Contacts of the helix formed by residues 90 - 97 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLN* 3.8 15.3 + - - +
88A ARG* 5.8 0.3 + - - -
101A THR* 4.4 10.9 - - - +
102A ILE 4.9 8.6 + - - +
105A GLY 5.4 5.8 - - - -
61I GLU* 5.3 2.1 - - - +
65I LEU* 4.9 13.0 - - + +
86I ALA 3.2 13.1 + - - +
87I ILE 3.0 14.4 - - - +
88I ARG 4.3 0.2 - - - -
89I ASN* 1.3 74.1 - - - +
91I GLU* 1.3 64.3 + - - +
92I GLU* 2.9 20.4 + - - +
93I LEU* 3.2 46.4 + - + +
94I ASN* 3.1 10.7 + - - +
106J LEU* 5.0 1.6 - - - +
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Residues in contact with GLU 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLN* 3.8 4.1 - - - +
88A ARG* 2.6 42.5 + - + +
94A ASN* 3.7 16.6 + - - +
98A GLY* 2.4 31.4 - - - +
100A VAL 3.8 5.5 - - - +
88I ARG 5.2 1.1 - - - -
89I ASN 3.3 6.3 + - - +
90I ASP* 1.3 75.3 + - - +
92I GLU* 1.3 61.2 + - - +
94I ASN* 3.6 7.2 + - - +
95I LYS* 3.6 31.8 + - - +
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Residues in contact with GLU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 3.9 5.4 - - - +
100A VAL* 3.0 10.2 + - - +
101A THR* 0.6 145.2 + - + +
90I ASP* 2.9 6.4 + - - +
91I GLU* 1.3 79.8 + - - +
93I LEU* 1.3 62.3 + - - +
95I LYS* 3.4 15.1 + - + +
96I LEU 3.6 1.4 + - - -
103J PRO* 3.4 43.4 - - + +
104J GLY* 4.0 2.9 + - - -
105J GLU 3.3 10.2 + - - -
106J LEU* 2.8 26.3 + - + +
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Residues in contact with LEU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I LEU* 4.9 4.0 - - + -
61I GLU* 4.9 4.0 - - + +
62I ILE* 3.6 44.2 - - + +
65I LEU* 4.3 13.7 - - + -
86I ALA 5.1 0.2 - - - +
87I ILE* 3.9 19.0 - - - +
90I ASP* 3.2 31.4 + - + +
92I GLU* 1.3 75.6 - - - +
94I ASN* 1.3 64.8 + - - +
95I LYS 3.2 0.4 - - - -
96I LEU* 3.3 14.2 + - + +
97I LEU* 3.1 34.3 + - + +
65J PHE* 5.9 0.4 - - + -
106J LEU* 3.4 29.6 - - + -
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Residues in contact with ASN 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G GLU* 3.7 13.4 + - - +
87I ILE* 3.3 9.8 + - - +
88I ARG* 3.0 48.8 - - - +
90I ASP 3.1 19.4 + - - +
91I GLU* 3.6 9.4 - - - +
93I LEU* 1.3 78.2 - - - +
95I LYS* 1.3 60.5 + - + +
97I LEU 3.6 0.2 - - - -
98I GLY* 3.2 21.5 + - - -
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Residues in contact with LYS 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY 4.3 4.1 + - - -
99A LYS* 4.1 32.1 - - - +
91I GLU* 3.6 26.9 + - + +
92I GLU* 3.4 10.2 + - - +
93I LEU 3.2 0.6 - - - -
94I ASN* 1.3 75.1 - - + +
96I LEU* 1.3 68.3 + - - +
98I GLY* 3.1 13.0 + - - -
103J PRO* 3.8 23.5 - - + +
104J GLY 5.6 2.4 - - - +
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Residues in contact with LEU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I LEU* 4.5 21.8 - - + -
92I GLU 3.6 8.1 + - - +
93I LEU* 3.3 14.3 + - + +
95I LYS* 1.3 81.5 - - - +
97I LEU* 1.3 72.3 + - + +
98I GLY 3.4 1.9 + - - -
99I LYS 5.2 0.3 + - - -
65J PHE* 4.6 8.1 - - + -
69J ILE* 4.9 6.3 - - + -
72J ARG* 3.0 43.8 + - - +
101J LEU* 3.8 23.3 - - + +
102J LEU* 3.9 27.8 - - + -
103J PRO* 4.0 10.9 - - + +
106J LEU* 4.6 7.4 - - + -
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Residues in contact with LEU 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I ILE* 5.1 1.3 - - + -
87I ILE* 3.6 42.8 - - + -
88I ARG* 2.5 33.4 + - - +
93I LEU* 3.1 21.6 + - + +
94I ASN 3.6 4.4 - - - -
96I LEU* 1.3 98.4 - - + +
98I GLY* 1.3 53.9 + - - +
99I LYS 3.5 1.8 - - - -
100I VAL* 3.7 30.7 + - + +
102I ILE* 5.9 0.2 - - + -
65J PHE* 3.9 35.0 - - + -
68J ASP* 5.0 1.6 - - - +
69J ILE* 4.8 3.1 - - + -
72J ARG* 4.0 10.5 - - - +
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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