Contacts of the helix formed by residues 90 - 99 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 2.9 29.8 + - - -
2B SER* 3.0 17.5 + - - +
3B GLU* 3.1 42.3 + - + +
88B GLY 3.6 7.0 + - - +
89B ILE* 1.3 76.8 - - - +
91B GLY* 1.4 73.5 + - - +
92B THR 3.1 0.7 + - - -
93B GLN* 2.9 35.4 + - + +
94B MET* 3.6 11.7 - - - +
280H LEU* 5.7 2.1 - - - +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER 6.0 0.4 - - - -
90B GLU* 1.4 84.3 + - - +
92B THR* 1.3 57.1 + - - -
94B MET* 3.6 5.3 - - - +
95B ALA* 3.1 29.9 + - - +
280H LEU* 3.5 23.6 - - - +
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU 3.1 1.4 + - - -
91B GLY* 1.3 70.2 - - - -
93B GLN* 1.3 64.9 + - - +
95B ALA* 3.4 5.0 + - - +
96B HIS* 2.9 33.1 + - - +
141B LEU* 3.7 21.6 - - + +
144B GLN* 3.5 37.9 - - + +
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.1 40.5 + - - +
9B MET* 4.8 15.6 - - + +
89B ILE* 4.3 7.9 - - - +
90B GLU* 2.9 17.5 + - + +
92B THR* 1.3 80.3 - - - +
94B MET* 1.3 64.0 + - - +
96B HIS* 4.1 6.0 + - - +
97B CYS* 3.2 23.9 + - - +
144B GLN* 3.6 9.3 + - - -
145B ALA* 3.2 37.2 + - - +
146B GLY* 5.2 3.0 - - - -
147B GLU 5.7 1.2 + - - +
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Residues in contact with MET 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.7 28.0 - - + +
90B GLU* 3.2 26.1 + - - +
91B GLY 3.6 10.1 - - - +
93B GLN* 1.3 74.4 - - - +
95B ALA* 1.3 65.6 + - - +
97B CYS* 3.0 12.8 + - - +
98B LEU* 3.1 39.7 + - + +
277H LEU* 3.2 37.7 - - + +
278H LEU* 3.8 9.9 - - + -
279H GLY 3.6 13.5 - - - +
280H LEU* 3.8 30.1 - - + +
281H PHE* 5.2 0.2 - - + -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLY 3.1 15.7 + - - +
92B THR* 3.8 4.7 - - - +
94B MET* 1.3 79.5 - - - +
96B HIS* 1.3 58.0 + - - +
98B LEU* 4.1 0.9 - - - -
99B GLY* 3.0 29.3 + - - -
137B PHE* 3.3 29.4 - - + -
141B LEU* 4.9 2.9 - - + -
280H LEU* 3.8 34.1 - - + +
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 6.1 3.0 - - - -
92B THR* 2.9 19.6 + - + +
93B GLN* 4.2 7.0 + - - +
95B ALA* 1.3 75.0 - - - +
97B CYS* 1.4 65.0 + - - +
100B ALA* 3.3 9.6 - - + +
101B TYR* 3.2 25.8 + + + +
134B ASP* 2.9 42.4 + - - -
137B PHE* 3.7 16.3 - + + -
138B MET* 3.4 25.9 - - + +
144B GLN* 3.4 28.7 + - + +
145B ALA 4.9 3.0 + - - -
146B GLY* 5.1 6.0 - - - -
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Residues in contact with CYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.8 27.1 - - + -
11B PHE* 3.9 24.9 - - - -
86B ILE* 4.0 15.5 - - - -
89B ILE* 4.1 13.2 - - + -
93B GLN 3.2 19.6 + - - +
94B MET 3.0 5.8 + - - +
96B HIS* 1.4 76.5 + - - +
98B LEU* 1.3 58.7 + - + +
101B TYR* 3.1 16.6 + - - +
102B CYS* 2.9 31.2 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL* 4.0 22.8 - - + +
86B ILE* 4.1 22.2 - - + -
89B ILE* 4.5 2.9 - - + -
94B MET* 3.2 44.2 - - + +
95B ALA* 4.1 1.6 - - - +
97B CYS* 1.3 77.7 - - - +
99B GLY* 1.4 60.7 + - - +
100B ALA 3.6 0.4 - - - -
102B CYS* 3.5 13.0 - - - -
103B PRO* 3.1 16.0 - - - +
278H LEU* 4.2 16.4 - - + -
280H LEU 3.1 25.8 - - - +
281H PHE* 3.0 38.7 - - + -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR* 6.1 0.2 - - - -
95B ALA 3.0 20.0 + - - -
98B LEU* 1.4 79.1 - - - +
100B ALA* 1.4 60.7 + - - +
103B PRO* 3.8 8.6 - - - +
133B PHE* 5.1 1.9 - - - +
137B PHE* 4.0 17.5 - - - +
281H PHE* 3.8 17.5 - - - -
286H MET* 5.0 10.6 - - - +
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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