Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1AVZ
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 TYR 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 1.3 73.5 - - - +
82A LYS* 1.3 63.6 + - + +
84A ALA* 3.2 2.6 + - - +
85A VAL* 2.9 47.1 + - + +
139A PHE* 3.2 60.8 - + + +
140A GLY* 3.8 14.6 - - - -
190A ALA* 2.5 33.2 + - - +
191A PHE* 4.8 6.9 - - - -
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Residues in contact with LYS 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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80A THR* 3.3 22.2 - - - +
81A TYR* 1.3 85.4 - - + +
83A ALA* 1.3 60.6 + - + +
85A VAL* 3.4 4.0 + - - +
86A ASP* 3.0 42.1 + - - +
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Residues in contact with ALA 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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78A PRO 4.6 0.9 - - - +
79A MET* 4.2 4.0 - - - -
80A THR* 3.1 25.9 + - - +
82A LYS* 1.3 81.3 - - + +
84A ALA* 1.3 65.0 + - - +
86A ASP* 3.9 6.1 - - - +
87A LEU* 3.1 24.9 + - - +
120A TYR* 3.1 38.5 + - + +
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Residues in contact with ALA 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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79A MET* 3.8 18.5 - - + -
80A THR 2.8 16.8 + - - +
81A TYR 3.4 7.4 - - - +
83A ALA* 1.3 72.0 - - - +
85A VAL* 1.3 54.0 + - - +
87A LEU* 3.3 7.1 + - - +
88A SER* 2.7 35.7 + - - -
138A THR* 4.0 13.2 - - + -
139A PHE 4.1 0.9 - - - +
140A GLY* 3.1 26.0 - - - -
141A TRP* 3.6 8.9 - - + +
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Residues in contact with VAL 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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81A TYR* 2.9 41.3 + - + +
82A LYS* 3.7 5.8 - - - +
84A ALA* 1.3 73.1 - - - +
86A ASP* 1.3 71.5 + - - +
88A SER* 2.9 15.8 + - - -
89A HIS* 3.0 40.7 + - + +
140A GLY* 3.3 24.2 - - - +
142A CYS* 4.8 3.6 - - - -
190A ALA* 4.3 10.5 - - + -
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Residues in contact with ASP 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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82A LYS* 3.0 23.6 + - - +
83A ALA* 3.9 6.5 - - - +
85A VAL* 1.3 81.5 - - - +
87A LEU* 1.3 57.1 + - - +
89A HIS* 3.4 12.7 + - - +
90A PHE* 3.1 26.2 + - - +
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Residues in contact with LEU 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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79A MET* 3.6 31.4 - - + -
83A ALA 3.1 16.4 + - - +
84A ALA 3.3 3.4 - - - +
86A ASP* 1.3 75.1 - - - +
88A SER* 1.3 64.8 + - - +
90A PHE* 3.1 10.1 + - + +
91A LEU* 3.0 47.2 + - + +
114A ILE* 3.8 32.3 - - + -
118A GLN* 4.3 15.7 - - + +
120A TYR* 4.6 5.4 - - + -
124A TRP* 4.2 14.4 - - + -
141A TRP* 3.9 13.7 - - + -
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Residues in contact with SER 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 ALA 2.7 20.0 + - - -
85A VAL 2.9 6.5 + - - -
87A LEU* 1.3 75.4 - - - +
89A HIS* 1.3 61.8 + - - +
91A LEU 3.8 0.2 + - - -
92A LYS* 3.2 24.8 + - - +
140A GLY 3.2 1.9 + - - -
141A TRP* 3.3 17.4 - - - -
142A CYS* 3.0 46.1 + - - -
143A TYR* 3.8 10.3 + - - -
185A PHE* 3.6 8.1 - - - -
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Residues in contact with HIS 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 VAL* 3.0 37.9 + - + +
86A ASP* 3.4 14.5 + - - +
88A SER* 1.3 77.1 - - - +
90A PHE* 1.3 60.0 + - - +
92A LYS* 3.3 4.8 + - - +
93A GLU* 2.9 48.4 + - - +
142A CYS* 5.5 4.1 - - - -
185A PHE* 4.5 17.6 - + - -
187A SER* 6.0 2.6 - - - -
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Residues in contact with PHE 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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86A ASP 3.1 13.6 + - - +
87A LEU* 3.1 15.0 - - + +
89A HIS* 1.3 73.9 - - - +
91A LEU* 1.3 81.9 + - + +
93A GLU* 2.9 20.1 + - + +
94A LYS* 2.9 59.1 + - + +
113A TRP* 4.4 11.9 - + - -
114A ILE* 5.9 0.4 - - + -
118A GLN* 4.2 20.9 - - - -
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Residues in contact with LEU 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 LEU* 3.0 25.5 + - + +
90A PHE* 1.3 93.9 - - + +
92A LYS* 1.3 56.8 + - - +
94A LYS* 4.4 9.4 - - + -
95A GLY* 3.5 22.9 + - - +
97A LEU* 4.2 19.6 + - + +
98A GLU* 5.1 1.2 + - - +
110A LEU* 4.6 13.0 - - + -
113A TRP* 4.0 24.7 - - + -
114A ILE* 4.6 0.2 - - + -
141A TRP* 3.4 36.1 - - + -
143A TYR* 3.1 18.9 + - + +
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Residues in contact with LYS 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 SER 3.2 19.2 + - - +
89A HIS* 3.6 5.4 - - - +
90A PHE 3.0 1.0 - - - -
91A LEU* 1.3 76.5 - - - +
93A GLU* 1.3 68.1 + - - +
95A GLY* 3.4 10.8 + - - -
98A GLU* 3.4 37.5 + - + +
143A TYR* 3.5 5.4 - - - +
185A PHE* 3.7 44.2 + - + +
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Residues in contact with GLU 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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89A HIS* 2.9 36.6 + - - +
90A PHE* 2.9 14.2 + - + +
92A LYS* 1.3 79.4 - - + +
94A LYS* 1.3 62.8 + - - +
95A GLY* 3.4 0.5 + - - -
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Residues in contact with LYS 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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90A PHE* 2.9 52.0 + - + +
91A LEU* 4.4 7.9 - - + -
93A GLU* 1.3 79.9 - - - +
95A GLY* 1.3 66.0 + - - +
113A TRP* 4.3 19.3 - - + -
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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