Contacts of the helix formed by residues 79 - 90 (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 ILE 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LYS* 4.1 25.1 - - + +
77A ARG* 4.4 12.3 - - + +
78A ILE* 1.3 77.8 - - - +
80A PRO* 1.3 65.1 - - + +
81A ARG* 4.2 18.4 - - + +
82A HIS* 2.7 53.7 + - + +
83A LEU 3.5 1.9 + - - -
55B SER* 3.7 20.4 - - - +
58B ALA* 4.0 2.9 - - - -
68I ASN* 5.7 4.5 - - - +
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Residues in contact with PRO 80 (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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79A ILE* 1.3 88.2 - - + +
81A ARG* 1.3 62.1 + - - +
83A LEU* 2.8 12.1 + - + +
84A GLN* 2.8 22.9 + - - +
102A ILE* 4.1 1.6 - - + +
103A ALA 3.5 15.3 - - - +
104A GLN* 3.6 14.8 - - + +
105A GLY* 4.2 3.8 - - - +
55B SER* 3.7 5.2 - - - +
57B LYS* 4.1 17.3 - - + -
58B ALA* 3.7 19.9 - - + +
61B ILE* 3.4 33.0 - - + -
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Residues in contact with ARG 81 (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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73A ASN* 5.7 3.6 - - - +
79A ILE* 2.9 21.1 + - + +
80A PRO* 1.3 77.9 - - - +
82A HIS* 1.3 62.5 + - + +
84A GLN* 3.4 9.3 + - - +
85A LEU* 2.8 63.6 + - + +
104A GLN 3.9 5.9 + - - +
105A GLY 3.3 28.3 + - - -
65I LEU* 5.8 3.4 - - - +
68I ASN* 5.6 10.6 - - - +
72I ASP* 5.6 5.9 + - - -
89I ASN* 4.4 32.5 + - - +
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Residues in contact with HIS 82 (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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66A ALA* 3.7 19.1 - - - +
69A ALA* 3.9 16.7 + - + +
70A ALA* 3.7 29.6 + - + -
73A ASN* 4.2 22.2 - - + -
75A LYS* 4.6 10.2 - - + +
77A ARG 3.9 6.1 + - - -
78A ILE* 3.6 17.0 - - + -
79A ILE* 2.7 54.2 + - + +
81A ARG* 1.3 75.9 - - + +
83A LEU* 1.3 65.4 + - - +
85A LEU* 3.3 6.9 + - + +
86A ALA* 2.7 28.4 + - - +
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Residues in contact with LEU 83 (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* 4.6 11.0 - - + +
63A LEU* 4.8 4.3 - - + -
66A ALA* 3.7 20.2 - - + -
78A ILE* 4.3 11.2 - - + -
79A ILE 3.5 0.4 + - - -
80A PRO* 2.8 9.2 + - + +
82A HIS* 1.3 75.5 - - - +
84A GLN* 1.3 54.2 + - - +
86A ALA* 3.1 4.6 + - - +
87A ILE* 2.7 49.9 + - + +
102A ILE* 4.7 2.5 - - + -
54B ILE* 5.3 0.2 - - + -
58B ALA* 3.6 27.1 - - + +
61B ILE* 3.5 39.7 - - + -
62B MET* 4.0 25.4 - - + -
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Residues in contact with GLN 84 (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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80A PRO 2.8 9.7 + - - +
81A ARG* 3.4 11.7 - - - +
83A LEU* 1.3 77.4 - - - +
85A LEU* 1.3 66.5 + - - +
86A ALA 2.9 1.0 + - - -
87A ILE* 3.5 1.5 - - - +
88A ARG* 2.8 70.5 + - + +
102A ILE* 3.5 16.5 - - + +
105A GLY* 3.1 36.0 - - - +
89I ASN 3.8 21.0 + - - +
90I ASP* 3.8 12.3 + - - +
91I GLU 3.8 14.1 - - - +
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Residues in contact with LEU 85 (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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69A ALA* 4.6 11.9 - - + -
73A ASN* 4.6 13.7 - - - +
81A ARG* 2.8 65.1 + - + +
82A HIS* 3.8 14.1 - - + +
84A GLN* 1.3 75.3 - - - +
86A ALA* 1.3 61.0 + - - +
88A ARG* 4.4 3.8 - - - +
89A ASN* 3.1 41.0 + - - +
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Residues in contact with ALA 86 (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* 4.5 3.6 - - - +
65A LEU* 3.8 19.1 - - + +
66A ALA* 3.7 29.6 - - + +
69A ALA* 5.0 2.9 - - + +
82A HIS 2.7 22.5 + - - +
83A LEU* 3.2 6.3 - - - +
84A GLN 2.9 0.8 + - - -
85A LEU* 1.3 70.4 - - - +
87A ILE* 1.3 67.5 + - + +
89A ASN* 3.3 4.0 + - - +
90A ASP* 3.2 23.7 + - - +
93A LEU* 5.3 1.8 - - + -
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Residues in contact with ILE 87 (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* 4.9 21.1 - - + -
83A LEU* 2.7 30.9 + - + +
84A GLN 3.6 2.9 - - - +
86A ALA* 1.3 74.4 - - + +
88A ARG* 1.3 75.2 + - - +
90A ASP 3.0 22.2 + - - +
93A LEU* 3.9 21.2 - - + +
94A ASN* 3.3 8.4 + - - -
97A LEU* 3.6 42.8 - - + -
102A ILE* 3.9 29.4 - - + -
61B ILE* 5.9 1.3 - - + -
65B PHE* 5.9 0.4 - - + -
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Residues in contact with ARG 88 (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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84A GLN* 2.8 64.3 + - + +
85A LEU* 4.4 3.6 - - - +
87A ILE* 1.3 84.8 - - - +
89A ASN* 1.3 66.8 + - - +
90A ASP 3.9 4.0 - - - +
91A GLU* 5.2 0.9 - - - -
94A ASN* 3.0 33.1 - - - +
97A LEU* 2.5 30.7 + - - +
100A VAL* 3.5 16.8 + - - +
102A ILE* 3.9 13.7 - - - +
89I ASN 5.4 3.6 - - - +
90I ASP* 5.8 0.4 + - - -
91I GLU* 2.6 41.7 + - + +
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Residues in contact with ASN 89 (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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85A LEU* 3.1 33.7 + - - +
86A ALA* 3.3 2.9 + - - +
88A ARG* 1.3 79.8 + - - +
90A ASP* 1.3 63.2 + - - +
91A GLU* 3.3 4.0 + - - +
81C ARG* 4.4 29.2 + - - +
84C GLN* 3.8 10.7 + - - +
88C ARG* 5.4 3.6 - - - +
105C GLY 6.4 0.2 - - - -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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