Contacts of the strand formed by residues 88 - 95 (chain J) in PDB entry 2NX5
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 88 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36J ARG* 3.7 22.2 - - - +
37J GLN 2.6 28.2 + - - -
38J ASP* 3.1 17.3 + - - -
86J GLN 3.3 3.0 + - - -
87J THR* 1.3 77.3 - - - +
89J VAL* 1.3 72.5 + - - +
90J TYR* 3.6 12.2 - - - -
113J ARG* 5.6 1.6 - - - -
114J LEU 3.2 29.7 + - - +
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Residues in contact with VAL 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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40I GLY* 5.8 1.8 - - - +
36J ARG* 3.3 1.4 - - - -
37J GLN* 2.7 44.6 + - + +
88J SER* 1.3 81.1 + - - +
90J TYR* 1.3 61.6 + - - +
91J PHE* 3.7 30.1 + - + -
111J GLY* 5.2 0.9 - - - -
112J THR 3.4 19.1 - - - +
113J ARG* 4.2 31.9 - - + +
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Residues in contact with TYR 90 (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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6J GLN* 3.1 6.4 - - - +
21J LEU* 3.7 20.2 - - + -
34J TRP* 3.9 15.7 - + + -
35J TYR 3.4 4.9 - - - +
36J ARG* 3.1 17.2 + - + -
46J ILE* 3.8 24.9 - - + -
65J TYR* 2.6 39.9 + + - -
77J LEU* 4.1 10.5 - - + -
79J LEU* 4.8 2.5 - - + +
86J GLN* 2.7 25.4 + - - +
88J SER* 3.6 15.3 - - - -
89J VAL* 1.3 72.8 - - - +
91J PHE* 1.3 62.2 + - - +
111J GLY* 3.5 1.2 - - - -
112J THR* 2.8 44.0 + - - +
114J LEU* 3.6 29.3 - - + +
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Residues in contact with PHE 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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37I GLN* 3.6 15.0 - - - -
40I GLY* 4.6 7.0 - - - -
41I GLU 3.9 5.6 - - - -
42I ALA* 3.8 17.7 - - - -
43I PRO* 4.2 11.2 - - + -
6J GLN* 3.7 1.8 - - - +
34J TRP* 3.7 3.7 - - - -
35J TYR* 2.7 45.6 + - + +
37J GLN* 3.5 19.3 - - + -
43J LEU* 4.0 22.4 - - + -
89J VAL* 3.7 31.9 - - + -
90J TYR* 1.3 76.1 - - - +
92J CYS* 1.3 58.2 + - - +
108J PHE* 4.3 15.5 - + + -
109J GLY 3.3 17.7 - - - -
110J ASP 3.7 21.1 - - - -
111J GLY* 3.9 4.5 - - - -
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Residues in contact with CYS 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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4J ILE* 3.6 16.8 - - - -
6J GLN* 3.1 23.0 - - - +
23J CYS* 2.0 52.9 - - + -
33J TYR 3.2 12.8 - - - +
34J TRP* 3.7 15.7 - - + -
91J PHE* 1.3 76.4 - - - +
93J ALA* 1.3 61.8 + - - +
108J PHE* 3.5 5.0 - - - -
109J GLY 3.1 23.9 + - - -
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Residues in contact with ALA 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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4J ILE* 4.6 1.6 - - - -
23J CYS* 5.1 0.5 - - - -
32J MET* 3.0 5.9 - - - +
33J TYR* 2.7 58.0 + - + +
35J TYR* 4.6 0.9 - - + -
92J CYS* 1.3 76.6 - - - +
94J THR* 1.3 65.1 + - - +
106J GLN* 4.4 10.3 - - + +
107J HIS 3.0 13.9 - - - +
108J PHE* 4.1 21.3 - - + -
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Residues in contact with THR 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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4J ILE* 3.4 23.4 - - + +
23J CYS* 5.0 2.2 - - - -
25J GLN* 3.5 35.2 + - + +
27J GLU* 5.8 0.5 - - - +
29J HIS* 3.3 22.5 + - - -
31J TYR 3.1 8.5 - - - -
32J MET* 3.8 15.7 - - + -
33J TYR* 4.2 4.8 - - - -
93J ALA* 1.3 80.1 - - - +
95J GLY* 1.3 60.2 + - - +
106J GLN* 3.7 7.1 - - - +
107J HIS* 2.9 35.0 + - - +
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Residues in contact with GLY 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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29J HIS* 3.2 22.4 + - - +
30J ARG 3.5 0.9 + - - -
31J TYR* 2.9 37.9 + - - +
33J TYR* 4.8 3.8 - - - -
94J THR* 1.3 78.0 - - - +
96J THR* 1.3 60.8 + - - -
97J GLY 3.3 2.9 - - - -
105J PRO 4.7 10.8 - - - -
106J GLN* 5.3 0.7 - - - -
107J HIS* 4.7 0.4 - - - -
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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