Contacts of the helix formed by residues 89 - 97 (chain B) in PDB entry 1UIR
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 GLY 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLY 3.0 12.8 + - - -
87B GLY 3.2 1.0 - - - -
88B GLU* 1.3 77.7 - - - +
90B ALA* 1.3 58.1 + - - +
91B THR 3.3 2.5 - - - -
92B LEU* 3.5 10.4 + - - +
93B ARG* 3.0 24.4 + - - +
106B MET* 5.1 0.2 - - - -
125B HIS* 3.7 11.8 - - - -
128B ALA* 3.7 3.2 - - - +
129B PHE* 3.7 24.7 - - - -
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Residues in contact with ALA 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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60B GLU* 3.8 1.6 - - - +
64B HIS* 3.3 37.2 - - + +
88B GLU* 3.4 3.0 - - + +
89B GLY* 1.3 76.3 - - - +
91B THR* 1.3 61.3 + - - +
93B ARG* 3.2 22.5 + - - +
94B GLU* 3.0 32.7 + - - +
124B TRP* 3.6 22.6 + - + +
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Residues in contact with THR 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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64B HIS* 3.3 15.1 + - - -
67B LEU* 3.5 19.7 - - + +
68B VAL* 3.8 15.9 - - + +
83B ILE* 3.9 26.5 - - + -
86B GLY* 3.9 11.7 - - - -
89B GLY* 4.4 0.4 - - - +
90B ALA* 1.3 76.9 - - - +
92B LEU* 1.3 64.6 + - - +
94B GLU* 3.2 2.6 + - - -
95B VAL* 3.0 23.0 + - + +
156B ILE* 4.0 10.1 - - + -
158B ASP* 2.6 28.0 + - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.5 22.3 - - + +
86B GLY 5.4 0.8 + - - -
89B GLY* 3.5 10.6 + - - +
91B THR* 1.3 79.5 - - - +
93B ARG* 1.3 62.8 - - - +
95B VAL* 3.0 2.4 + - - +
96B LEU* 2.8 44.6 + - + +
104B ALA* 3.7 30.1 - - + +
106B MET* 4.4 19.9 - - + -
128B ALA* 3.6 28.3 - - + +
129B PHE* 4.0 19.7 - - + +
134B ALA* 3.8 15.0 - - + -
135B VAL 6.5 0.2 - - - -
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Residues in contact with ARG 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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60B GLU* 2.7 43.2 + - - -
61B TYR* 4.2 11.1 - - - +
64B HIS* 4.2 3.4 - - - +
89B GLY 3.0 15.6 + - - +
90B ALA* 3.2 16.4 + - - +
92B LEU* 1.3 79.1 - - - +
94B GLU* 1.3 92.4 + - - +
96B LEU* 3.3 11.5 + - - +
97B LYS* 3.3 21.2 + - + +
123B GLU 3.4 1.0 + - - -
124B TRP 2.8 25.1 + - - -
125B HIS 4.0 11.2 - - - +
126B GLN* 3.3 37.7 + - + +
128B ALA* 3.7 9.8 - - + +
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Residues in contact with GLU 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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61B TYR* 5.9 0.3 - - - +
64B HIS* 3.8 25.1 - - + +
65B GLU* 3.8 9.8 - - - +
68B VAL* 3.8 14.4 - - + -
69B HIS* 2.7 49.4 + - + +
90B ALA 3.0 20.0 + - - +
91B THR 3.8 3.8 - - - +
93B ARG* 1.3 106.6 + - - +
95B VAL* 1.3 64.3 + - - +
97B LYS* 2.8 45.8 + - - +
98B HIS* 3.6 2.6 - - - -
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Residues in contact with VAL 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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68B VAL* 3.7 20.6 - - + -
72B MET* 3.7 7.6 - - + +
81B VAL* 3.9 41.1 - - + -
83B ILE* 3.9 17.5 - - + -
91B THR 3.0 17.1 + - - +
92B LEU 3.0 8.5 + - - +
94B GLU* 1.3 75.5 - - - +
96B LEU* 1.3 63.4 + - - +
97B LYS 3.1 1.4 + - - -
98B HIS* 3.2 14.7 + - - +
101B VAL* 3.5 15.3 - - + +
104B ALA* 4.1 17.9 - - + -
156B ILE* 4.3 8.7 - - + -
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Residues in contact with LEU 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 LEU* 2.8 38.4 + - + +
93B ARG* 3.6 6.7 - - - +
94B GLU 3.3 0.4 - - - -
95B VAL* 1.3 72.8 - - - +
97B LYS* 1.3 63.6 + - - +
98B HIS 3.1 4.9 + - - -
99B PRO* 5.3 0.2 - - - +
101B VAL* 4.3 7.9 - - + -
104B ALA* 4.0 25.8 - - + -
128B ALA* 3.7 14.1 - - + +
131B ASP* 3.4 40.4 - - + +
133B ARG* 3.1 46.9 + - + +
134B ALA* 4.5 0.7 - - + -
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Residues in contact with LYS 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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65B GLU* 4.6 6.3 + - - -
69B HIS* 4.6 0.9 - - - +
93B ARG* 3.3 18.2 + - + +
94B GLU* 2.8 52.1 + - - +
95B VAL 3.1 1.6 - - - -
96B LEU* 1.3 77.3 - - - +
98B HIS* 1.3 57.7 + - - +
99B PRO* 3.0 13.9 - - - +
260B ARG 4.1 3.1 - - - +
261B ASN 5.3 0.9 - - - +
262B LEU* 3.6 26.1 - - + +
263B ALA* 3.0 37.3 + - + +
265B ARG* 6.1 2.4 - - - +
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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