Contacts of the helix formed by residues 482 - 490 (chain N) in PDB entry 6LTJ
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 THR 482 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225M ASP* 3.1 38.8 - - + +
226M LEU* 6.0 0.2 - - - +
480N TYR* 3.4 32.0 + - + +
481N LEU* 1.3 75.1 - - - +
483N SER* 1.3 62.6 + - - +
484N THR* 3.5 4.5 + - - -
485N ALA* 3.2 27.7 + - - +
486N CYS* 3.3 19.2 + - - -
501N HIS* 3.8 0.2 - - - -
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Residues in contact with SER 483 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221M ILE* 4.5 12.1 - - - -
225M ASP* 3.9 11.1 + - - -
480N TYR* 5.2 0.4 + - - -
482N THR* 1.3 73.3 - - - +
484N THR* 1.3 57.9 + - - +
486N CYS* 3.3 3.5 + - - +
487N ARG* 2.9 27.4 + - - +
497N ILE* 5.4 0.5 - - - +
498N MET* 3.1 38.0 - - - +
501N HIS* 3.7 34.8 + - - +
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Residues in contact with THR 484 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218M PHE* 6.0 0.2 - - + -
221M ILE* 5.2 1.6 - - + -
222M LEU* 3.6 33.4 - - + +
225M ASP* 3.2 34.5 + - + +
226M LEU* 4.0 12.1 - - - +
482N THR* 3.5 2.9 + - - -
483N SER* 1.3 76.4 - - - +
485N ALA* 1.3 67.3 + - - +
487N ARG* 3.3 25.7 - - - +
488N ARG* 2.9 38.0 + - - +
498N MET* 5.7 3.4 - - + -
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Residues in contact with ALA 485 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481N LEU* 4.7 2.7 - - + -
482N THR* 3.2 26.6 + - - +
484N THR* 1.3 83.7 + - - +
486N CYS* 1.3 56.6 + - - +
488N ARG* 3.6 6.1 + - - +
489N ASN* 2.7 28.4 + - - +
45R GLN* 3.1 43.1 - - + +
46R THR* 3.9 9.1 - - + +
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Residues in contact with CYS 486 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468N PHE* 4.8 9.4 - - + -
469N MET* 3.5 39.3 - - + -
481N LEU* 3.5 43.1 - - - -
482N THR 3.3 4.4 + - - +
483N SER 3.3 8.0 + - - +
484N THR 3.1 0.8 - - - -
485N ALA* 1.3 74.9 - - - +
487N ARG* 1.3 57.9 + - - +
488N ARG 3.0 3.8 - - - -
489N ASN* 2.8 26.3 + - - +
490N LEU* 3.3 16.2 + - + +
497N ILE* 5.0 0.2 - - + -
501N HIS* 4.1 7.6 - - + -
46R THR* 5.5 0.2 - - - -
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Residues in contact with ARG 487 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M ASP* 2.9 41.9 + - - -
203M ALA 5.2 1.0 + - - -
204M PHE* 3.7 15.1 - - - +
218M PHE* 3.9 24.4 - - - -
222M LEU* 3.8 23.8 - - - +
309M THR* 3.7 4.5 - - - +
483N SER 2.9 16.7 + - - +
484N THR* 3.3 20.3 - - - +
486N CYS* 1.3 74.4 - - - +
488N ARG* 1.3 75.5 + - - +
489N ASN 3.4 0.4 - - - -
490N LEU 3.0 20.4 - - - +
494N VAL* 3.7 26.9 - - + +
497N ILE* 3.7 32.3 - - + +
498N MET* 4.7 10.8 - - + -
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Residues in contact with ARG 488 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M LEU* 4.7 1.4 - - - +
201M ARG 4.5 7.4 + - - -
202M ASP* 2.8 33.7 + - - +
222M LEU* 4.6 1.0 - - - +
226M LEU* 3.4 40.1 - - - +
306M GLU* 3.1 35.9 - - + -
309M THR* 3.1 14.5 + - - +
484N THR* 2.9 24.1 + - - +
485N ALA 3.8 5.8 - - - +
486N CYS 2.9 0.6 + - - -
487N ARG* 1.3 100.9 - - - +
489N ASN* 1.3 59.1 + - - +
490N LEU 3.4 0.2 - - - -
45R GLN* 3.3 52.0 - - - +
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Residues in contact with ASN 489 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305M GLY* 3.1 28.0 + - - +
306M GLU 4.1 1.4 - - - +
308M VAL* 3.2 19.8 - - - +
468N PHE* 3.3 36.3 - - + -
485N ALA 2.7 23.4 - - - +
486N CYS 2.8 3.2 + - - +
488N ARG* 1.3 78.4 - - - +
490N LEU* 1.3 64.1 + - - +
43R ASP* 2.4 33.1 + - - +
44R SER 4.5 2.9 + - - +
45R GLN* 4.7 1.4 + - - -
46R THR* 3.5 10.8 + - - +
50R GLN* 4.1 1.3 - - - +
56R TRP* 6.0 0.2 - - - -
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Residues in contact with LEU 490 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309M THR* 3.2 7.1 - - - +
465N TYR* 3.7 43.3 - - + +
468N PHE* 4.0 38.1 - - + -
469N MET* 4.0 21.5 - - + -
486N CYS 3.3 15.1 + - - +
487N ARG 3.0 17.3 - - - +
488N ARG 3.4 0.2 - - - -
489N ASN* 1.3 86.7 - - - +
491N ALA* 1.3 59.2 + - - +
492N GLY 3.9 0.9 + - - +
497N ILE* 3.3 23.8 - - + +
56R TRP* 4.2 18.2 - - + -
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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