Contacts of the helix formed by residues 386 - 392 (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 SER 386 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2843 GLU 5.1 1.9 + - - -
3853 ALA* 1.3 76.6 - - - +
3873 LEU* 1.3 62.0 + - - +
3883 GLU* 3.4 14.4 + - - +
3893 ASP* 3.0 30.9 + - - +
3903 LEU* 2.9 23.0 + - - +
5333 LEU* 5.9 0.4 - - - +
6183 GLU* 3.2 6.7 - - - -
6203 ARG* 3.9 13.8 + - - -
6753 ARG* 2.9 29.6 - - - +
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Residues in contact with LEU 387 (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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2613 VAL* 6.1 0.2 - - + -
2843 GLU 4.0 9.4 + - - +
2853 VAL* 3.5 46.7 - - + +
3853 ALA 4.5 0.2 - - - +
3863 SER* 1.3 74.7 + - - +
3883 GLU* 1.3 57.8 + - - +
3903 LEU* 2.8 24.3 + - + +
3913 LEU* 3.0 16.2 + - - +
4083 ILE* 3.6 13.7 - - + -
4093 LEU* 3.5 26.0 - - + -
4123 ARG* 4.5 17.3 + - + +
5333 LEU* 3.6 21.8 - - + -
6173 LEU* 5.4 7.4 - - + -
6183 GLU* 3.1 17.2 + - - +
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Residues in contact with GLU 388 (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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2833 PRO* 3.7 24.0 - - - +
2843 GLU* 4.6 20.1 + - - +
3863 SER* 3.3 8.5 + - - +
3873 LEU* 1.3 77.3 - - - +
3893 ASP* 1.3 59.9 + - - +
3913 LEU* 3.1 13.6 + - + +
3923 GLN* 2.9 32.1 + - - +
4123 ARG* 4.7 9.6 + - - +
4223 PRO* 4.1 25.5 - - + +
4233 PRO* 4.4 13.9 - - + +
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Residues in contact with ASP 389 (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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3853 ALA* 5.3 1.1 - - + -
3863 SER* 3.0 40.3 + - - +
3883 GLU* 1.3 77.4 - - - +
3903 LEU* 1.3 51.6 + - - +
3923 GLN* 3.3 10.3 - - - +
3933 ALA* 2.6 34.2 + - - +
5043 VAL* 4.7 2.1 - - - +
5313 LYS* 4.3 24.8 - - + +
6753 ARG* 3.6 13.3 + - - -
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Residues in contact with LEU 390 (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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3853 ALA* 6.3 0.7 - - + -
3863 SER 2.9 6.3 + - - +
3873 LEU* 2.8 22.9 + - + +
3893 ASP* 1.3 73.7 - - - +
3913 LEU* 1.3 60.4 + - + +
3933 ALA* 2.9 25.7 + - + +
3963 ALA* 4.5 11.9 - - + -
4093 LEU* 4.5 22.4 - - + -
4123 ARG* 4.5 17.3 - - + +
4133 LEU* 4.3 20.4 - - + -
4163 PHE* 3.7 17.2 - - + -
5043 VAL* 3.8 36.3 - - + +
5063 ILE* 4.3 14.4 - - + -
5333 LEU* 5.3 3.6 - - + -
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Residues in contact with LEU 391 (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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3873 LEU 3.0 16.5 + - - +
3883 GLU* 3.1 14.1 + - + +
3903 LEU* 1.3 78.9 - - + +
3923 GLN* 1.3 61.5 + - - +
3933 ALA 3.5 4.5 + - - +
4123 ARG* 3.3 43.1 - - + +
4153 GLU* 3.2 31.0 - - + +
4163 PHE* 3.4 29.6 - - + +
4203 LEU 3.9 19.7 - - - +
4213 LYS* 4.6 19.3 - - - +
4223 PRO* 4.5 13.2 - - + -
4233 PRO* 5.7 2.5 - - + -
4473 LYS* 5.5 2.4 + - - -
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Residues in contact with GLN 392 (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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3883 GLU 2.9 19.8 + - - +
3893 ASP* 3.3 10.1 - - - +
3913 LEU* 1.3 72.3 - - - +
3933 ALA* 1.3 65.6 + - - +
3943 ASP* 3.8 8.1 - - - +
4213 LYS* 4.5 10.7 - - - +
4223 PRO* 3.7 31.2 - - + +
5023 ASN* 4.9 1.6 - - - +
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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