Contacts of the helix formed by residues 473 - 483 (chain D) in PDB entry 6K4Y
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1285C TYR* 4.9 3.4 - - + -
1289C GLU* 3.0 17.8 + - + +
1304C MET* 5.0 3.6 - - - -
1313C HIS* 3.6 20.9 + - - +
1314C GLN* 4.0 7.1 - - - +
1315C MET* 4.3 24.8 + - - +
472D LEU* 1.3 85.0 - - - +
474D LEU* 1.3 69.4 + - - +
475D GLU* 2.8 19.8 + - + +
476D ALA* 3.3 24.4 + - + +
477D GLN* 3.2 20.7 + - - +
28E ARG* 4.2 0.2 + - - -
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Residues in contact with LEU 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313C HIS* 4.1 22.3 - - + +
473D THR* 1.3 78.4 + - - +
475D GLU* 1.3 66.8 + - - +
477D GLN* 3.0 27.1 + - - +
478D LEU* 3.0 21.6 + - + +
24E ALA* 4.2 9.2 - - - +
27E ALA* 3.7 29.4 - - + +
28E ARG* 3.8 24.7 - - + +
31E GLN* 4.6 12.1 - - + +
46E THR* 4.0 13.5 - - - +
47E THR* 3.7 23.1 - - - +
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Residues in contact with GLU 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C TYR* 3.6 48.7 - - + -
1315C MET* 5.5 2.3 - - - +
473D THR* 2.8 22.9 + - + +
474D LEU* 1.3 73.8 - - - +
476D ALA* 1.3 57.5 + - - +
478D LEU* 3.3 7.3 + - - +
479D GLU* 2.9 32.4 + - - +
20E VAL* 4.9 3.7 - - + +
21E LEU* 6.3 0.7 - - + -
24E ALA* 3.7 26.4 - - + +
28E ARG* 3.0 29.9 + - - -
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Residues in contact with ALA 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C TYR* 4.4 0.6 - - - +
1286C THR* 3.3 30.1 + - - +
1289C GLU* 3.4 27.1 - - - +
471D PRO* 3.8 12.8 - - + +
473D THR* 3.3 18.8 + - + +
474D LEU 3.2 0.6 - - - -
475D GLU* 1.3 76.4 - - - +
477D GLN* 1.3 59.5 + - - +
479D GLU* 3.4 2.0 + - - -
480D ALA* 2.9 28.9 + - - +
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Residues in contact with GLN 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313C HIS* 4.9 11.5 + - - -
418D GLU 5.3 1.4 - - - +
419D HIS* 3.0 45.4 + - + +
420D PRO* 4.9 10.9 - - + +
471D PRO* 4.5 7.9 - - + +
472D LEU 4.1 11.3 + - - -
473D THR 3.2 11.8 + - - +
474D LEU* 3.0 20.2 + - - +
476D ALA* 1.3 77.4 - - - +
478D LEU* 1.3 60.2 + - - +
480D ALA* 3.4 6.0 + - - +
481D ARG* 2.9 31.7 + - - +
45E LYS* 5.2 8.9 - - - +
47E THR* 3.1 25.7 + - + +
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Residues in contact with LEU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D LEU* 3.0 20.1 + - + +
475D GLU 3.3 6.3 + - - +
477D GLN* 1.3 76.6 - - - +
479D GLU* 1.3 60.3 + - - +
481D ARG* 4.4 0.9 - - + +
482D ALA* 2.9 34.9 + - + +
19E LEU 5.5 0.2 - - - +
20E VAL* 3.7 18.4 - - + +
23E ALA* 3.6 15.7 - - + +
24E ALA* 3.5 39.5 - - + +
27E ALA* 5.2 2.2 - - + -
47E THR* 3.7 30.1 - - + +
51E LEU* 3.9 26.0 - - + -
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Residues in contact with GLU 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282C GLY 4.4 1.3 - - - +
1283C ALA* 3.3 15.3 - - + +
1284C ALA* 2.7 18.5 + - - -
1285C TYR* 2.6 40.8 + - + -
1286C THR* 2.8 32.1 + - - +
475D GLU 2.9 17.1 + - - +
476D ALA 3.8 4.5 - - - +
477D GLN 3.4 0.2 - - - -
478D LEU* 1.3 76.0 - - - +
480D ALA* 1.3 60.6 + - - +
482D ALA* 4.9 0.7 - - - -
483D LEU* 3.2 28.8 + - + +
484D MET* 3.3 11.4 + - + +
1361D THR* 3.6 7.7 + - - +
20E VAL* 4.1 18.8 - - + -
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Residues in contact with ALA 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286C THR* 5.0 1.3 + - - +
420D PRO* 4.6 9.9 - - + -
422D LEU* 4.2 16.6 - - + -
436D ALA* 3.9 17.2 - - + +
471D PRO* 4.3 7.9 - - + -
476D ALA 2.9 17.9 + - - +
477D GLN* 3.7 5.8 - - - +
479D GLU* 1.3 78.6 - - - +
481D ARG* 1.3 58.7 + - - +
484D MET* 3.1 13.2 + - + -
485D MET* 2.9 30.4 + - - -
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Residues in contact with ARG 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D GLU* 2.5 43.0 + - - +
420D PRO* 3.4 20.8 - - + +
438D GLU* 3.0 26.5 + - - +
477D GLN 2.9 16.5 + - - +
478D LEU* 4.3 3.8 - - - +
480D ALA* 1.3 76.9 - - - +
482D ALA* 1.3 61.5 + - - +
485D MET* 3.5 21.6 - - + +
488D ASN* 3.3 13.3 + - - -
3E ARG* 3.4 32.0 - - + +
6E VAL* 3.9 15.7 - - + +
47E THR* 3.4 18.0 - - - +
48E VAL* 4.2 8.7 - - - +
51E LEU* 3.7 20.4 - - + -
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Residues in contact with ALA 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D LEU* 2.9 19.4 + - + +
481D ARG* 1.3 81.1 - - - +
483D LEU* 1.3 68.9 + - + +
488D ASN* 2.9 5.9 + - - -
6E VAL* 3.8 17.0 - - + +
16E ARG* 2.8 36.1 + - + +
19E LEU* 5.6 8.3 - - + -
20E VAL* 4.5 11.2 - - + -
51E LEU* 6.0 5.4 - - + -
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Residues in contact with LEU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281C TYR* 3.4 17.4 - - + -
1282C GLY 4.2 24.2 - - - +
1283C ALA* 4.6 2.7 - - - +
479D GLU* 3.2 21.5 + - + +
481D ARG 3.5 0.2 - - - -
482D ALA* 1.3 94.4 - - + +
484D MET* 1.3 66.0 + - - +
485D MET 3.2 4.0 + - - +
488D ASN* 4.5 2.4 - - - +
489D ASN* 3.3 23.4 + - - +
905D ARG* 3.6 15.5 + - - +
16E ARG* 3.4 33.7 - - + +
17E PHE* 4.0 27.1 - - + -
20E VAL* 5.6 3.6 - - + -
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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