Residues in contact with GLN 345 (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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341B ILE 5.0 0.4 - - - +
342B LYS* 2.8 38.0 - - - +
344B ARG* 1.3 73.5 - - + +
346B GLU* 1.3 72.1 + - + +
347B MET 3.5 0.4 + - - -
348B PRO* 5.5 3.3 - - - +
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Residues in contact with GLU 346 (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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328B GLU* 4.4 1.0 - - - +
331B ARG* 4.5 4.3 + - - -
332B VAL* 3.3 34.1 - - + +
342B LYS 4.8 4.0 - - - +
343B ASP* 3.0 17.1 + - - +
345B GLN* 1.3 94.0 - - + +
347B MET* 1.3 61.8 + - - +
348B PRO* 3.6 11.6 - - - +
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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