Contacts of the helix formed by residues 83 - 95 (chain L) in PDB entry 1O1F
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 THR 83 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786J ILE* 5.9 2.5 - - - -
80L ASP 5.2 4.0 - - - +
81L GLN* 3.1 15.7 + - - +
82L GLY* 1.3 71.3 - - - +
84L PHE* 1.3 63.9 + - - +
85L GLU* 3.2 15.8 + - - +
86L ASP* 3.1 38.6 + - + +
87L PHE* 3.4 18.0 + - + -
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Residues in contact with PHE 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L GLY 3.8 4.1 + - - -
83L THR* 1.3 70.2 + - - +
85L GLU* 1.3 94.6 + - - +
86L ASP 3.3 0.2 - - - -
87L PHE* 3.6 11.1 - - + +
88L VAL* 3.2 35.2 + - + +
147L MET* 3.6 33.0 - - + -
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Residues in contact with GLU 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L THR* 3.2 12.0 + - - +
84L PHE* 1.3 112.0 - - - +
86L ASP* 1.3 63.9 + - - +
88L VAL* 3.3 3.4 + - - +
89L GLU* 2.9 52.6 + - - +
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Residues in contact with ASP 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786J ILE* 3.1 56.2 - - + +
83L THR* 3.1 36.2 + - + +
85L GLU* 1.3 81.4 - - - +
87L PHE* 1.3 57.8 + - + +
89L GLU* 3.6 11.7 - - - +
90L GLY* 2.9 23.2 + - - -
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Residues in contact with PHE 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786J ILE* 3.0 17.5 - - - -
789J ALA* 3.0 36.8 - - + -
790J THR* 1.2 73.8 - - + +
793J ARG* 5.3 6.3 - - + -
82L GLY* 4.0 6.7 - - - -
83L THR* 3.4 31.0 - - + -
84L PHE* 3.3 13.4 + - - +
85L GLU 3.3 0.4 - - - -
86L ASP* 1.3 81.6 - - - +
88L VAL* 1.3 61.6 + - - +
90L GLY* 3.4 7.1 + - - -
91L LEU* 3.4 22.0 + - - +
143L VAL* 4.2 14.6 - - + -
147L MET* 4.0 20.6 - - + -
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Residues in contact with VAL 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L PHE* 3.2 25.8 + - + +
85L GLU* 4.0 3.4 - - - +
87L PHE* 1.3 76.8 - - - +
89L GLU* 1.3 60.3 + - + +
91L LEU* 3.4 6.9 + - - +
92L ARG* 2.9 32.4 + - + +
139L TYR* 4.1 17.9 - - + +
140L GLU* 5.3 11.4 - - + +
143L VAL* 4.0 27.4 - - + -
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Residues in contact with GLU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786J ILE* 5.5 1.9 - - + +
85L GLU* 2.9 46.3 + - - +
86L ASP* 3.6 13.4 - - - +
88L VAL* 1.3 76.8 - - + +
90L GLY* 1.3 64.9 + - - +
92L ARG* 3.6 8.1 - - + +
93L VAL* 3.0 33.3 + - + +
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Residues in contact with GLY 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783J LEU* 6.3 3.4 - - - -
786J ILE* 5.2 9.6 - - - +
86L ASP 2.9 18.1 + - - -
87L PHE 3.8 1.8 - - - -
88L VAL 3.3 0.4 - - - -
89L GLU* 1.3 77.8 - - - +
91L LEU* 1.3 65.1 + - - +
93L VAL* 3.2 13.7 + - - +
94L PHE* 3.3 11.1 + - - +
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Residues in contact with LEU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790J THR* 6.0 5.8 - - + -
87L PHE 3.4 9.8 + - - +
88L VAL 3.4 4.5 + - - +
90L GLY* 1.3 77.3 - - - +
92L ARG* 1.3 58.3 + - - +
94L PHE* 3.1 33.5 + - + +
95L ASP* 2.9 25.1 - - - +
102L VAL* 4.5 6.1 - - + -
107L LEU* 4.7 10.5 - - + -
139L TYR* 3.4 42.2 - - + -
142L PHE* 4.5 11.9 - - + -
143L VAL* 3.8 20.9 - - + -
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Residues in contact with ARG 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L VAL* 2.9 23.7 + - + +
89L GLU* 3.2 12.1 + - + +
91L LEU* 1.3 76.6 - - - +
93L VAL* 1.3 60.1 + - + +
94L PHE 3.2 0.2 - - - -
95L ASP 3.2 20.8 - - - +
97L GLU 4.8 8.7 - - - -
98L GLY* 3.9 9.1 - - - -
99L ASN* 3.7 20.4 - - - +
100L GLY* 3.7 21.7 - - - +
139L TYR* 3.0 25.2 + - - -
140L GLU* 3.8 24.5 + - - +
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Residues in contact with VAL 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779J ARG* 4.6 17.7 - - - +
89L GLU* 3.0 19.4 + - + +
90L GLY* 3.2 7.6 + - - +
92L ARG* 1.3 79.8 - - + +
94L PHE* 1.3 60.6 + - - +
95L ASP 3.4 1.7 + - - -
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Residues in contact with PHE 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L GLY 3.3 9.7 + - - +
91L LEU* 3.1 27.1 + - + +
93L VAL* 1.3 79.3 - - - +
95L ASP* 1.3 58.9 + - - +
102L VAL* 3.6 40.4 - - + -
106L GLU* 3.8 29.9 - - + +
107L LEU* 4.3 4.9 - - + -
110L VAL* 3.7 34.3 - - + -
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Residues in contact with ASP 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L LEU 2.9 8.5 + - - +
92L ARG* 3.2 15.0 - - - +
93L VAL 3.4 2.4 - - - -
94L PHE* 1.3 83.0 - - - +
96L LYS* 1.3 79.6 + - - +
97L GLU 4.1 3.6 - - - +
99L ASN 3.7 6.4 - - - +
101L THR 3.1 30.2 + - - +
102L VAL* 3.4 15.1 - - - +
106L GLU* 5.1 4.9 - - - +
139L TYR* 2.8 42.5 + - - -
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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