Contacts of the helix formed by residues 87 - 96 (chain B) in PDB entry 1DIZ
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 ASN 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 5.1 5.5 + - - +
7B GLN* 5.3 12.3 - - - +
85B GLN 3.5 4.5 + - - +
86B CYS* 1.3 75.6 - - - +
88B PRO* 1.3 67.2 - - - +
89B GLN* 3.2 23.3 - - - +
90B ILE* 3.0 48.7 + - + +
91B VAL* 3.4 12.0 + - - +
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Residues in contact with PRO 88 (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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7B GLN* 3.5 17.5 - - + +
8B PRO 3.2 28.0 - - - +
9B PRO* 3.5 22.0 - - + +
86B CYS* 3.0 22.8 - - - +
87B ASN* 1.3 83.5 - - - +
89B GLN* 1.3 66.4 + - + +
90B ILE 3.1 0.3 + - - -
91B VAL* 3.3 3.4 + - + +
92B ASN* 2.8 42.2 + - - +
103B PRO 4.2 7.0 - - - +
106B ARG* 3.9 7.4 - - - +
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Residues in contact with GLN 89 (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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7B GLN* 5.1 10.9 - - - +
8B PRO 5.6 4.3 + - - +
9B PRO* 5.5 0.4 - - - +
87B ASN* 3.2 17.9 + - - +
88B PRO* 1.3 80.3 - - + +
90B ILE* 1.3 59.4 + - + +
92B ASN* 4.2 3.3 - - - +
93B GLY* 3.2 23.0 + - - -
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Residues in contact with ILE 90 (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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87B ASN* 3.0 35.5 + - + +
89B GLN* 1.3 75.5 - - + +
91B VAL* 1.3 67.1 + - + +
93B GLY* 3.1 12.5 + - - -
94B ALA* 3.4 11.1 + - - +
263B TRP* 4.1 26.9 - - + +
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Residues in contact with VAL 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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86B CYS* 4.2 12.3 - - - -
87B ASN 3.4 10.5 + - - +
88B PRO* 3.3 8.3 + - + +
90B ILE* 1.3 76.3 - - + +
92B ASN* 1.3 63.0 + - - +
94B ALA* 3.1 4.7 + - - +
95B LEU* 3.0 50.3 + - + +
263B TRP* 4.3 25.1 - - + +
266B TYR* 3.7 44.2 - - + -
270B HIS* 5.6 1.8 - - + -
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Residues in contact with ASN 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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9B PRO* 5.1 1.8 - - - +
88B PRO* 2.8 31.2 + - - +
89B GLN* 4.4 3.1 - - - +
91B VAL* 1.3 77.8 - - - +
93B GLY* 1.3 56.8 + - - +
94B ALA 3.0 9.7 + - - -
95B LEU* 3.6 12.0 + - - +
96B GLY* 3.6 17.9 + - - +
99B GLY* 4.4 12.1 - - - +
103B PRO* 3.5 41.5 + - - +
270B HIS* 4.7 9.2 - - - -
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Residues in contact with GLY 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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89B GLN 3.2 14.5 + - - -
90B ILE 3.1 10.9 + - - -
92B ASN* 1.3 74.3 - - - +
94B ALA* 1.3 57.8 + - - +
96B GLY* 4.9 0.9 - - - -
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Residues in contact with ALA 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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90B ILE 3.8 5.2 - - - +
91B VAL 3.1 3.1 + - - +
92B ASN 3.0 0.4 - - - -
93B GLY* 1.3 80.4 - - - +
95B LEU* 1.3 66.2 + - - +
96B GLY 3.3 2.5 + - - -
259B ARG 5.1 5.0 - - - +
260B TRP* 5.0 6.2 - - - +
261B LYS 5.6 3.4 - - - +
262B PRO* 5.9 0.4 - - + -
263B TRP* 3.6 32.3 - - + +
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Residues in contact with LEU 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 VAL* 3.0 39.6 + - + +
92B ASN* 3.6 5.6 + - - +
94B ALA* 1.3 81.0 - - - +
96B GLY* 1.3 62.1 + - - +
98B LEU* 3.1 23.1 + - + +
99B GLY* 4.3 11.2 - - - +
260B TRP* 3.8 32.6 + - + +
263B TRP* 4.2 15.9 - - + +
266B TYR* 4.0 8.3 - - + -
267B ALA* 3.9 18.6 - - + +
270B HIS* 3.7 30.5 - - + +
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Residues in contact with GLY 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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92B ASN* 3.6 15.2 + - - +
93B GLY 4.9 0.8 - - - -
94B ALA 3.3 4.8 + - - +
95B LEU* 1.3 80.1 - - - +
97B ARG* 1.3 60.8 + - - -
98B LEU 3.3 0.3 + - - -
99B GLY* 3.6 6.8 + - - -
100B ALA* 3.9 6.4 + - - +
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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