Contacts of the helix formed by residues 344 - 348 (chain L) in PDB entry 4XLN
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 TYR 344 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530J VAL* 4.9 14.4 - - + +
534J ARG* 6.0 1.9 - - - +
536J ALA* 4.4 17.4 - - + +
330L VAL* 5.0 13.1 - - + +
331L SER 4.1 9.0 - - - -
332L LEU* 3.3 24.7 + - + +
334L THR* 3.1 30.8 + - + +
336L ILE* 4.9 8.1 - - + -
343L PHE* 1.3 75.5 - - - +
345L GLY* 1.3 59.9 + - - +
346L ASP 2.9 11.2 + - - -
347L PHE* 2.9 28.5 + + + +
348L ILE* 3.5 23.6 - - + +
18S G 5.5 15.9 - + + -
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Residues in contact with GLY 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014I SER* 4.0 6.0 + - - -
1015I LEU* 5.2 1.6 + - - +
1016I ILE* 5.0 8.6 - - - +
332L LEU* 3.0 32.1 + - - -
343L PHE* 4.6 0.4 - - - +
344L TYR* 1.3 77.3 - - - +
346L ASP* 1.3 59.3 + - - +
347L PHE 3.0 2.0 - - - -
348L ILE* 3.2 33.1 + - - +
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Residues in contact with ASP 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014I SER* 4.3 8.7 - - - -
1016I ILE* 5.2 4.0 - - + +
1021I LEU* 3.2 28.5 - - - +
1026I GLN* 4.6 2.8 + - - -
611J GLN* 5.4 1.4 - - - +
622J ARG* 5.9 5.6 - - - +
343L PHE* 3.0 56.5 + - - +
344L TYR 3.8 0.2 - - - -
345L GLY* 1.3 73.0 - - - +
347L PHE* 1.3 66.8 + - + +
348L ILE 3.3 0.7 - - - -
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Residues in contact with PHE 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021I LEU* 3.9 8.2 - - - +
1026I GLN* 3.7 37.5 - - + +
336L ILE* 3.5 18.8 - - + -
342L SER* 4.0 8.1 - - - -
343L PHE 3.5 20.2 - - - -
344L TYR* 2.9 21.0 + + + +
346L ASP* 1.3 89.1 - - + +
348L ILE* 1.3 62.5 + - + +
349L PRO* 3.3 11.3 - - - +
16S G 5.2 8.1 - - - -
17S G 3.1 28.3 - + - -
18S G 3.3 25.1 - - - +
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Residues in contact with ILE 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014I SER* 3.5 6.8 + - - -
1015I LEU* 3.2 44.6 + - + -
1021I LEU* 4.3 2.1 - - - +
528J VAL* 4.4 11.9 - - + -
530J VAL* 4.3 20.6 - - + -
536J ALA* 5.5 0.9 - - + -
332L LEU* 4.6 8.7 - - + -
344L TYR* 3.5 47.3 - - + +
345L GLY* 3.2 18.3 + - - +
346L ASP 3.3 0.2 - - - -
347L PHE* 1.3 83.4 - - + +
349L PRO* 1.3 75.0 - - + +
351L GLU* 5.4 2.2 - - - +
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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