Contacts of the helix formed by residues 2161 - 2170 (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 LEU2161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2159A PHE 3.2 10.8 - - - +
2160A GLY* 1.3 73.7 - - - +
2162A ALA* 1.3 56.3 + - - +
2163A PHE 3.2 6.1 - - - -
2164A PRO* 3.2 27.5 - - + +
2165A GLY 4.0 1.6 + - - -
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Residues in contact with ALA2162 (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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2159A PHE 4.5 4.4 + - - +
2160A GLY* 3.2 2.9 - - - -
2161A LEU* 1.3 73.6 - - - +
2163A PHE* 1.3 61.4 + - - +
2164A PRO 3.2 2.0 - - - -
2165A GLY* 3.3 6.8 + - - +
2166A SER* 3.2 19.9 + - - -
2209A SER* 3.9 33.4 - - - +
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Residues in contact with PHE2163 (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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2160A GLY 3.8 13.1 + - - +
2161A LEU 3.2 0.4 - - - -
2162A ALA* 1.3 78.5 - - - +
2164A PRO* 1.3 57.7 - - - +
2166A SER* 3.5 7.6 + - - +
2167A VAL* 2.9 25.8 + - - +
2176A LEU* 5.4 12.3 - - + -
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Residues in contact with PRO2164 (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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2161A LEU* 3.2 15.0 - - + +
2162A ALA 3.2 0.4 - - - -
2163A PHE* 1.3 77.0 - - - +
2165A GLY* 1.3 59.8 + - - +
2167A VAL* 3.1 11.2 + - + +
2168A LEU* 2.9 26.5 + - - +
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Residues in contact with GLY2165 (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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2161A LEU 4.0 2.0 + - - -
2162A ALA* 3.3 11.3 + - - +
2164A PRO* 1.3 77.0 - - - +
2166A SER* 1.3 58.3 + - - +
2168A LEU* 3.3 8.4 + - - +
2169A LYS* 2.9 25.5 + - - +
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Residues in contact with SER2166 (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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2162A ALA 3.2 12.3 + - - -
2163A PHE* 3.7 10.5 - - - -
2164A PRO 3.3 0.2 - - - -
2165A GLY* 1.3 75.3 - - - +
2167A VAL* 1.3 56.9 + - - +
2169A LYS* 4.0 8.1 - - - -
2170A GLU* 2.6 39.4 + - - +
2199A LYS* 5.7 8.7 - - - -
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Residues in contact with VAL2167 (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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2163A PHE 2.9 16.3 + - - +
2164A PRO* 3.1 15.8 + - + +
2166A SER* 1.3 76.1 - - - +
2168A LEU* 1.3 56.3 + - - +
2170A GLU* 2.9 18.3 - - - +
2171A LYS* 4.3 3.3 - - - +
2173A ARG* 3.5 27.9 - - + +
2174A ASN 5.8 1.3 - - - +
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Residues in contact with LEU2168 (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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2164A PRO 2.9 10.7 + - - +
2165A GLY* 3.7 9.4 - - - +
2166A SER 3.2 0.2 - - - -
2167A VAL* 1.3 78.3 - - - +
2169A LYS* 1.3 64.2 + - - +
2171A LYS* 4.4 7.3 + - - +
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Residues in contact with LYS2169 (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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2165A GLY 2.9 16.8 + - - +
2166A SER* 3.7 8.1 - - - +
2168A LEU* 1.3 77.2 - - - +
2170A GLU* 1.3 61.1 + - - +
2171A LYS* 3.1 9.0 + - - +
2194A LEU 5.5 2.6 - - - +
2198A LYS* 5.6 11.6 - - + +
2199A LYS* 5.7 9.2 - - + +
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Residues in contact with GLU2170 (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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2166A SER* 2.6 19.3 + - - +
2167A VAL* 2.9 22.8 - - - +
2169A LYS* 1.3 69.6 - - - +
2171A LYS* 1.3 64.0 + - - +
2172A HIS* 3.2 10.9 + - + +
2173A ARG* 3.6 6.0 + - - -
2194A LEU 5.7 1.1 - - - -
2195A SER* 4.6 28.3 - - - +
2199A LYS* 5.7 3.8 - - + -
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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