Contacts of the helix formed by residues 461 - 470 (chain B) in PDB entry 4L0D
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 LEU 461 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ILE* 4.0 26.2 - - + +
438B LEU* 4.0 13.1 - - + +
439B ARG* 4.1 33.2 - - + +
443B PHE 4.4 11.4 - - - +
444B ASP* 2.7 31.1 + - - +
460B THR* 1.3 72.6 + - - +
462B GLY* 1.3 57.2 + - - +
464B MET* 3.4 2.5 + - - +
465B LEU* 2.9 53.4 + - + +
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Residues in contact with GLY 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 5.4 0.2 - - - +
199A SER* 3.9 8.1 - - - -
200A PRO* 3.8 22.6 - - - +
444B ASP* 4.2 3.8 + - - -
460B THR* 3.3 4.9 + - - -
461B LEU* 1.3 80.7 - - - +
463B ASN* 1.3 56.7 + - - +
465B LEU* 3.8 5.6 - - - +
466B SER* 2.9 30.1 + - - -
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Residues in contact with ASN 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN 4.1 6.5 + - - +
196A ARG* 3.2 35.0 + - - +
199A SER* 3.7 9.5 - - - -
460B THR* 3.4 15.9 + - + +
461B LEU 3.3 0.2 - - - -
462B GLY* 1.3 73.3 - - - +
464B MET* 1.3 57.1 + - - +
466B SER* 4.3 1.1 - - - -
467B SER* 2.3 43.1 + - - -
482B VAL* 3.5 25.6 + - + +
484B TYR* 3.1 43.9 - - - +
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Residues in contact with MET 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B CYS* 3.5 53.2 - - - +
434B THR* 4.0 20.2 - - + +
435B ILE* 4.1 15.5 - - + -
459B VAL* 4.4 7.2 - - + -
460B THR 3.0 19.8 + - - +
461B LEU* 3.6 5.4 - - - +
463B ASN* 1.3 77.1 - - - +
465B LEU* 1.3 57.3 + - - +
467B SER* 3.1 5.8 + - - -
468B LEU* 2.9 33.2 + - - +
473B VAL* 5.3 0.7 - - - -
479B VAL* 3.7 25.1 - - + +
482B VAL* 3.9 29.5 - - + +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 4.3 21.8 - - + -
439B ARG* 5.4 5.6 - - - -
461B LEU* 2.9 43.5 + - + +
462B GLY* 3.8 5.4 - - - +
464B MET* 1.3 74.1 - - - +
466B SER* 1.3 67.4 + - - +
467B SER 3.2 0.2 + - - -
468B LEU* 3.3 8.6 + - + +
469B LEU* 2.9 40.1 + - + +
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 3.2 25.8 + - - +
198A ASP* 2.7 42.9 + - - +
199A SER 4.5 0.9 - - - -
462B GLY 2.9 19.4 + - - -
463B ASN* 3.9 4.5 - - - -
465B LEU* 1.3 74.6 - - - +
467B SER* 1.3 65.2 + - - +
469B LEU* 3.8 5.5 - - - +
470B ALA* 2.9 27.4 + - - +
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Residues in contact with SER 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 4.5 7.9 - - - +
463B ASN* 2.3 35.1 + - - -
464B MET 3.1 5.1 + - - -
466B SER* 1.3 76.8 - - - +
468B LEU* 1.3 62.2 + - - +
470B ALA* 3.2 5.3 + - - +
471B GLY 3.1 3.6 + - - -
472B LYS* 3.0 33.4 + - - +
473B VAL* 3.8 11.9 - - - -
482B VAL* 3.3 28.1 - - - +
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Residues in contact with LEU 468 (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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431B CYS* 4.7 8.1 - - + -
432B GLY* 5.0 1.6 - - - +
435B ILE* 3.5 31.4 - - + -
464B MET 2.9 13.9 + - - +
465B LEU* 3.7 9.2 - - + +
467B SER* 1.3 75.3 - - - +
469B LEU* 1.3 58.5 + - + +
471B GLY* 2.7 26.5 + - - -
473B VAL* 3.2 33.9 - - + +
474B GLN* 3.4 24.2 - - - +
475B PRO* 3.5 17.9 - - + -
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Residues in contact with LEU 469 (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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465B LEU* 2.9 31.6 + - + +
466B SER* 3.8 5.4 - - - +
468B LEU* 1.3 80.9 - - + +
470B ALA* 1.3 58.9 + - - +
471B GLY 3.1 1.2 + - - -
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Residues in contact with ALA 470 (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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196A ARG* 3.6 30.3 - - - +
198A ASP* 5.6 0.9 - - - +
466B SER 2.9 18.1 + - - +
467B SER 3.7 3.8 - - - +
468B LEU 3.1 0.4 - - - -
469B LEU* 1.3 76.9 - - - +
471B GLY* 1.3 61.8 + - - +
472B LYS* 3.3 19.1 + - + +
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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