Contacts of the helix formed by residues 81 - 92 (chain A) in PDB entry 1IXR
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 GLY 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY* 2.9 6.9 - - - +
80A VAL* 1.3 75.2 - - - +
82A PRO* 1.3 56.7 - - - +
83A LYS* 2.6 12.0 + - - -
84A VAL* 2.7 17.8 + - - +
85A ALA* 2.3 37.8 + - - +
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Residues in contact with PRO 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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29A GLN* 5.6 1.1 - - - +
51A LEU* 3.8 18.2 - - + -
53A LYS* 5.1 9.2 - - - +
60A TYR* 3.2 36.8 - - + +
71A PHE* 4.0 3.6 - - + -
75A LEU* 3.7 13.5 - - + -
80A VAL* 2.7 17.7 - - + +
81A GLY* 1.3 79.5 - - - +
83A LYS* 1.3 54.2 + - - +
85A ALA* 3.4 12.1 - - + -
86A LEU* 2.6 40.9 + - - +
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Residues in contact with LYS 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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29A GLN* 5.9 1.8 - - - -
81A GLY* 2.6 4.4 - - - -
82A PRO* 1.3 78.3 - - + +
84A VAL* 1.3 54.4 + - + +
86A LEU* 2.6 14.1 + - - +
87A ALA* 2.4 35.6 + - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 4.5 9.2 - - - +
81A GLY* 2.7 26.9 + - - +
83A LYS* 1.3 73.2 - - + +
85A ALA* 1.3 53.5 + - - +
87A ALA* 2.9 9.4 - - + +
88A LEU* 2.6 47.0 + - + +
113A SER 5.0 1.1 - - - -
114A GLY* 5.0 4.0 - - - +
115A VAL* 3.5 30.5 - - + +
119A LEU* 3.7 27.6 - - + -
123A ILE* 4.9 2.5 - - + -
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Residues in contact with ALA 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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71A PHE* 3.4 30.3 - - + -
74A LEU* 4.5 25.3 - - + +
75A LEU* 4.2 7.6 - - + +
79A GLY 5.6 0.2 + - - -
80A VAL 4.8 0.4 - - - +
81A GLY 2.3 30.5 + - - +
82A PRO* 3.3 7.6 - - + +
84A VAL* 1.3 68.8 - - - +
86A LEU* 1.3 65.8 + - - +
88A LEU* 3.1 3.0 + - - +
89A LEU* 3.0 23.3 + - - +
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Residues in contact with LEU 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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15A GLY 5.3 0.7 - - - +
29A GLN* 4.0 32.5 - - + +
30A ALA* 4.1 12.6 - - - +
31A PRO* 4.1 13.2 - - + -
60A TYR* 4.0 11.4 - - + -
62A PHE* 3.5 37.0 - - + -
71A PHE* 4.0 8.3 - - + -
82A PRO 2.6 30.1 + - - +
83A LYS* 2.6 5.5 + - - +
85A ALA* 1.3 73.2 - - - +
87A ALA* 1.3 65.0 + - - +
89A LEU* 4.4 3.4 - - + -
90A SER* 3.0 30.4 + - - +
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Residues in contact with ALA 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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83A LYS* 2.4 24.4 + - + +
84A VAL* 2.8 25.9 + - + +
86A LEU* 1.3 70.7 - - - +
88A LEU* 1.3 58.2 + - - +
90A SER* 3.2 11.3 + - - -
91A ALA* 3.2 11.1 + - - +
112A ALA* 3.6 14.4 - - + +
113A SER* 3.4 33.3 + - - +
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Residues in contact with LEU 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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74A LEU* 3.4 39.3 - - + -
84A VAL* 2.6 31.8 + - + +
85A ALA 3.6 4.9 - - - +
87A ALA* 1.3 67.0 - - - +
89A LEU* 1.3 56.9 + - - +
90A SER 3.0 4.5 - - - -
91A ALA* 2.9 4.7 + - - +
92A LEU* 2.9 35.3 + - + +
97A LEU* 4.5 9.4 - - + -
109A LEU* 3.5 38.4 - - + +
112A ALA* 3.1 23.8 - - + -
115A VAL* 3.8 8.1 - - + -
123A ILE* 4.4 12.3 - - + -
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Residues in contact with LEU 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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31A PRO* 4.2 21.4 - - + +
33A PRO* 4.8 3.8 - - - +
62A PHE* 3.6 22.0 - - + -
67A ASN* 2.9 40.8 - - + +
70A LEU* 4.4 8.3 - - + -
71A PHE* 3.7 32.1 - - + +
74A LEU* 5.6 2.2 - - + -
85A ALA 3.0 14.9 + - - +
86A LEU* 4.0 4.0 - - - +
88A LEU* 1.3 77.5 - - - +
90A SER* 1.3 58.7 + - - +
92A LEU 3.5 16.4 - - - +
93A PRO* 5.3 0.7 - - - +
94A PRO* 5.3 3.4 - - + +
97A LEU* 4.4 15.0 - - + +
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Residues in contact with SER 90 (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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31A PRO* 3.5 6.2 - - - +
32A THR* 3.0 39.6 + - - -
33A PRO* 3.5 24.8 - - - +
86A LEU* 3.0 22.3 + - - +
87A ALA* 3.4 5.6 - - - -
89A LEU* 1.3 78.7 - - - +
91A ALA* 1.3 62.9 + - - +
92A LEU 5.1 0.6 - - - -
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Residues in contact with ALA 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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87A ALA 3.2 4.1 + - - +
88A LEU 2.9 6.1 + - - +
90A SER* 1.3 80.4 - - - +
92A LEU* 1.3 69.8 + - + +
93A PRO* 4.0 4.4 - - - +
111A SER* 4.1 13.0 - - - +
112A ALA* 3.7 36.3 - - + +
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Residues in contact with LEU 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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88A LEU* 2.9 13.8 + - + +
89A LEU* 3.5 20.5 - - - +
90A SER 5.1 0.2 - - - -
91A ALA* 1.3 92.5 - - + +
93A PRO* 1.3 78.0 - - + +
94A PRO 3.7 0.7 - - - -
96A LEU* 4.5 8.3 - - + -
97A LEU* 4.3 22.5 - - + +
100A ALA* 5.2 0.7 - - + -
108A LEU* 3.5 46.9 - - + -
109A LEU* 4.3 25.1 - - + +
111A SER* 3.8 15.7 - - - +
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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