Contacts of the helix formed by residues 90 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU* 5.3 1.9 - - - +
65A LEU* 4.9 12.9 - - + +
86A ALA 3.2 12.1 + - - +
87A ILE 3.0 14.4 - - - +
88A ARG 4.3 0.2 - - - -
89A ASN* 1.3 73.4 - - - +
91A GLU* 1.3 64.9 + - - +
92A GLU* 2.9 21.2 + - - +
93A LEU* 3.2 46.0 + - + +
94A ASN* 3.1 10.4 + - - +
106B LEU* 5.0 1.7 - - - +
84C GLN* 3.8 14.9 + - - +
88C ARG* 5.8 0.2 + - - -
101C THR* 4.4 10.7 - - - +
102C ILE 4.9 8.7 + - - +
105C GLY 5.4 5.2 - - - -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG 5.2 0.9 - - - -
89A ASN 3.3 5.6 + - - +
90A ASP* 1.3 74.4 + - - +
92A GLU* 1.3 61.4 + - - +
94A ASN* 3.6 7.7 + - - +
95A LYS* 3.6 33.5 + - - +
84C GLN* 3.8 3.9 - - - +
88C ARG* 2.6 42.4 + - + +
94C ASN* 3.7 16.5 + - - +
98C GLY* 2.4 31.4 - - - +
100C VAL 3.8 5.8 - - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP* 2.9 6.6 + - - +
91A GLU* 1.3 79.6 + - - +
93A LEU* 1.3 62.9 + - - +
95A LYS* 3.4 13.5 + - + +
96A LEU 3.6 1.0 + - - -
103B PRO* 3.4 45.0 - - + +
104B GLY* 4.0 2.8 + - - -
105B GLU 3.3 10.2 + - - -
106B LEU* 2.8 26.6 + - + +
99C LYS 3.9 4.9 - - - +
100C VAL* 3.0 9.8 + - - +
101C THR* 0.6 144.6 + - + +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.9 4.5 - - + -
61A GLU* 4.9 3.1 - - + +
62A ILE* 3.6 45.1 - - + +
65A LEU* 4.3 13.0 - - + -
86A ALA 5.1 0.9 - - - +
87A ILE* 3.9 18.8 - - + +
90A ASP* 3.2 32.1 + - + +
92A GLU* 1.3 75.8 - - - +
94A ASN* 1.3 64.8 + - - +
95A LYS 3.2 0.8 + - - -
96A LEU* 3.3 14.6 + - + +
97A LEU* 3.1 34.5 + - + +
65B PHE* 5.9 0.2 - - + -
106B LEU* 3.4 29.8 - - + -
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 3.3 10.5 + - - +
88A ARG* 3.0 48.9 - - - +
90A ASP 3.1 18.3 + - - +
91A GLU* 3.6 9.2 - - - +
93A LEU* 1.3 78.5 - - - +
95A LYS* 1.3 61.1 + - + +
97A LEU 3.6 1.2 - - - -
98A GLY* 3.2 21.3 + - - -
91I GLU* 3.7 13.8 + - - +
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLU* 3.6 26.4 + - - +
92A GLU* 3.4 10.8 + - - +
93A LEU 3.2 0.8 - - - -
94A ASN* 1.3 75.9 - - + +
96A LEU* 1.3 68.5 + - - +
98A GLY* 3.1 12.4 + - - -
103B PRO* 3.8 24.4 - - + +
104B GLY 5.6 2.4 - - - +
98C GLY 4.3 4.1 + - - -
99C LYS* 4.1 32.1 - - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.5 21.3 - - + -
92A GLU 3.6 8.3 + - - +
93A LEU* 3.3 13.4 + - + +
95A LYS* 1.3 82.3 - - - +
97A LEU* 1.3 72.7 + - + +
98A GLY 3.4 2.3 + - - -
99A LYS 5.2 0.2 + - - -
65B PHE* 4.6 7.9 - - + -
69B ILE* 4.9 6.3 - - + -
72B ARG* 3.0 45.9 + - - +
101B LEU* 3.8 23.1 - - + +
102B LEU* 3.9 28.3 - - + -
103B PRO* 4.0 11.1 - - + +
106B LEU* 4.6 7.4 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 5.1 1.6 - - + -
87A ILE* 3.6 42.0 - - + -
88A ARG* 2.5 34.0 + - - +
93A LEU* 3.1 22.9 + - + +
94A ASN 3.6 4.5 - - - -
96A LEU* 1.3 96.4 - - + +
98A GLY* 1.3 54.3 + - - +
99A LYS 3.5 2.7 - - - -
100A VAL* 3.7 29.5 + - + +
65B PHE* 3.9 35.4 - - + -
68B ASP* 5.0 1.8 - - - +
69B ILE* 4.8 2.7 - - + -
72B 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