Contacts of the helix formed by residues 90 - 97 (chain E) in PDB entry 2XQL
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 ASP 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E GLU* 5.3 2.1 - - - +
65E LEU* 4.9 12.3 - - + +
86E ALA 3.2 12.5 + - - +
87E ILE 3.0 14.6 - - - +
88E ARG 4.3 0.2 - - - -
89E ASN* 1.3 72.8 - - - +
91E GLU* 1.3 64.7 + - - +
92E GLU* 2.9 20.7 + - - +
93E LEU* 3.2 45.7 + - + +
94E ASN* 3.1 10.9 + - - +
106F LEU* 5.0 1.6 - - - +
84G GLN* 3.8 13.7 + - - +
88G ARG* 5.8 0.2 + - - -
101G THR* 4.4 10.8 - - - +
102G ILE 4.9 9.0 + - - +
105G GLY 5.4 6.5 - - - -
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Residues in contact with GLU 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ARG 5.2 0.9 - - - -
89E ASN 3.3 6.1 + - - +
90E ASP* 1.3 74.2 + - - +
92E GLU* 1.3 61.6 + - - +
94E ASN* 3.6 7.7 + - - +
95E LYS* 3.6 33.1 + - - +
84G GLN* 3.8 4.3 - - - +
88G ARG* 2.6 41.8 + - + +
94G ASN* 3.7 17.0 + - - +
98G GLY* 2.4 32.5 - - - +
100G VAL 3.8 5.9 - - - +
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Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASP* 2.9 5.2 + - - +
91E GLU* 1.3 80.4 + - - +
93E LEU* 1.3 63.5 + - - +
95E LYS* 3.4 13.8 + - + +
96E LEU 3.6 1.7 + - - -
103F PRO* 3.4 44.3 - - + +
104F GLY* 4.0 2.6 - - - -
105F GLU 3.3 9.8 + - - -
106F LEU* 2.8 26.8 + - + +
99G LYS* 3.9 4.9 - - - +
100G VAL* 3.0 10.5 + - - +
101G THR* 0.6 144.9 + - + +
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 4.9 4.5 - - + -
61E GLU* 4.9 3.4 - - + +
62E ILE* 3.6 43.3 - - + +
65E LEU* 4.3 13.5 - - + -
86E ALA 5.1 0.9 - - - +
87E ILE* 3.9 18.6 - - - +
90E ASP* 3.2 30.6 + - + +
92E GLU* 1.3 75.7 - - - +
94E ASN* 1.3 64.7 + - - +
95E LYS 3.2 0.8 + - - -
96E LEU* 3.3 15.0 + - + +
97E LEU* 3.1 35.7 + - + +
65F PHE* 5.9 0.2 - - + -
106F LEU* 3.4 29.4 - - + -
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Residues in contact with ASN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU* 3.7 13.8 + - - +
87E ILE* 3.3 10.3 + - - +
88E ARG* 3.0 48.0 - - - +
90E ASP 3.1 18.6 + - - +
91E GLU* 3.6 9.6 - - - +
92E GLU 3.3 0.2 - - - -
93E LEU* 1.3 79.0 - - - +
95E LYS* 1.3 59.4 + - - +
97E LEU 3.6 0.5 - - - -
98E GLY* 3.2 22.2 + - - -
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Residues in contact with LYS 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLU* 3.6 26.9 + - - +
92E GLU* 3.4 10.6 + - - +
93E LEU 3.2 0.8 - - - -
94E ASN* 1.3 74.2 - - + +
96E LEU* 1.3 67.2 + - - +
98E GLY* 3.1 13.0 + - - -
103F PRO* 3.8 23.3 - - + +
104F GLY 5.6 2.2 - - - +
98G GLY 4.3 3.3 + - - -
99G LYS* 4.1 33.3 - - - +
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 4.5 21.5 - - + -
92E GLU 3.6 8.1 + - - +
93E LEU* 3.3 14.1 + - + +
95E LYS* 1.3 82.8 - - - +
97E LEU* 1.3 73.5 + - + +
98E GLY 3.4 1.9 + - - -
99E LYS 5.2 0.2 + - - -
65F PHE* 4.6 8.3 - - + -
69F ILE* 4.9 6.7 - - + -
72F ARG* 3.0 43.9 + - - +
101F LEU* 3.8 23.3 - - + +
102F LEU* 3.9 26.2 - - + -
103F PRO* 4.0 10.5 - - + +
106F LEU* 4.6 7.4 - - + -
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ILE* 5.1 1.3 - - + -
87E ILE* 3.6 44.0 - - + -
88E ARG* 2.5 33.4 + - - +
93E LEU* 3.1 22.0 + - + +
94E ASN 3.6 3.4 - - - -
96E LEU* 1.3 98.9 - - + +
98E GLY* 1.3 53.3 + - - +
99E LYS 3.5 1.6 - - - -
100E VAL* 3.7 29.3 + - + +
65F PHE* 3.9 34.3 - - + -
68F ASP* 5.0 1.3 - - - +
69F ILE* 4.8 3.1 - - + -
72F ARG* 4.0 11.0 - - - +
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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