Contacts of the helix formed by residues 487 - 500 (chain 3) in PDB entry 6Q8W
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 SER 487 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4663 GLU* 2.9 41.4 + - - -
4863 GLY* 1.3 75.5 - - - +
4883 GLU* 1.3 59.2 + - - +
4893 MET 3.2 5.7 + - - -
4903 VAL* 3.3 16.0 + - - +
4913 ALA* 2.8 28.4 + - - +
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Residues in contact with GLU 488 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4663 GLU* 5.1 0.2 + - - -
4873 SER* 1.3 74.3 - - - +
4893 MET* 1.3 61.5 + - + +
4913 ALA* 3.2 7.5 + - - +
4923 LYS* 2.9 41.0 + - + +
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Residues in contact with MET 489 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4513 PHE* 3.5 8.1 - - + -
4633 ALA 3.6 7.6 - - - +
4643 ILE* 3.0 17.4 - - - +
4653 HIS* 2.8 47.8 - - + +
4663 GLU* 3.3 32.5 + - + +
4873 SER* 3.2 1.6 + - - -
4883 GLU* 1.3 82.2 - - + +
4903 VAL* 1.3 57.0 + - - +
4923 LYS* 3.3 41.0 + - + +
4933 ALA 3.0 23.0 + - - -
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Residues in contact with VAL 490 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4513 PHE* 3.8 21.3 - - + -
4663 GLU* 4.8 3.8 - - + +
4763 ILE* 3.6 41.1 - - + +
4793 ALA* 3.9 24.9 - - + -
4803 LEU* 4.0 6.2 - - + +
4863 GLY* 4.3 3.4 - - - -
4873 SER* 3.2 31.9 + - - +
4893 MET* 1.3 75.8 - - - +
4913 ALA* 1.3 57.7 + - - +
4933 ALA* 3.8 0.7 - - - +
4943 LYS* 2.9 27.8 + - - +
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Residues in contact with ALA 491 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4853 GLU* 6.1 3.4 - - + -
4863 GLY* 4.9 5.8 - - - +
4873 SER 2.8 16.8 + - - +
4883 GLU* 3.6 7.2 - - - +
4903 VAL* 1.3 76.9 - - - +
4923 LYS* 1.3 59.9 + - - +
4943 LYS* 3.5 11.6 - - + +
4953 GLU* 2.8 31.9 + - - +
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Residues in contact with LYS 492 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4633 ALA* 4.6 11.5 + - - +
4643 ILE* 3.6 23.8 - - + +
4883 GLU* 2.9 23.7 + - + +
4893 MET* 3.3 38.2 + - + +
4913 ALA* 1.3 74.1 - - - +
4933 ALA* 1.3 60.4 + - - +
4953 GLU* 3.5 7.9 + - - +
4963 ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 493 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3953 PHE* 4.3 3.3 - - + -
3973 LEU* 4.3 11.6 - - + +
4493 ALA* 4.0 13.9 - - + -
4513 PHE* 3.4 32.5 - - + -
4643 ILE* 3.6 10.0 - - + +
4803 LEU* 4.0 5.4 - - + -
4893 MET 3.0 10.0 + - - +
4903 VAL 3.9 3.4 - - - +
4923 LYS* 1.3 76.5 - - - +
4943 LYS* 1.3 58.6 + - - +
4963 ALA* 3.4 3.9 + - - +
4973 TRP* 2.9 32.4 + - - +
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Residues in contact with LYS 494 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4793 ALA* 3.1 24.7 - - + +
4803 LEU* 3.5 31.5 - - + +
4823 GLY* 4.1 17.3 - - - -
4843 LYS 5.4 2.0 - - - +
4903 VAL* 2.9 19.8 + - + +
4913 ALA* 3.5 11.4 - - + +
4933 ALA* 1.3 75.5 - - - +
4953 GLU* 1.3 57.0 + - - +
4973 TRP* 3.2 4.6 + - - +
4983 GLU* 2.8 52.5 + - + +
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Residues in contact with GLU 495 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4913 ALA 2.8 21.0 + - - +
4923 LYS* 3.9 7.4 - - - +
4943 LYS* 1.3 74.3 - - - +
4963 ALA* 1.3 59.8 + - - +
4983 GLU* 3.1 9.2 + - - +
4993 LYS* 2.9 59.5 + - + +
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Residues in contact with ALA 496 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3953 PHE* 3.7 34.5 - - + -
4463 ASP 5.6 1.1 - - - +
4643 ILE* 5.2 6.1 - - + -
4923 LYS 2.9 19.6 + - - +
4933 ALA 3.9 0.2 - - - +
4953 GLU* 1.3 78.3 - - - +
4973 TRP* 1.3 57.5 + - - +
4993 LYS* 4.1 5.4 - - - +
5003 ALA* 3.2 28.6 + - - +
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Residues in contact with TRP 497 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3953 PHE* 4.3 9.4 - + + -
3973 LEU* 3.9 26.9 - - + -
4803 LEU* 5.0 4.9 - - + -
4933 ALA 2.9 19.2 + - - +
4943 LYS* 3.5 4.9 - - - +
4963 ALA* 1.3 76.1 - - - +
4983 GLU* 1.3 82.2 + - - +
5003 ALA* 3.9 6.0 + - - +
5033 PRO* 3.6 23.8 - - + -
5043 VAL 3.7 20.6 - - - -
5053 LEU* 3.7 24.2 - - + -
5243 LEU* 3.3 50.9 + - + +
5253 ALA* 4.4 1.1 - - - -
5283 LYS* 3.1 43.7 - - + +
5303 ALA* 3.8 17.9 - - + -
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Residues in contact with GLU 498 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4803 LEU 4.1 13.8 - - - +
4813 LEU 5.0 3.8 - - - +
4943 LYS* 2.8 48.5 + - + +
4953 GLU* 3.1 7.2 + - + +
4973 TRP* 1.3 99.9 + - - +
4993 LYS* 1.3 63.4 + - + +
5003 ALA 3.5 1.6 + - - +
5243 LEU* 5.3 0.9 - - - +
5283 LYS* 3.7 16.7 + - - +
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Residues in contact with LYS 499 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4953 GLU* 2.9 44.7 + - + +
4963 ALA* 4.3 4.9 - - - +
4983 GLU* 1.3 79.5 - - + +
5003 ALA* 1.3 63.3 + - - +
5013 LYS* 3.5 17.3 + - - +
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Residues in contact with ALA 500 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3943 ASP* 4.3 9.9 - - + -
3953 PHE* 3.9 13.7 - - + -
4963 ALA 3.2 19.1 + - - +
4973 TRP 4.3 2.0 - - - +
4983 GLU 3.4 1.1 - - - +
4993 LYS* 1.3 77.3 - - - +
5013 LYS* 1.3 65.3 + - - +
5023 ASN 3.8 0.2 + - - -
5033 PRO* 3.8 28.9 - - + +
5283 LYS* 3.0 27.4 + - - -
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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