Contacts of the helix formed by residues 88 - 101 (chain e) in PDB entry 5JPQ
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 88 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49e SER* 3.2 14.4 + - - -
70e CYS* 6.3 0.4 - - + -
84e ILE 4.9 2.2 - - - +
85e SER* 4.3 10.8 - - - +
86e GLU 3.8 0.2 - - - -
87e ALA* 1.3 77.4 - - - +
89e PRO* 1.3 62.9 - - - +
90e ASP* 3.1 5.2 - - + +
91e ILE* 3.0 26.2 + - + +
92e THR* 4.1 0.9 + - - -
208e ALA 4.3 7.4 - - - +
209e MET* 5.4 0.4 - - - -
210e ALA* 5.2 15.7 - - + +
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Residues in contact with PRO 89 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49e SER* 3.1 27.4 - - - +
50e LEU* 5.2 0.9 - - - -
67e LEU* 5.0 11.7 - - + -
68e LEU 4.4 12.5 - - - +
69e ASN* 5.0 8.1 - - + -
87e ALA 3.7 2.2 - - - -
88e ARG* 1.3 72.5 - - - +
90e ASP* 1.3 64.1 + - - +
92e THR* 3.1 11.9 + - - +
93e HIS* 2.9 21.3 + - - +
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Residues in contact with ASP 90 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88e ARG* 3.0 3.7 + - + +
89e PRO* 1.3 77.7 - - - +
91e ILE* 1.3 52.5 + - - +
93e HIS* 3.0 8.9 + - - +
94e GLN* 2.6 38.0 + - - +
134e PHE* 5.8 9.0 - - + -
132f ARG 5.3 8.1 - - - +
133f THR* 5.8 8.1 - - - -
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Residues in contact with ILE 91 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88e ARG* 3.0 19.4 + - + +
90e ASP* 1.3 77.8 - - - +
92e THR* 1.3 62.8 + - - +
94e GLN* 3.2 8.3 + - - +
95e CYS* 2.9 24.8 + - - +
208e ALA* 3.8 26.2 - - - +
209e MET* 4.6 4.7 - - - +
234e ALA* 5.3 9.2 - - + +
235e SER* 5.5 0.5 - - - -
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Residues in contact with THR 92 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48e ALA* 4.7 15.7 - - - -
49e SER 5.4 2.2 - - - -
88e ARG 4.1 0.8 + - - -
89e PRO* 3.1 14.8 + - - -
91e ILE* 1.3 78.9 - - - +
93e HIS* 1.3 63.0 + - - -
95e CYS* 3.1 6.0 + - - +
96e LEU* 2.9 25.1 + - - +
208e ALA* 4.3 18.9 + - - +
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Residues in contact with HIS 93 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89e PRO 2.9 13.3 + - - +
90e ASP* 3.4 11.2 - - - +
92e THR* 1.3 76.3 - - - +
94e GLN* 1.3 65.3 + - - +
96e LEU* 3.4 7.0 + - - +
97e LEU* 3.3 19.9 + - - +
134e PHE* 5.2 10.1 - - + -
137e PHE* 4.8 18.6 - - + -
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Residues in contact with GLN 94 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90e ASP 2.6 17.0 + - - +
91e ILE* 3.3 13.9 - - - +
93e HIS* 1.3 74.9 - - - +
95e CYS* 1.3 56.7 + - - +
97e LEU* 3.3 5.6 + - - +
98e THR* 3.0 26.7 + - - -
235e SER* 4.5 14.1 - - - -
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Residues in contact with CYS 95 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91e ILE 2.9 16.1 + - - +
92e THR* 3.6 7.0 - - - +
94e GLN* 1.3 74.0 - - - +
96e LEU* 1.3 55.8 + - - +
98e THR* 3.2 9.3 + - - -
99e LEU* 2.7 39.3 + - + +
208e ALA* 5.9 3.4 - - + -
234e ALA* 5.4 5.4 - - + +
235e SER* 4.4 15.8 - - - +
238e CYS* 5.3 7.1 - - + +
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Residues in contact with LEU 96 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92e THR 2.9 15.6 + - - +
93e HIS* 3.7 8.7 - - - +
94e GLN 3.3 0.2 - - - -
95e CYS* 1.3 75.3 - - - +
97e LEU* 1.3 57.7 + - - +
99e LEU* 3.9 4.9 - - - +
100e LEU* 2.8 35.2 + - - +
130e ILE* 4.8 16.4 - - + -
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Residues in contact with LEU 97 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93e HIS 3.3 8.3 + - - +
94e GLN* 3.3 10.2 + - - +
95e CYS 3.2 0.4 - - - -
96e LEU* 1.3 77.4 - - - +
98e THR* 1.3 64.6 + - - +
100e LEU* 5.2 1.1 - - - -
101e ASP* 3.0 33.2 + - + +
130e ILE* 5.6 3.8 - - - +
132e ARG* 6.4 1.6 - - - -
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Residues in contact with THR 98 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94e GLN 3.0 10.7 + - - -
95e CYS* 3.5 13.2 - - - -
97e LEU* 1.3 79.2 - - - +
99e LEU* 1.3 58.3 + - - +
101e ASP* 4.6 3.0 - - - +
102e SER* 4.0 15.1 + - - -
235e SER* 4.4 22.2 - - - -
238e CYS* 4.9 6.5 - - - -
239e SER* 5.5 8.1 + - - -
242e CYS* 5.7 2.3 - - - +
235f SER* 6.6 0.4 - - - -
236f VAL* 5.8 3.5 - - - +
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Residues in contact with LEU 99 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43e VAL* 6.0 6.3 - - + -
95e CYS* 2.7 21.7 + - + +
96e LEU* 3.9 4.7 - - - +
98e THR* 1.3 72.3 - - - +
100e LEU* 1.3 65.6 + - - +
101e ASP 3.2 1.3 - - - -
102e SER* 3.3 19.5 - - - -
105e ASN* 3.7 8.8 - - - +
110e LEU* 5.5 2.8 - - - +
112e VAL* 5.3 14.1 - - + -
238e CYS* 5.6 7.9 - - + -
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Residues in contact with LEU 100 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96e LEU 2.8 20.9 + - - +
97e LEU* 4.5 1.6 - - - +
99e LEU* 1.3 72.4 - - - +
101e ASP* 1.3 60.5 + - - +
102e SER 3.2 3.9 + - - +
105e ASN* 3.8 17.6 - - - +
106e LYS* 5.1 1.2 + - - +
126e PRO 5.1 8.2 - - - +
128e VAL 4.5 16.4 - - - +
130e ILE* 5.6 7.2 - - + +
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Residues in contact with ASP 101 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97e LEU* 3.0 21.2 + - + +
98e THR* 4.6 3.8 - - - +
100e LEU* 1.3 77.2 - - - +
102e SER* 1.3 64.3 + - - +
103e PRO 3.7 0.9 - - - -
106e LYS* 5.8 0.7 - - - +
231f PRO 5.1 6.8 - - - +
232f LEU* 5.2 4.5 - - - +
233f SER* 4.6 20.6 - - - +
236f VAL* 4.5 16.6 - - + +
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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