Contacts of the helix formed by residues 90 - 100 (chain A) in PDB entry 5JTP
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 GLU 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ILE* 1.3 76.1 - - - +
91A GLY* 1.3 70.1 + - - +
92A THR 3.6 1.7 + - - -
93A GLN* 3.8 11.6 + - - +
94A MET* 3.5 37.6 + - + +
450E ASN* 3.2 40.3 - - - +
451E VAL* 3.4 2.2 + - - -
452E VAL 4.3 7.9 + - - +
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Residues in contact with GLY 91 (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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90A GLU* 1.3 81.6 - - - +
92A THR* 1.3 59.2 - - - -
94A MET* 3.5 9.5 + - - +
95A ALA* 2.9 27.7 + - - +
153C GLN* 6.1 0.2 - - - -
454E LEU* 6.0 0.3 - - - +
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Residues in contact with THR 92 (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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90A GLU 3.6 0.6 + - - -
91A GLY* 1.3 69.3 - - - -
93A GLN* 1.3 62.9 + - - +
94A MET 3.3 0.2 - - - -
95A ALA* 3.3 10.6 + - - +
96A HIS* 3.1 26.2 + - - +
137A PHE* 4.3 4.9 - - - -
141A LEU* 4.8 6.9 - - - +
150C GLU 5.2 1.6 - - - -
151C GLU* 3.2 45.4 + - - +
152C HIS 4.4 10.1 - - - -
153C GLN* 3.6 36.6 - - + +
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Residues in contact with GLN 93 (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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9A MET* 3.9 14.8 - - - +
88A GLY 5.4 0.4 + - - -
89A ILE* 3.6 40.2 - - + +
90A GLU 3.8 9.2 + - - +
92A THR* 1.3 82.5 + - - +
94A MET* 1.3 59.8 + - - +
96A HIS* 3.3 12.0 + - - +
97A CYS* 3.2 27.3 + - - -
149C THR* 5.9 6.3 - - - +
150C GLU 5.7 1.5 + - - -
151C GLU* 6.3 0.9 - - + -
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Residues in contact with MET 94 (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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86A ILE* 5.7 2.0 - - + -
89A ILE* 4.2 5.6 - - + -
90A GLU* 3.5 37.8 + - + +
91A GLY* 3.5 9.8 + - - +
92A THR 3.3 0.4 - - - -
93A GLN* 1.3 75.4 - - - +
95A ALA* 1.3 61.1 + - - +
96A HIS 3.1 2.0 - - - -
97A CYS* 2.9 27.0 + - + +
98A LEU* 2.9 31.6 + - + +
451E VAL* 2.9 59.9 - - + +
452E VAL 4.1 2.9 - - - +
454E LEU* 3.6 29.2 - - + -
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Residues in contact with ALA 95 (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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91A GLY 2.9 18.3 + - - +
92A THR* 3.3 13.2 + - - +
94A MET* 1.3 74.7 - - - +
96A HIS* 1.4 55.5 + - - +
98A LEU* 3.8 12.5 - - + +
99A GLY* 3.1 26.6 + - - -
137A PHE* 3.4 23.8 - - + -
153C GLN* 4.1 14.1 - - - +
454E LEU* 5.2 7.4 - - + -
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Residues in contact with HIS 96 (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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92A THR 3.1 12.4 + - - +
93A GLN* 3.3 13.4 + - - +
95A ALA* 1.4 75.6 - - - +
97A CYS* 1.3 67.5 + - - +
100A ALA* 3.0 39.0 + - + +
101A TYR* 3.1 11.2 + + + -
134A ASP* 2.8 31.4 + - + +
137A PHE* 3.8 16.1 - + + -
138A MET* 3.8 14.1 - - + -
141A LEU* 6.1 0.2 - - + -
147C GLU* 3.3 22.7 + - - +
149C THR* 3.5 34.9 + - + +
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Residues in contact with CYS 97 (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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11A PHE* 5.7 5.6 - - + -
86A ILE* 6.4 2.9 - - + -
89A ILE* 4.3 17.9 - - + -
93A GLN* 3.2 21.3 - - - -
94A MET* 2.9 22.5 + - + +
96A HIS* 1.3 84.2 - - - +
98A LEU* 1.3 55.3 + - + +
101A TYR* 3.1 15.1 + - + -
102A CYS* 2.8 41.4 + - - -
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Residues in contact with LEU 98 (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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46A THR* 4.7 2.9 - - - +
48A SER* 5.7 2.5 - - - +
56A TYR* 3.6 34.5 - - + -
58A VAL* 3.3 43.3 - - + +
86A ILE* 6.6 0.2 - - + -
94A MET* 2.9 43.0 + - + +
95A ALA* 3.8 9.4 - - + +
97A CYS* 1.3 73.5 - - + +
99A GLY* 1.3 75.9 + - - +
100A ALA 3.5 0.2 - - - -
102A CYS* 3.8 11.6 - - - -
103A PRO* 3.3 6.1 - - - +
451E VAL 4.6 0.2 - - - +
454E LEU* 3.5 34.3 - - + -
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Residues in contact with GLY 99 (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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46A THR* 5.4 2.9 - - - -
95A ALA 3.1 21.5 + - - -
98A LEU* 1.3 83.2 - - - +
100A ALA* 1.3 60.2 + - - +
103A PRO* 3.9 5.5 - - - +
133A PHE* 4.7 0.7 - - - +
137A PHE* 4.4 11.4 - - - -
460E LEU* 3.5 34.7 - - - +
461E PHE* 5.0 1.0 - - - -
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Residues in contact with ALA 100 (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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96A HIS* 3.0 16.2 + - + +
98A LEU 3.5 1.0 - - - -
99A GLY* 1.3 80.0 - - - +
101A TYR* 1.3 63.4 + - - +
102A CYS 3.5 1.1 - - - -
103A PRO* 3.4 5.5 - - - +
104A ASN* 3.1 24.1 + - - +
133A PHE* 3.4 34.9 - - - +
134A ASP* 3.6 19.3 - - - +
137A PHE* 3.9 11.9 - - + -
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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