Contacts of the helix formed by residues 79 - 90 (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 ILE 79 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68G ASN* 5.7 4.7 - - - +
75I LYS* 4.1 25.1 - - + +
77I ARG* 3.6 12.8 + - + +
78I ILE* 1.3 78.2 - - - +
80I PRO* 1.3 66.2 - - + +
81I ARG* 4.2 17.9 - - + +
82I HIS* 2.7 54.1 + - + +
83I LEU 3.5 1.7 + - - -
55J SER* 3.7 20.0 - - - +
58J ALA* 4.0 2.9 - - - -
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Residues in contact with PRO 80 (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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79I ILE* 1.3 88.5 - - + +
81I ARG* 1.3 62.9 + - - +
83I LEU* 2.8 12.0 + - + +
84I GLN* 2.8 22.7 + - - +
102I ILE* 4.1 1.4 - - - +
103I ALA 3.5 14.1 - - - +
104I GLN* 3.6 15.0 - - + +
105I GLY* 4.2 3.6 - - - +
55J SER* 3.7 5.4 - - - +
57J LYS* 4.1 16.8 - - + -
58J ALA* 3.7 20.3 - - + +
61J ILE* 3.4 32.3 - - + -
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Residues in contact with ARG 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G LEU* 5.8 3.4 - - - +
68G ASN* 5.6 10.8 - - - +
72G ASP* 5.6 6.1 + - - -
89G ASN* 4.4 31.7 + - - +
73I ASN* 5.7 4.0 - - - +
79I ILE* 3.1 20.5 - - + +
80I PRO* 1.3 78.0 - - - +
82I HIS* 1.3 63.8 + - + +
84I GLN* 3.4 9.3 + - - +
85I LEU* 2.8 62.4 + - + +
104I GLN 3.9 6.4 + - - +
105I GLY 3.3 28.2 + - - -
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Residues in contact with HIS 82 (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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66I ALA* 3.7 18.3 - - - +
69I ALA* 3.9 17.2 + - + +
70I ALA* 3.7 28.0 + - + -
73I ASN* 4.2 22.4 - - + -
75I LYS* 4.6 10.2 - - + +
77I ARG 3.8 6.4 + - - -
78I ILE* 3.6 17.3 - - + -
79I ILE* 2.7 54.6 + - + +
81I ARG* 1.3 75.9 - - + +
83I LEU* 1.3 66.7 + - - +
85I LEU* 3.8 6.3 - - - +
86I ALA* 2.7 28.5 + - - +
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Residues in contact with LEU 83 (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* 4.6 10.8 - - + +
63I LEU* 4.8 4.0 - - + -
66I ALA* 3.7 21.1 - - + -
78I ILE* 4.3 11.7 - - + -
79I ILE 3.5 0.2 + - - -
80I PRO* 2.8 8.8 + - + +
82I HIS* 1.3 76.5 - - - +
84I GLN* 1.3 52.9 + - - +
86I ALA* 3.2 4.2 - - - +
87I ILE* 2.7 50.4 + - + +
102I ILE* 4.7 2.9 - - + -
54J ILE* 5.3 0.2 - - + -
58J ALA* 3.6 26.9 - - + +
61J ILE* 3.5 40.4 - - + -
62J MET* 4.0 24.9 - - + -
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Residues in contact with GLN 84 (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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89G ASN 3.8 19.7 + - - +
90G ASP* 3.8 12.3 + - - +
91G GLU 3.8 14.5 - - - +
80I PRO 2.8 10.2 + - - +
81I ARG* 3.4 11.4 - - - +
83I LEU* 1.3 77.4 - - - +
85I LEU* 1.3 67.1 + - - +
86I ALA 2.9 1.0 + - - -
87I ILE* 2.9 1.5 + - - +
88I ARG* 2.8 68.4 + - + +
102I ILE* 3.5 16.5 - - + +
105I GLY* 3.1 36.4 - - - +
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Residues in contact with LEU 85 (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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69I ALA* 4.6 12.3 - - + -
73I ASN* 4.6 13.9 - - - +
81I ARG* 2.8 62.8 + - + +
82I HIS* 3.8 13.9 - - - +
84I GLN* 1.3 73.8 - - - +
86I ALA* 1.3 61.0 + - - +
88I ARG* 4.1 3.8 - - - +
89I ASN* 3.1 40.4 + - - +
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Residues in contact with ALA 86 (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* 4.5 4.0 - - + +
65I LEU* 3.8 19.4 - - + +
66I ALA* 3.7 29.4 - - + +
69I ALA* 5.0 3.1 - - + +
82I HIS 2.7 22.6 + - - +
83I LEU* 3.2 5.6 - - - +
84I GLN 2.9 0.8 + - - -
85I LEU* 1.3 71.2 - - - +
87I ILE* 1.3 65.8 + - + +
89I ASN* 3.3 5.0 + - - +
90I ASP* 3.2 23.6 + - - +
93I LEU* 5.3 1.6 - - + -
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Residues in contact with ILE 87 (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* 4.9 20.6 - - + -
83I LEU* 2.7 30.8 + - + +
84I GLN 3.6 3.1 - - - +
86I ALA* 1.3 74.4 - - + +
88I ARG* 1.3 73.7 + - - +
90I ASP 3.0 22.3 + - - +
93I LEU* 3.9 22.1 - - + +
94I ASN* 3.3 8.7 + - - -
97I LEU* 3.6 42.8 - - + -
102I ILE* 3.9 29.2 - - + -
61J ILE* 5.9 1.1 - - + -
65J PHE* 5.9 0.7 - - + -
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Residues in contact with ARG 88 (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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89G ASN 5.4 3.6 - - - +
90G ASP* 5.8 0.4 + - - -
91G GLU* 2.6 42.4 + - + +
84I GLN* 2.8 65.8 + - + +
85I LEU* 4.4 4.0 - - - +
87I ILE* 1.3 83.3 - - - +
89I ASN* 1.3 65.2 + - - +
90I ASP 3.7 4.3 + - - +
91I GLU* 5.2 0.9 - - - -
94I ASN* 3.0 34.4 - - - +
97I LEU* 2.5 30.9 + - - +
100I VAL* 3.5 16.8 + - - +
102I ILE* 3.9 14.1 - - - +
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Residues in contact with ASN 89 (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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81A ARG* 4.4 30.2 + - - +
84A GLN* 3.8 10.7 + - - +
88A ARG* 5.4 3.6 - - - +
105A GLY 6.4 0.2 - - - -
85I LEU* 3.1 34.4 + - - +
86I ALA* 3.3 2.9 + - - +
88I ARG* 1.3 80.6 + - - +
90I ASP* 1.3 63.4 + - - +
91I GLU* 3.3 4.0 + - - +
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Residues in contact with ASP 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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