Contacts of the helix formed by residues 473 - 483 (chain J) in PDB entry 6XAV
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 473 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1285I TYR* 5.2 1.2 + - - +
1289I GLU* 2.7 24.7 + - - +
1304I MET* 3.7 18.8 - - + -
1313I HIS* 3.6 14.1 - - - +
1315I MET* 3.6 39.5 - - + +
472J LEU* 1.3 78.3 - - - +
474J LEU* 1.3 65.0 + - - +
475J GLU* 3.8 12.8 + - - +
476J ALA* 3.3 13.7 + - - +
477J GLN* 3.2 23.7 + - - +
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Residues in contact with LEU 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313I HIS* 3.3 35.4 + - + +
473J THR* 1.3 73.0 - - - +
475J GLU* 1.3 68.1 + - - +
477J GLN* 3.3 7.9 + - - +
478J LEU* 2.9 36.0 + - + +
24W ALA* 3.9 12.3 - - + +
27W ALA* 3.7 19.5 - - + +
28W ARG* 3.5 46.0 - - - +
31W GLN* 3.7 20.0 - - - +
46W THR* 4.3 6.1 - - - +
47W THR* 4.6 9.6 - - + +
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Residues in contact with GLU 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285I TYR* 3.7 50.5 - - + -
1315I MET* 5.8 1.4 - - - +
473J THR* 3.8 9.8 + - - +
474J LEU* 1.3 81.5 + - - +
476J ALA* 1.3 58.7 + - - +
478J LEU* 3.8 5.6 - - - +
479J GLU* 2.9 36.8 + - - +
20W VAL* 4.6 8.1 - - + +
21W LEU* 5.7 2.2 - - + -
24W ALA* 3.4 29.0 - - + +
28W ARG* 4.3 17.5 + - - -
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Residues in contact with ALA 476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285I TYR* 4.8 1.0 - - - +
1286I THR* 3.3 32.3 + - + +
1289I GLU* 3.3 28.0 - - - +
471J PRO* 3.6 23.1 - - + +
473J THR* 3.3 8.4 + - - +
474J LEU 3.3 0.6 - - - -
475J GLU* 1.3 79.5 - - - +
477J GLN* 1.3 61.9 + - - +
479J GLU* 4.2 0.4 - - - -
480J ALA* 3.2 21.8 + - - +
484J MET* 4.6 1.2 - - - +
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Residues in contact with GLN 477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313I HIS* 4.2 14.1 - - - -
380J PHE* 4.9 0.2 - - - -
418J GLU 4.8 5.2 - - - +
419J HIS* 3.1 47.2 + - + +
420J PRO* 4.5 9.7 - - + +
471J PRO* 4.2 10.1 - - + -
472J LEU 3.3 18.1 + - - +
473J THR 3.2 15.9 + - - +
474J LEU* 3.7 5.5 - - - +
476J ALA* 1.3 75.4 - - - +
478J LEU* 1.3 66.0 + - - +
480J ALA* 3.3 14.4 + - - +
481J ARG* 3.3 19.7 + - - +
45W LYS* 5.3 4.8 - - - +
47W THR* 3.3 27.7 + - + +
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Residues in contact with LEU 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474J LEU* 2.9 23.9 + - + +
477J GLN* 1.3 73.9 - - - +
479J GLU* 1.3 61.2 + - - +
481J ARG* 3.2 5.2 + - - +
482J ALA* 2.8 33.0 + - + +
20W VAL* 3.7 24.7 - - + +
23W ALA* 3.7 15.9 - - + +
24W ALA* 3.5 36.3 - - + +
27W ALA* 5.5 1.6 - - + -
47W THR* 3.8 40.8 - - + +
50W ALA* 5.6 0.7 - - + -
51W LEU* 4.0 23.7 - - + +
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Residues in contact with GLU 479 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282I GLY 3.4 3.3 - - - +
1283I ALA* 3.3 19.2 - - + -
1284I ALA 3.4 4.3 + - - -
1285I TYR* 3.4 10.6 + - - -
1286I THR* 2.4 44.3 + - - +
475J GLU 2.9 22.2 + - - +
477J GLN 3.3 0.2 - - - -
478J LEU* 1.3 75.0 - - - +
480J ALA* 1.3 58.2 + - - +
483J LEU* 3.0 54.3 + - + +
484J MET* 3.3 7.7 + - + +
1361J THR* 2.9 28.3 + - + +
20W VAL* 3.8 13.4 - - + +
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Residues in contact with ALA 480 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420J PRO* 4.2 13.5 - - + -
422J LEU* 4.3 5.4 - - + -
436J ALA* 3.3 26.9 - - + +
471J PRO* 4.6 5.8 - - + -
476J ALA 3.2 14.9 + - - +
477J GLN* 3.5 11.2 - - - +
478J LEU 3.2 0.4 - - - -
479J GLU* 1.3 77.7 - - - +
481J ARG* 1.3 56.2 + - - +
484J MET* 3.7 18.8 - - + +
485J MET* 3.1 24.8 + - - +
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Residues in contact with ARG 481 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418J GLU* 3.5 41.2 + - - +
420J PRO* 3.5 28.6 - - + +
438J GLU* 3.7 25.1 + - - +
477J GLN* 3.3 12.9 + - - +
478J LEU* 3.2 8.5 + - - +
480J ALA* 1.3 78.6 - - - +
482J ALA* 1.3 53.2 + - - +
483J LEU 3.5 0.2 - - - -
485J MET* 3.2 18.4 - - + +
488J ASN* 2.7 30.0 + - - -
3W ARG* 3.7 33.1 + - + +
6W VAL* 4.2 7.8 - - + +
47W THR* 4.4 13.0 + - - -
48W VAL* 3.9 13.9 - - - +
51W LEU* 4.5 24.0 - - + -
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Residues in contact with ALA 482 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478J LEU* 2.8 16.2 + - + +
481J ARG* 1.3 76.9 - - + +
483J LEU* 1.3 64.0 + - + +
488J ASN* 4.3 0.7 - - - -
6W VAL* 4.2 17.3 - - + -
10W VAL* 5.9 2.7 - - + -
16W ARG* 2.9 35.0 + - + +
19W LEU* 6.0 4.0 - - + -
20W VAL* 4.2 19.3 - - + -
51W LEU* 5.4 10.1 - - + -
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Residues in contact with LEU 483 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281I TYR* 3.3 21.2 - - + -
1282I GLY* 3.5 43.5 - - - +
1283I ALA* 4.1 1.3 - - + +
479J GLU* 3.0 35.2 + - + +
481J ARG 3.5 0.2 - - - -
482J ALA* 1.3 91.1 - - + +
484J MET* 1.3 61.3 + - + +
485J MET 3.7 2.0 - - - -
488J ASN* 5.4 1.8 - - - -
489J ASN* 3.6 10.3 - - - +
905J ARG* 3.9 9.4 + - - +
1361J THR* 4.7 0.9 - - + -
16W ARG* 3.3 39.0 - - + +
17W PHE* 4.1 13.7 - - + -
20W VAL* 4.6 6.5 - - + -
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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