Contacts of the helix formed by residues 205 - 209 (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 ARG 205 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1781 GLY 3.5 22.6 + - - -
1791 ALA* 3.9 4.5 - - - +
1811 ILE* 5.4 0.4 - - - -
1961 ARG* 4.0 2.5 - - - +
3501 HIS* 3.0 33.5 + - - +
3511 GLU* 3.9 21.6 + - - +
3521 SER 3.6 14.1 - - - +
3531 CYS* 4.3 6.1 - - - +
652 SER 4.7 0.4 + - - +
662 PHE* 2.4 71.0 + - + +
672 TYR* 3.6 11.3 - - - +
682 SER* 3.6 14.4 + - - +
2043 GLU* 1.3 80.8 - - - +
2063 GLY* 1.3 68.8 + - - +
2073 VAL 3.9 0.5 + - - -
2083 HIS* 4.0 10.0 + - - +
2093 THR* 3.1 6.3 + - - -
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Residues in contact with GLY 206 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3491 ALA 4.5 9.6 - - - -
3501 HIS 5.6 1.3 - - - -
3521 SER* 2.7 37.6 + - - -
3531 CYS 4.4 3.0 - - - -
3541 GLY* 4.7 3.9 - - - -
3601 ARG* 4.5 11.2 - - - -
3641 ALA* 5.7 0.2 - - - -
2053 ARG* 1.3 72.8 - - - +
2073 VAL* 1.3 60.0 + - - -
2093 THR* 2.3 30.0 + - - -
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Residues in contact with VAL 207 (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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3491 ALA 5.8 0.4 - - - +
3601 ARG* 3.3 46.4 - - + +
3611 GLU* 4.7 6.7 - - - +
3641 ALA* 3.4 28.4 - - + +
3651 GLY* 4.4 7.2 - - - +
1143 ASN* 5.5 3.4 - - - +
1623 ARG* 3.3 32.4 + - + +
1833 HIS* 4.7 0.5 + - - -
2053 ARG 3.9 0.2 + - - -
2063 GLY* 1.3 67.9 - - - -
2083 HIS* 1.3 72.7 + - + +
2093 THR* 3.0 12.4 + - - +
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Residues in contact with HIS 208 (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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1623 ARG* 5.6 7.3 - - - +
1643 VAL* 5.4 9.3 - - - +
2043 GLU* 4.0 25.7 - - - +
2053 ARG 4.0 7.1 + - - +
2063 GLY 3.3 1.6 - - - -
2073 VAL* 1.3 88.2 - - + +
2093 THR* 1.3 64.4 + - - +
2103 PHE* 3.4 19.2 - - - +
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Residues in contact with THR 209 (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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1961 ARG* 4.6 1.6 - - - +
3531 CYS 5.1 0.2 + - - -
3541 GLY* 5.1 5.4 - - - -
3601 ARG* 5.8 0.2 - - - -
1623 ARG* 4.7 3.8 + - - -
1783 ARG 5.6 0.2 - - - +
1833 HIS* 2.4 41.5 + - + -
2023 PHE* 3.5 34.5 - - + -
2043 GLU 3.2 22.0 - - - +
2053 ARG* 3.1 17.8 + - - -
2063 GLY 2.3 27.0 + - - -
2073 VAL 3.0 3.5 - - - +
2083 HIS* 1.3 79.1 - - - +
2103 PHE* 1.3 61.7 + - - +
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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