Contacts of the helix formed by residues 75 - 88 (chain A) in PDB entry 5AJQ
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 LEU 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 6.2 2.5 - - + -
28A ARG* 6.1 3.6 - - + -
72A GLU* 3.7 27.8 - - + +
73A GLU 3.4 1.0 - - - -
74A GLU* 1.3 81.2 - - - +
76A GLU* 1.3 61.6 + - + +
77A ASP 3.0 4.5 - - - +
78A TYR* 2.9 25.3 + - - +
79A ILE* 3.4 23.5 + - + +
101A TYR* 3.7 51.1 - - + -
106A LEU* 4.4 24.1 - - + +
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Residues in contact with GLU 76 (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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72A GLU* 3.5 19.2 + - + +
73A GLU* 4.9 1.1 - - - +
75A LEU* 1.3 75.8 - - + +
77A ASP* 1.3 64.6 + - - +
78A TYR 3.3 0.4 - - - -
79A ILE* 3.7 33.6 + - + +
80A VAL* 4.4 10.2 + - - +
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Residues in contact with ASP 77 (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 GLU 3.3 21.9 + - - +
74A GLU* 3.7 9.4 - - - +
75A LEU 3.0 0.4 - - - +
76A GLU* 1.3 79.0 - - - +
78A TYR* 1.3 77.3 + - + +
80A VAL* 4.3 5.2 + - - +
81A GLU* 3.6 16.3 - - - +
181A LYS* 4.0 26.0 - - + +
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Residues in contact with TYR 78 (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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67A ILE* 4.0 28.0 - - + +
74A GLU* 3.5 26.2 - - + -
75A LEU 2.9 5.7 + - - +
77A ASP* 1.3 82.2 - - + +
79A ILE* 1.3 65.2 + - + +
80A VAL 3.3 2.9 - - - -
81A GLU* 3.1 12.0 + - - +
82A ILE* 3.1 28.5 + - + +
106A LEU* 3.7 30.7 - - + -
108A ILE* 5.0 2.0 - - + -
178A VAL* 3.9 44.0 - - + -
181A LYS* 3.5 18.1 + - + -
182A ASN* 3.3 28.2 + - - +
185A THR* 5.2 3.8 - - - +
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.6 21.3 - - + -
75A LEU* 3.4 21.4 + - + +
76A GLU* 4.0 36.6 - - + +
77A ASP 3.5 1.6 - - - -
78A TYR* 1.3 77.4 - - - +
80A VAL* 1.3 60.4 + - + +
82A ILE* 3.9 6.3 - - + +
83A GLU* 3.0 31.7 + - + +
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Residues in contact with VAL 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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76A GLU 4.5 10.8 - - - +
77A ASP 4.3 3.5 + - - +
78A TYR 3.3 0.8 - - - -
79A ILE* 1.3 80.0 - - + +
81A GLU* 1.3 69.0 + - - +
83A GLU* 3.6 4.8 + - - +
84A ILE* 3.1 47.1 + - + +
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Residues in contact with GLU 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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77A ASP 3.6 16.0 - - - +
78A TYR* 3.1 9.2 + - - +
80A VAL* 1.3 89.1 - - - +
82A ILE* 1.3 57.8 + - + +
84A ILE* 3.3 12.7 + - + +
85A LEU* 2.9 35.3 + - + +
156A ARG* 6.5 0.4 - - - -
176A PHE* 3.3 34.7 - - + +
177A GLY 4.1 1.4 - - - -
178A VAL* 3.6 35.6 + - + +
181A LYS* 3.5 30.6 - - - +
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Residues in contact with ILE 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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25A HIS* 4.6 9.9 - - - -
26A VAL* 4.2 23.6 - - + -
78A TYR 3.1 22.9 + - - +
79A ILE* 4.1 5.8 - - + +
81A GLU* 1.3 75.1 - - + +
83A GLU* 1.3 60.8 + - - +
85A LEU* 3.5 6.6 + - + +
86A ALA* 3.0 29.1 + - - +
96A LEU* 3.7 22.3 - - + +
99A ALA* 3.8 15.9 - - + -
106A LEU* 4.2 17.3 - - + -
108A ILE* 4.1 37.0 - - + -
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Residues in contact with GLU 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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24A GLU 4.9 5.8 - - - +
25A HIS* 6.2 0.4 - - - +
79A ILE* 3.0 21.5 + - + +
80A VAL* 3.8 6.5 - - - +
82A ILE* 1.3 72.9 - - - +
84A ILE* 1.3 57.1 + - - +
86A ALA* 3.6 5.3 + - - +
87A THR* 2.7 41.0 + - + +
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Residues in contact with ILE 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 VAL* 3.1 37.7 + - + +
81A GLU* 3.4 16.2 - - + +
82A ILE 3.2 0.2 - - - -
83A GLU* 1.3 75.9 - - + +
85A LEU* 1.3 66.9 + - - +
87A THR* 3.1 7.3 + - - -
88A CYS* 2.9 45.4 + - - -
153A ILE* 3.8 34.3 - - + -
154A ILE 5.3 3.1 - - - +
176A PHE* 3.9 32.1 - - + +
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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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81A GLU* 2.9 25.6 + - + +
82A ILE* 4.1 6.5 - - + +
84A ILE* 1.3 77.6 - - + +
86A ALA* 1.3 60.6 + - - +
88A CYS* 4.0 13.6 - - - +
93A ILE* 4.5 2.5 - - + -
94A VAL* 3.6 39.3 - - + +
95A LYS* 4.7 1.7 - - - +
96A LEU* 3.9 27.5 + - + +
108A ILE* 5.0 7.4 - - + -
110A ILE* 3.7 24.7 - - + -
175A ASP* 5.5 8.1 - - - +
176A PHE* 3.7 33.2 - - + -
178A VAL* 5.9 2.9 - - + -
800A DB8 6.4 0.9 - - + -
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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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24A GLU* 3.4 46.3 - - + +
82A ILE 3.0 18.0 + - - +
83A GLU 3.7 4.3 - - - +
84A ILE 3.1 0.2 - - - -
85A LEU* 1.3 78.9 - - - +
87A THR* 1.3 61.8 + - + +
88A CYS 3.5 4.5 + - - +
96A LEU* 4.1 12.5 - - + +
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Residues in contact with THR 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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24A GLU* 5.5 7.0 - - + +
83A GLU* 2.7 26.3 + - + +
84A ILE* 3.4 6.8 + - - -
86A ALA* 1.3 77.6 - - + +
88A CYS* 1.3 61.7 + - - +
89A ASP* 3.6 4.3 + - - +
147A PHE* 4.9 0.3 - - - -
151A LYS* 3.0 28.1 + - - -
153A ILE* 5.1 3.5 - - - +
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Residues in contact with CYS 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 ILE* 2.9 41.3 + - - +
85A LEU 4.0 11.8 + - - +
86A ALA 3.4 4.6 - - - +
87A THR* 1.3 75.9 - - - +
89A ASP* 1.3 59.8 + - - +
90A HIS 3.6 2.8 + - - -
93A ILE* 4.1 21.7 - - + +
94A VAL 5.2 2.4 - - - +
95A LYS* 4.7 12.1 + - - +
147A PHE* 3.9 18.4 - - + -
148A LEU* 3.8 23.1 - - - -
151A LYS* 5.1 1.1 - - - -
153A ILE* 4.0 11.2 - - - -
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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