Contacts of the helix formed by residues 470 - 476 (chain B) in PDB entry 1LV5
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 GLN 470 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400B LEU* 3.7 26.6 + - + +
401B LEU* 4.2 1.7 - - - +
465B LEU* 2.6 35.5 + - + +
468B ASN* 2.9 40.9 + - + +
469B GLU* 1.3 75.6 - - - +
471B ASP* 1.3 62.8 + - - +
472B ARG 3.2 3.1 - - - -
473B LEU* 3.0 30.1 + - + +
474B LEU* 3.3 11.4 + - - +
768B HIS* 3.0 29.6 + - + +
769B ARG* 4.2 2.0 - - - +
770B ARG* 3.7 20.4 - - - +
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Residues in contact with ASP 471 (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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462B LEU* 4.9 8.9 - - + +
465B LEU* 3.4 12.7 + - + -
466B ARG* 3.4 54.6 + - + +
469B GLU* 4.0 6.2 - - - -
470B GLN* 1.3 82.5 + - - +
472B ARG* 1.3 79.2 + - - +
474B LEU* 3.6 3.5 + - - +
475B VAL* 3.3 29.1 + - + +
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Residues in contact with ARG 472 (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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204B SO4 3.7 26.0 + - - +
469B GLU 5.2 2.9 + - - +
470B GLN 3.2 0.8 - - - -
471B ASP* 1.3 90.0 + - - +
473B LEU* 1.3 60.7 + - - +
474B LEU 3.1 2.2 - - - -
475B VAL* 5.0 1.1 - - - -
476B GLU* 2.7 76.7 + - + +
477B LEU 3.5 0.7 + - - -
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Residues in contact with LEU 473 (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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204B SO4 4.3 7.3 + - - +
400B LEU* 3.4 32.8 - - + -
470B GLN* 3.0 21.0 + - + +
472B ARG* 1.3 78.8 - - - +
474B LEU* 1.3 57.4 + - - +
477B LEU* 3.4 34.2 - - + +
478B GLU* 2.9 30.0 + - + +
767B LEU* 3.8 31.0 - - + +
768B HIS* 4.2 4.7 - - + +
769B ARG* 3.9 34.8 - - - +
802B ASP* 5.0 0.2 - - - +
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Residues in contact with LEU 474 (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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392B PHE* 3.8 22.2 - - + -
393B ASP 4.3 0.9 - - - +
396B LEU* 3.5 35.2 - - + -
397B ALA* 3.7 12.6 - - + +
400B LEU* 3.9 15.7 - - + +
462B LEU* 4.2 7.2 - - + -
465B LEU* 3.6 25.8 - - + -
470B GLN 3.3 6.2 + - - +
471B ASP 4.1 5.6 - - - +
472B ARG 3.1 0.2 - - - -
473B LEU* 1.3 79.9 - - - +
475B VAL* 1.3 65.6 + - + +
478B GLU* 4.5 0.9 - - + -
479B GLN* 2.9 60.0 + - + +
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Residues in contact with VAL 475 (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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391B SER 4.9 6.5 - - - +
392B PHE* 6.3 0.2 - - + -
462B LEU* 5.1 9.4 - - + -
471B ASP* 3.3 17.4 + - + +
472B ARG* 5.0 0.7 - - - -
474B LEU* 1.3 85.6 - - + +
476B GLU* 1.3 67.7 + - + +
479B GLN* 4.1 17.1 + - - +
480B PRO* 3.4 16.9 - - - +
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Residues in contact with GLU 476 (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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204B SO4 3.2 21.9 + - - +
472B ARG* 2.7 61.1 + - - +
475B VAL* 1.3 86.5 - - + +
477B LEU* 1.3 56.7 + - - +
480B PRO* 2.9 20.9 - - - +
809B ILE* 3.7 8.3 - - - +
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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