Contacts of the helix formed by residues 90 - 100 (chain B) in PDB entry 2EZT
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 LEU 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B GLU* 3.5 23.8 - - + +
60B GLU* 4.8 0.2 - - - -
62B GLY* 5.7 0.2 - - - -
63B ALA* 3.2 17.7 - - + +
79B CYS* 4.0 10.5 - - + -
80B PHE 3.7 23.1 - - - +
81B GLY 4.0 8.1 - - - +
86B GLY 3.8 6.1 - - - +
87B GLY* 3.0 18.1 + - - +
89B HIS* 1.3 76.8 - - - +
91B MET* 1.3 64.1 + - - +
92B ASN 3.3 0.4 - - - -
93B GLY 3.0 14.7 + - - -
94B LEU* 3.1 29.7 + - + -
106B ALA* 4.4 8.1 - - + -
108B ILE* 3.4 33.0 - - + -
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Residues in contact with MET 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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88B THR* 3.1 24.9 - - + +
89B HIS 3.2 1.8 - - - -
90B LEU* 1.3 76.6 - - - +
92B ASN* 1.3 68.9 + - - +
94B LEU* 4.4 5.2 - - - -
95B TYR* 2.9 56.6 + - + +
129B ILE* 3.3 46.9 - - + +
130B TYR* 3.7 24.0 - - + +
133B VAL* 4.6 6.5 - - + -
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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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60B GLU* 3.8 22.9 + - + +
64B MET* 3.9 3.8 - - + -
89B HIS 4.3 3.4 + - - -
90B LEU 3.1 1.0 + - - -
91B MET* 1.3 80.3 - - - +
93B GLY* 1.3 57.3 + - - +
96B ASP* 3.1 27.2 + - - +
419B PHE* 3.7 21.8 - - - -
421B THR* 2.9 34.0 + - - +
1614B TDM 4.1 16.6 - - - +
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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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60B GLU* 4.6 2.2 + - - +
63B ALA* 3.6 19.9 - - - +
64B MET* 3.7 25.4 - - - +
67B ALA* 4.1 4.9 - - - +
90B LEU 3.0 7.7 + - - -
92B ASN* 1.3 77.1 - - - +
94B LEU* 1.3 59.1 + - - +
96B ASP* 3.3 5.4 + - - +
97B ALA* 2.9 27.6 + - - +
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Residues in contact with LEU 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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63B ALA* 4.3 3.1 - - + +
79B CYS* 4.2 9.9 - - - -
90B LEU* 3.1 31.9 + - + +
91B MET* 3.9 9.0 - - - +
93B GLY* 1.3 76.0 - - - +
95B TYR* 1.3 57.3 + - - +
97B ALA* 3.1 1.8 + - - -
98B ARG 2.9 23.0 + - - -
104B VAL* 4.1 16.2 - - + -
106B ALA* 3.8 31.9 - - + -
130B TYR* 4.2 25.1 - - + -
133B VAL* 3.4 20.0 - - + +
163B VAL* 3.2 31.1 - - + +
165B VAL* 4.4 1.6 - - + -
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Residues in contact with TYR 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 MET* 2.9 45.8 + - + +
94B LEU* 1.3 72.9 - - - +
96B ASP* 1.3 60.1 + - - +
98B ARG* 3.2 31.7 + - - +
99B GLU* 2.8 36.1 + - - +
129B ILE 5.3 3.8 + - - -
132B ASP* 2.7 40.0 + - - +
133B VAL* 3.5 25.0 + - + +
419B PHE* 3.3 44.2 - + + -
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Residues in contact with ASP 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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64B MET* 5.0 2.8 - - - +
67B ALA* 3.8 9.5 - - - +
71B LYS* 2.6 29.2 + - - -
92B ASN 3.1 19.9 + - - +
93B GLY* 3.4 8.5 - - - +
95B TYR* 1.3 76.9 - - - +
97B ALA* 1.3 56.0 + - - +
100B ASP* 2.8 40.0 + - - +
416B SER* 2.5 40.4 + - - +
419B PHE* 3.8 10.3 - - - +
421B THR* 4.1 7.4 - - + -
424B VAL* 4.5 5.8 - - + +
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Residues in contact with ALA 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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63B ALA 5.8 0.2 - - - +
67B ALA* 4.0 4.9 - - + -
93B GLY 2.9 13.1 + - - +
94B LEU* 3.1 9.4 + - - +
96B ASP* 1.3 73.8 + - - +
98B ARG* 1.3 61.0 + - - +
101B HIS* 2.9 23.6 + - - -
102B VAL* 3.1 29.3 + - + +
104B VAL* 3.7 28.0 - - + -
161B GLN 4.6 0.5 - - - +
162B GLY* 4.8 0.4 - - - -
163B VAL* 3.6 15.3 - - + -
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Residues in contact with ARG 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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94B LEU 2.9 12.4 + - - +
95B TYR* 3.2 30.5 + - - +
97B ALA* 1.3 76.9 - - - +
99B GLU* 1.3 88.5 + - - +
101B HIS* 3.2 15.0 + - - +
132B ASP* 2.8 45.8 + - - -
133B VAL* 3.5 28.0 - - + +
161B GLN 5.0 0.7 - - - +
162B GLY* 5.1 7.2 - - - -
163B VAL* 3.9 6.6 - - + +
419B PHE* 5.9 0.4 - - - -
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Residues in contact with GLU 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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95B TYR* 2.8 23.5 + - - +
96B ASP 4.2 0.9 - - - +
98B ARG* 1.3 114.7 + - - +
100B ASP* 1.3 60.8 + - - +
101B HIS* 3.2 13.0 + - - -
418B LEU* 3.7 35.7 - - + +
419B PHE* 3.8 43.5 - - + +
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Residues in contact with ASP 100 (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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71B LYS* 3.3 32.5 + - + +
96B ASP* 2.8 23.3 + - - +
97B ALA 3.6 0.4 - - - -
99B GLU* 1.3 76.2 - - - +
101B HIS* 1.3 84.7 + - - +
102B VAL* 3.3 12.7 + - + +
415B THR 3.5 2.8 - - - +
417B ASN* 3.1 48.1 + - - +
418B LEU* 3.4 12.3 + - - +
419B PHE 4.6 0.7 + - - -
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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