Contacts of the helix formed by residues 85 - 95 (chain J) in PDB entry 5XVO
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 ASP 85 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208I PHE* 3.5 38.4 + - - +
209I ASN 6.6 0.2 - - - -
210I ASP* 4.9 0.4 - - - -
83J ARG* 4.6 14.5 + - - +
84J HIS* 1.3 83.6 - - - +
86J SER* 1.3 64.9 + - - +
87J SER* 3.0 4.0 - - - +
88J LEU* 3.0 27.0 + - + +
89J GLN* 4.2 1.7 + - - +
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Residues in contact with SER 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I GLN* 4.0 17.7 + - - -
210I ASP* 3.4 14.9 + - - -
80J PHE 4.7 3.8 + - - -
81J TYR* 5.0 1.6 - - - -
82J GLY 4.7 5.1 + - - -
83J ARG* 3.3 36.0 + - - +
84J HIS 3.4 1.2 + - - -
85J ASP* 1.3 76.3 - - - +
87J SER* 1.3 62.3 + - - +
88J LEU 3.2 0.6 + - - -
89J GLN* 3.5 3.7 + - - +
90J LEU* 3.4 22.7 + - - +
195J GLY* 3.9 17.6 + - - +
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Residues in contact with SER 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I GLN* 3.4 19.4 + - - +
200I LEU* 4.3 7.5 - - - +
208I PHE* 3.8 22.9 - - - -
209I ASN 2.6 28.8 + - - -
210I ASP* 4.0 2.1 + - - -
212I ASN* 5.3 0.7 - - - -
85J ASP 3.0 0.4 - - - -
86J SER* 1.3 80.0 - - - +
88J LEU* 1.3 64.2 + - - +
90J LEU* 3.4 19.1 + - - +
91J THR* 3.4 17.7 + - - +
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Residues in contact with LEU 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I PHE 4.9 4.6 - - - +
85J ASP* 3.0 22.5 + - + +
87J SER* 1.3 78.3 - - - +
89J GLN* 1.3 60.8 + - - +
91J THR* 2.6 28.1 + - - +
92J ARG* 3.4 45.7 + - + +
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Residues in contact with GLN 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J ARG* 5.8 0.9 - - - -
85J ASP 4.2 0.8 + - - +
86J SER* 3.5 4.2 + - - +
88J LEU* 1.3 76.2 - - - +
90J LEU* 1.3 61.9 + - - +
92J ARG* 3.1 16.4 + - - +
93J GLN* 2.8 28.2 + - - +
96J TRP* 3.9 7.1 - - - -
194J THR 3.4 26.4 - - - +
195J GLY* 3.6 21.3 - - - +
196J CYS* 3.7 15.1 - - - -
273J VAL* 3.6 17.4 - - - +
277J ASN* 3.1 40.8 + - - +
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Residues in contact with LEU 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I PHE* 4.6 8.5 - - + -
199I GLN* 3.7 46.0 - - + +
200I LEU* 4.5 10.1 - - + -
86J SER* 3.4 13.5 + - - +
87J SER* 3.4 8.5 + - - +
88J LEU 3.3 0.4 - - - -
89J GLN* 1.3 78.6 - - - +
91J THR* 1.3 63.5 + - - +
93J GLN* 3.1 10.2 + - - +
94J LEU* 2.9 36.0 + - + +
195J GLY 3.8 14.3 + - - +
197J PHE* 3.1 46.2 - - + -
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Residues in contact with THR 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I LEU* 3.4 35.9 - - + -
87J SER 3.4 5.5 + - - +
88J LEU* 2.6 31.2 + - - +
90J LEU* 1.3 78.0 - - - +
92J ARG* 1.3 60.2 + - - +
94J LEU* 3.3 10.5 + - + +
95J ALA* 3.2 21.0 + - - +
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Residues in contact with ARG 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J LEU* 3.6 48.1 - - + +
89J GLN* 3.1 27.0 + - - +
91J THR* 1.3 79.2 + - - +
93J GLN* 1.3 61.1 + - - +
95J ALA* 3.1 17.0 + - - +
96J TRP* 3.2 17.8 + - - -
277J ASN* 3.6 28.0 - - - +
279J GLU* 2.8 33.2 + - - -
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Residues in contact with GLN 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J GLN* 2.8 18.7 + - - +
90J LEU* 3.1 11.3 + - - +
92J ARG* 1.3 73.9 - - - +
94J LEU* 1.3 64.1 + - + +
96J TRP* 3.2 50.0 + - + +
195J GLY 4.4 0.9 - - - +
196J CYS* 3.1 14.3 - - - -
197J PHE* 2.8 53.3 + - - +
200J LEU* 3.7 28.0 - - + +
213J LEU* 3.8 12.9 - - - +
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Residues in contact with LEU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I LEU* 3.9 33.0 - - + -
197I PHE* 5.3 1.8 - - + -
200I LEU* 4.0 26.0 - - + -
90J LEU* 2.9 26.9 + - + +
91J THR* 3.6 10.1 - - + +
92J ARG 3.3 0.2 - - - -
93J GLN* 1.3 77.8 - - + +
95J ALA* 1.3 58.0 + - - +
96J TRP 3.3 4.4 + - - +
197J PHE* 5.6 0.4 - - + -
200J LEU* 4.3 20.6 - - + -
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Residues in contact with ALA 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J THR 3.2 12.2 + - - +
92J ARG* 3.1 13.6 + - - +
93J GLN 3.1 1.0 - - - -
94J LEU* 1.3 76.4 - - - +
96J TRP* 1.3 66.5 + - - +
97J THR* 3.1 12.5 + - - +
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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