Contacts of the helix formed by residues 472 - 482 (chain 3) in PDB entry 6Q8O
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 GLU 472 (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* 5.7 1.0 - - - +
4683 HIS* 3.9 12.8 - - - +
4693 ARG* 3.1 53.7 + - - +
4703 PRO 3.0 2.6 - - - +
4713 GLY* 1.3 77.8 - - - +
4733 GLU* 1.3 67.2 + - - +
4743 ARG* 3.3 2.5 - - - -
4753 GLU* 3.1 29.9 + - + +
4763 ILE* 3.1 21.9 + - + +
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Residues in contact with GLU 473 (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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3993 LEU* 4.5 8.3 - - + -
4533 PRO* 5.2 6.8 - - - +
4683 HIS* 3.4 26.6 + - + -
4703 PRO* 4.1 6.4 - - - +
4713 GLY* 3.4 18.2 + - - -
4723 GLU* 1.3 81.0 + - - +
4743 ARG* 1.3 55.9 + - - +
4763 ILE* 2.6 36.2 + - - +
4773 LEU* 2.9 26.0 + - + +
5103 GLY* 5.6 6.1 - - - -
5113 VAL* 4.2 23.1 - - + +
5143 ASP* 4.8 8.0 - - - +
5173 ALA* 4.8 1.8 - - + -
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Residues in contact with ARG 474 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4713 GLY* 4.0 23.2 + - - +
4733 GLU* 1.3 77.5 + - - +
4753 GLU* 1.3 71.0 + - + +
4773 LEU* 3.4 3.5 + - - +
4783 LEU 2.9 19.1 + - - -
5143 ASP* 3.4 27.3 + - - +
5163 VAL* 3.2 37.6 - - - +
5173 ALA* 3.8 30.6 - - + +
5203 ARG* 2.6 33.9 + - - +
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Residues in contact with GLU 475 (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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4713 GLY 5.2 2.7 - - - +
4723 GLU* 3.1 22.2 + - + +
4733 GLU 3.0 1.0 - - - -
4743 ARG* 1.3 93.1 - - + +
4763 ILE* 1.3 65.9 + - - +
4783 LEU* 3.4 14.0 - - + +
4793 ALA* 2.9 23.7 + - - +
4843 LYS* 6.1 4.0 - - + -
5203 ARG* 3.9 6.3 - - - +
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Residues in contact with ILE 476 (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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3993 LEU* 4.3 10.1 - - + -
4513 PHE* 4.3 25.6 - - + -
4663 GLU* 6.4 0.2 - - + -
4683 HIS* 3.8 32.5 - - + +
4723 GLU* 3.1 40.9 + - + +
4733 GLU* 2.6 17.4 + - - +
4753 GLU* 1.3 71.0 - - - +
4773 LEU* 1.3 57.2 + - - +
4793 ALA* 3.2 3.9 + - - +
4803 LEU* 2.9 48.2 + - + +
4903 VAL* 4.0 29.3 - - + +
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Residues in contact with LEU 477 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3993 LEU* 3.4 29.4 - - + -
4733 GLU* 2.9 37.7 + - + +
4743 ARG* 3.6 9.6 - - - +
4763 ILE* 1.3 74.7 - - - +
4783 LEU* 1.3 65.9 + - - +
4803 LEU* 3.2 13.4 + - + +
4813 LEU* 2.9 28.0 + - - +
5053 LEU* 5.8 1.3 - - + -
5073 LEU* 4.9 7.9 - - + -
5113 VAL* 4.7 3.6 - - + -
5173 ALA* 3.1 30.1 - - + +
5203 ARG* 4.0 10.3 - - + -
5213 ALA* 3.5 29.2 - - + +
5243 LEU* 5.7 5.6 - - + +
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Residues in contact with LEU 478 (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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4743 ARG 2.9 13.7 + - - +
4753 GLU* 3.2 18.8 + - + +
4773 LEU* 1.3 75.7 - - - +
4793 ALA* 1.3 63.0 + - - +
4813 LEU* 2.9 31.0 + - + +
4823 GLY 3.3 4.7 + - - -
4833 ASP* 3.7 27.9 + - + +
4843 LYS* 3.7 33.4 - - + -
5203 ARG* 3.5 32.2 - - - +
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Residues in contact with ALA 479 (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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4753 GLU 2.9 12.9 + - - +
4763 ILE 3.7 7.0 - - - +
4783 LEU* 1.3 77.7 - - - +
4803 LEU* 1.3 62.2 + - - +
4823 GLY* 3.2 10.6 + - - -
4843 LYS* 3.8 26.8 - - + +
4853 GLU 4.8 0.7 - - - -
4863 GLY* 4.2 15.3 - - - +
4903 VAL* 3.7 20.4 - - + -
4943 LYS* 3.4 18.3 - - - +
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Residues in contact with LEU 480 (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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3973 LEU* 3.6 31.6 - - + -
3993 LEU* 5.2 3.8 - - + -
4513 PHE* 5.2 0.4 - - + -
4763 ILE* 2.9 39.2 + - + +
4773 LEU* 3.6 14.8 - - + +
4793 ALA* 1.3 73.0 - - - +
4813 LEU* 1.3 65.6 + - - +
4823 GLY 3.4 0.3 + - - -
4903 VAL* 3.4 17.9 - - + +
4933 ALA* 4.0 9.6 - - + -
4943 LYS* 3.4 46.8 - - + +
4973 TRP* 5.4 4.6 - - + -
4983 GLU* 4.7 7.3 - - - +
5243 LEU* 4.3 23.0 - - + +
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Residues in contact with LEU 481 (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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4773 LEU 2.9 19.6 + - - +
4783 LEU* 2.9 20.1 + - + +
4803 LEU* 1.3 75.8 - - - +
4823 GLY* 1.3 57.1 + - - +
4833 ASP* 4.7 12.9 - - - +
4983 GLU* 5.3 3.9 - - - +
5203 ARG* 3.7 32.8 - - + +
5233 LEU* 4.3 12.8 - - + -
5243 LEU* 3.6 46.6 - - + +
5273 ARG* 4.4 22.7 + - - +
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Residues in contact with GLY 482 (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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4783 LEU 3.3 0.2 + - - -
4793 ALA 3.2 4.1 + - - -
4803 LEU 3.2 3.2 - - - -
4813 LEU* 1.3 78.7 - - - +
4833 ASP* 1.3 69.6 + - - +
4843 LYS 3.5 3.8 - - - -
4943 LYS* 3.6 25.9 - - - -
4983 GLU* 6.0 0.4 - - - -
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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