Contacts of the helix formed by residues 82 - 92 (chain L) in PDB entry 1IJ4
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 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47L PHE* 3.3 32.4 - - + -
80L THR* 3.5 15.7 + - - +
81L ASN* 1.3 72.1 - - - +
83L PHE* 1.3 58.3 + - - -
84L GLY 3.6 0.4 - - - -
85L ALA* 3.6 2.0 - - - +
86L ILE* 3.1 43.1 + - + +
110L ILE* 5.0 5.8 - - + -
112L THR* 5.8 2.5 - - + -
114L GLY 4.7 3.9 + - - +
115L GLU* 4.4 0.9 - - - +
116L ALA* 3.7 18.3 + - - +
118L ASP* 2.9 8.1 + - - -
151L PHE* 3.7 28.5 - - + -
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Residues in contact with PHE 83 (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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30I LEU* 4.4 8.7 - - + -
82L THR* 1.3 76.5 - - - +
84L GLY* 1.3 61.5 + - - +
86L ILE* 3.6 2.3 + - - +
87L ASN* 3.0 30.1 + - - -
116L ALA* 3.7 13.5 - - + -
118L ASP* 3.1 42.8 + - - +
119L SER* 3.9 7.0 - - - -
120L GLY* 3.7 23.1 - - - +
121L ASN 3.4 33.5 - - - +
122L ILE* 4.0 12.1 - - + -
150L LYS* 4.1 26.5 - - + -
151L PHE* 4.1 15.7 - + - -
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Residues in contact with GLY 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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51L TYR* 3.6 25.5 - - - -
83L PHE* 1.3 72.3 - - - +
85L ALA* 1.3 55.1 + - - +
87L ASN* 3.6 9.2 + - - +
88L TYR* 2.9 28.1 + - - +
118L ASP* 2.9 15.3 + - - -
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Residues in contact with ALA 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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9L LEU* 3.8 12.3 - - + +
45L VAL* 6.0 0.4 - - + -
47L PHE* 3.5 27.8 - - + -
51L TYR* 3.4 17.3 - - + -
81L ASN 3.1 22.0 - - - +
82L THR* 3.4 8.0 + - - +
84L GLY* 1.3 71.4 - - - +
86L ILE* 1.3 63.5 + - - +
88L TYR* 3.4 7.1 - - + +
89L VAL* 3.3 25.6 + - - +
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Residues in contact with ILE 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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9L LEU* 3.6 22.9 - - + -
82L THR* 3.1 26.2 + - + +
83L PHE 4.2 0.2 - - - +
85L ALA* 1.3 70.4 - - - +
87L ASN* 1.3 62.8 - - - +
89L VAL* 3.4 13.4 + - - +
90L ALA 3.7 3.6 + - - -
108L LEU* 4.1 11.9 - - + -
110L ILE* 3.7 22.0 - - + -
122L ILE* 3.8 28.0 - - + -
125L ALA* 3.6 28.2 - - + +
130L ARG* 4.3 9.2 - - - -
151L PHE* 3.6 33.7 - - + -
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Residues in contact with ASN 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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83L PHE 3.0 24.7 + - - -
84L GLY* 3.7 9.9 - - - +
85L ALA 3.5 0.2 - - - -
86L ILE* 1.3 72.2 - - - +
88L TYR* 1.3 61.3 + - - +
89L VAL 3.6 0.2 + - - -
90L ALA* 3.6 4.3 + - - +
91L THR* 2.9 30.1 + - + +
121L ASN* 3.1 35.4 + - - +
122L ILE* 4.2 0.8 - - - +
123L ASP 3.4 7.2 + - - -
124L ALA* 3.2 35.1 + - + +
125L ALA* 5.2 1.1 - - - -
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Residues in contact with TYR 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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45L VAL* 3.6 30.7 - - + -
51L TYR* 3.4 42.6 + + + -
53L THR* 2.7 40.0 + - - -
84L GLY 2.9 18.1 + - - +
85L ALA* 3.4 15.0 + - + +
87L ASN* 1.3 70.7 - - - +
89L VAL* 1.3 57.7 + - - +
91L THR* 3.5 8.1 - - - -
92L GLU* 2.9 56.1 + - + +
93L VAL* 3.7 7.8 + - + -
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Residues in contact with VAL 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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7L VAL* 3.8 34.5 - - + -
9L LEU* 3.9 27.8 - - + -
45L VAL* 4.6 2.5 - - + -
85L ALA 3.3 15.5 + - - +
86L ILE 3.4 9.0 + - - +
88L TYR* 1.3 74.9 - - + +
90L ALA* 1.3 57.6 + - - +
93L VAL* 3.5 12.5 - - + +
94L PHE* 3.2 49.0 + - + -
108L LEU* 3.9 20.6 - - + -
128L ILE* 4.4 1.3 - - + -
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Residues in contact with ALA 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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86L ILE 3.7 2.4 + - - -
87L ASN 3.6 3.7 + - - +
88L TYR 3.6 0.2 - - - -
89L VAL* 1.3 77.3 - - - +
91L THR* 1.3 62.5 + - - +
94L PHE* 4.2 16.8 - - - +
106L LYS* 6.3 0.7 - - - +
124L ALA* 3.4 45.1 - - + +
125L ALA* 3.7 10.1 - - + +
128L ILE* 3.9 12.3 - - + +
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Residues in contact with THR 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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87L ASN* 2.9 23.4 + - + +
88L TYR* 3.5 8.7 - - - -
90L ALA* 1.3 80.0 - - - +
92L GLU* 1.3 74.0 + - - +
93L VAL 3.3 5.6 + - - -
94L PHE 4.4 0.7 + - - -
95L ARG* 3.2 26.2 - - - +
124L ALA* 4.7 12.3 - - + -
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Residues in contact with GLU 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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53L THR* 4.0 10.0 + - - +
88L TYR* 2.9 41.2 + - + +
91L THR* 1.3 79.8 - - - +
93L VAL* 1.3 65.9 + - - +
95L ARG* 2.8 40.1 + - - +
98L LEU* 3.4 16.0 - - + +
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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