Contacts of the helix formed by residues 2103 - 2111 (chain A) in PDB entry 5XJY
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 SER2103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064A ASP* 5.6 1.3 - - - -
2101A SER* 3.1 8.5 - - - -
2102A HIS* 1.3 80.7 - - - +
2104A MET* 1.3 63.1 + - - +
2105A GLU* 3.1 7.0 + - - +
2106A GLU* 3.8 8.9 + - - +
2107A CYS* 3.6 20.6 + - - +
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Residues in contact with MET2104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A ASP* 5.2 12.3 - - + +
1945A LEU* 5.5 10.8 - - + -
2101A SER* 5.0 2.6 + - - -
2102A HIS 4.2 0.4 - - - -
2103A SER* 1.3 69.7 - - - +
2105A GLU* 1.3 52.7 + - - +
2107A CYS* 4.7 3.6 - - - -
2108A GLU* 2.6 45.5 + - + +
2143A VAL* 4.5 18.7 - - + +
2144A ARG* 5.6 3.8 - - + +
2147A GLY* 6.2 1.8 - - - -
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Residues in contact with GLU2105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A HIS* 6.4 2.0 - - + -
1092A ASP* 4.2 24.9 - - + -
2103A SER* 3.1 4.1 - - - -
2104A MET* 1.3 75.7 - - - +
2106A GLU* 1.3 63.2 + - + +
2108A GLU* 3.2 2.9 + - - +
2109A ALA* 2.9 30.7 + - - +
2143A VAL* 5.6 2.7 - - - -
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Residues in contact with GLU2106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2072A THR* 6.5 1.1 - - - -
2080A ARG* 4.9 22.0 - - + +
2084A TRP* 4.7 8.5 - - - +
2103A SER* 3.8 11.2 + - - +
2105A GLU* 1.3 79.1 - - + +
2107A CYS* 1.3 60.1 + - - +
2109A ALA* 4.0 7.2 + - - +
2110A LEU* 3.9 16.6 + - - +
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Residues in contact with CYS2107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2099A LEU* 5.5 11.0 - - + -
2101A SER* 3.8 21.5 - - - -
2103A SER 3.6 15.7 + - - +
2104A MET* 4.5 3.6 - - - +
2105A GLU 3.2 0.4 - - - -
2106A GLU* 1.3 78.6 - - - +
2108A GLU* 1.3 59.4 + - - +
2109A ALA 3.2 0.2 - - - -
2110A LEU* 3.2 5.2 + - - +
2111A CYS* 2.9 32.1 + - + +
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Residues in contact with GLU2108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104A MET* 2.6 25.8 + - + +
2105A GLU* 3.8 2.7 - - - +
2107A CYS* 1.3 75.0 - - - +
2109A ALA* 1.3 65.0 + - - +
2110A LEU 3.5 0.2 + - - -
2111A CYS* 3.8 14.6 + - - +
2128A VAL* 4.7 17.6 - - + +
2143A VAL* 3.9 22.7 - - + -
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Residues in contact with ALA2109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2105A GLU 2.9 16.1 + - - +
2106A GLU* 4.2 8.5 - - - +
2107A CYS 3.2 0.2 - - - -
2108A GLU* 1.3 79.2 - - - +
2110A LEU* 1.3 57.6 + - + +
2111A CYS 4.6 1.9 - - - +
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Residues in contact with LEU2110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941A CYS* 4.4 8.0 - - - +
2084A TRP* 4.3 28.9 - - + +
2087A ALA* 6.1 2.2 - - + -
2088A LEU* 5.6 8.1 - - + +
2106A GLU 3.9 10.0 + - - +
2107A CYS* 3.2 7.7 + - - +
2109A ALA* 1.3 76.9 - - + +
2111A CYS* 1.3 67.7 + - - +
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Residues in contact with CYS2111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941A CYS* 3.7 12.3 - - - +
1942A PHE 4.5 8.3 - - - +
1943A GLY* 5.3 3.6 - - - +
2099A LEU* 5.9 3.1 - - + -
2107A CYS* 2.9 19.2 + - + +
2108A GLU* 3.8 12.8 + - - +
2109A ALA 3.6 3.1 - - - +
2110A LEU* 1.3 81.0 - - - +
2112A THR* 1.3 63.1 + - - +
2113A ARG 4.4 9.0 - - - +
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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