Contacts of the helix formed by residues 90 - 99 (chain C) in PDB entry 5JTO
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89C ILE* 1.3 78.2 - - - +
91C GLY* 1.4 70.6 + - - +
92C THR 3.5 0.5 + - - -
93C GLN* 3.2 26.8 + - - +
94C MET* 3.3 15.0 + - - -
274F GLN* 5.1 11.1 + - - +
275F LYS 5.0 0.3 - - - -
276F PRO* 3.5 30.8 - - - +
277F LEU* 3.5 22.4 - - + +
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Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 1.4 80.6 + - - +
92C THR* 1.3 52.5 + - - -
94C MET* 3.4 0.9 + - - +
95C ALA* 2.9 34.2 + - - +
275F LYS 4.7 4.6 + - - -
277F LEU 4.5 0.6 - - - +
278F LEU 3.7 23.9 + - - +
279F GLY* 5.1 2.5 - - - -
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU 3.5 0.6 + - - -
91C GLY* 1.3 69.1 - - - -
93C GLN* 1.3 66.1 + - - +
95C ALA* 3.5 9.5 - - + +
96C HIS 3.2 16.8 + - - -
140C TYR* 6.5 0.9 - - + -
142C GLN* 3.0 39.5 + - - +
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Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU* 5.4 3.1 - - - +
9C MET* 5.1 2.6 - - - +
89C ILE* 3.4 43.0 - - + +
90C GLU* 3.2 17.3 + - - +
92C THR* 1.3 79.0 + - - +
94C MET* 1.3 60.2 + - - +
96C HIS* 3.4 18.5 + - - +
97C CYS* 3.7 5.2 + - - +
142C GLN* 3.2 26.1 - - - +
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Residues in contact with MET 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TYR* 4.3 13.9 - - + -
86C ILE* 3.7 52.9 - - + +
89C ILE* 3.8 19.1 - - + +
90C GLU* 3.3 21.0 + - - -
91C GLY 4.0 1.3 - - - +
93C GLN* 1.3 75.5 - - - +
95C ALA* 1.3 59.7 + - - +
96C HIS 3.2 2.2 - - - -
97C CYS* 3.0 5.4 + - + +
98C LEU* 2.9 44.9 + - + +
277F LEU* 3.2 50.7 - - + +
278F LEU 5.0 0.7 - - - +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLY 2.9 18.6 + - - +
92C THR* 3.5 13.0 - - + +
93C GLN 3.3 0.2 - - - -
94C MET* 1.3 77.0 - - - +
96C HIS* 1.3 55.8 + - - +
98C LEU* 4.2 11.0 - - - +
99C GLY* 3.0 27.9 + - - -
137C PHE* 3.8 11.4 - - + -
279F GLY 3.3 26.2 - - - +
280F LEU* 4.2 8.6 - - + +
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Residues in contact with HIS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C MET* 5.4 9.1 - - + +
92C THR 3.2 11.0 + - - +
93C GLN 3.4 12.4 + - - +
95C ALA* 1.3 77.7 - - - +
97C CYS* 1.3 61.6 + - - +
100C ALA* 3.1 26.3 - - - +
101C TYR* 3.7 5.1 + - + +
134C ASP* 2.9 27.4 + - - -
137C PHE* 3.5 37.8 - - + +
138C MET 5.1 0.2 + - - -
141C LEU 4.4 1.1 - - - -
142C GLN* 3.2 36.0 + - + +
143C GLN* 3.6 23.5 - - + +
145C ALA* 6.1 3.1 - - + -
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Residues in contact with CYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C MET* 3.3 36.3 - - - -
11C PHE* 3.3 35.2 - - - -
86C ILE* 3.7 16.6 - - + -
93C GLN 3.7 1.1 + - - +
94C MET* 3.0 14.4 + - - +
96C HIS* 1.3 81.3 + - - +
98C LEU* 1.3 59.0 + - - +
101C TYR* 2.9 36.9 + - - +
102C CYS* 3.0 10.7 + - - -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C SER* 4.8 0.2 - - - +
56C TYR* 6.5 0.9 - - + -
58C VAL* 4.5 11.2 - - + -
86C ILE* 5.1 3.6 - - + -
94C MET* 2.9 50.8 + - + +
95C ALA* 4.2 2.0 - - - +
97C CYS* 1.3 73.7 - - - +
99C GLY* 1.4 61.5 + - - +
102C CYS* 3.4 18.8 - - - +
103C PRO* 3.1 13.2 - - - +
278F LEU* 3.7 38.8 - - + -
279F GLY 4.0 2.9 - - - +
280F LEU* 3.6 30.1 - - + +
281F PHE* 3.0 40.4 - - + -
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Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA 3.0 19.0 + - - -
98C LEU* 1.4 77.3 - - - +
100C ALA* 1.3 59.2 + - - +
103C PRO* 4.1 9.8 - - - +
133C PHE* 4.3 5.4 - - - +
137C PHE* 3.8 15.3 - - - -
280F LEU* 3.9 20.3 - - - +
281F PHE* 3.9 15.4 - - - -
286F MET* 4.7 4.7 - - - +
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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