Contacts of the helix formed by residues 74 - 90 (chain A) in PDB entry 2A1X
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 PRO 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LEU 3.7 7.0 - - - +
73A VAL* 1.3 86.0 - - + +
75A ASP* 1.3 65.5 + - - +
76A ALA* 4.0 11.7 - - + +
77A ASP* 3.0 40.0 + - - +
78A ILE* 3.1 10.4 + - - +
136A LEU* 5.0 0.7 - - + -
138A GLU* 4.7 19.3 - - + +
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Residues in contact with ASP 75 (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 VAL 3.5 2.4 + - - +
74A PRO* 1.3 70.7 - - - +
76A ALA* 1.3 62.7 + - - +
78A ILE* 3.3 4.3 + - - +
79A GLN* 3.1 25.1 + - - +
252A LYS* 3.1 44.7 - - - +
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Residues in contact with ALA 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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74A PRO* 3.0 9.8 - - + +
75A ASP* 1.3 81.3 - - - +
77A ASP* 1.3 66.2 + - - +
79A GLN* 3.6 5.8 + - - +
80A ARG* 3.2 27.6 + - - +
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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
----------------------------------------------------------
73A VAL* 3.8 12.8 - - + -
74A PRO* 3.0 36.2 + - - +
76A ALA* 1.3 78.5 - - - +
78A ILE* 1.3 65.7 + - - +
80A ARG* 3.3 12.7 + - - +
81A PHE* 3.1 36.1 + - + -
132A ARG* 2.7 29.9 + - - +
136A LEU* 3.9 17.1 - - + +
138A GLU* 4.9 0.7 - - - +
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Residues in contact with ILE 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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73A VAL* 3.3 35.4 - - + +
74A PRO 3.1 14.2 + - - +
75A ASP* 3.3 8.7 + - - +
77A ASP* 1.3 76.5 - - - +
79A GLN* 1.3 58.5 + - - +
81A PHE* 3.2 16.4 + - + +
82A ARG* 2.9 30.7 + - - +
194A THR* 3.9 19.1 - - + -
195A ALA 4.0 4.5 - - - +
196A MET* 3.5 42.2 - - + +
252A LYS* 4.4 13.9 - - + -
253A GLY* 4.1 9.4 - - - +
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Residues in contact with GLN 79 (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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75A ASP 3.1 17.5 + - - +
76A ALA* 3.8 6.7 - - - +
78A ILE* 1.3 75.3 - - - +
80A ARG* 1.3 59.8 + - - +
82A ARG* 3.2 21.3 + - - +
83A ASN* 2.5 69.4 + - - +
252A LYS* 5.7 1.5 - - - +
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Residues in contact with ARG 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 ALA* 3.2 16.7 + - - +
77A ASP* 3.5 11.9 + - - +
79A GLN* 1.3 78.7 - - - +
81A PHE* 1.3 65.8 + - + +
83A ASN* 3.5 11.6 + - - +
84A GLU* 3.1 23.6 + - - +
129A GLU* 3.0 43.9 + - + +
132A ARG* 3.3 48.0 - - - +
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Residues in contact with PHE 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 VAL* 4.2 14.4 - - + -
77A ASP* 3.1 33.1 + - + -
78A ILE* 3.2 16.3 + - + +
80A ARG* 1.3 74.0 - - + +
82A ARG* 1.3 66.5 + - - +
84A GLU* 3.4 2.9 + - - +
85A PHE* 3.0 24.3 + - - +
129A GLU 3.2 29.2 - - - -
130A LEU* 4.0 9.9 - - + +
132A ARG* 4.6 10.3 - - + -
133A TYR* 3.8 46.0 - + + -
136A LEU* 5.2 4.0 - - + -
158A LEU* 4.4 1.2 - - + +
196A MET* 3.7 16.1 - - + +
278A ILE* 4.1 29.4 - - + -
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Residues in contact with ARG 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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78A ILE* 2.9 17.0 + - - +
79A GLN* 3.2 28.5 + - - +
81A PHE* 1.3 77.5 - - - +
83A ASN* 1.3 63.6 + - - +
85A PHE* 3.3 5.3 + - - +
86A GLU* 3.0 26.5 + - + +
196A MET* 3.3 38.6 - - + +
197A GLU* 5.9 0.7 - - - -
276A LYS* 4.3 19.9 - - + +
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Residues in contact with ASN 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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79A GLN* 2.5 57.0 + - - +
80A ARG* 3.6 11.6 - - - +
81A PHE 3.3 0.2 - - - -
82A ARG* 1.3 74.6 - - - +
84A GLU* 1.3 62.2 + - - +
86A GLU* 3.4 5.8 + - - +
87A LYS* 3.2 36.9 + - + +
90A ARG* 5.6 0.5 + - - -
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Residues in contact with GLU 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 ARG 3.1 12.8 + - - +
83A ASN* 1.3 75.1 - - - +
85A PHE* 1.3 65.9 + - - +
87A LYS* 3.3 19.0 + - - +
88A ILE* 3.0 24.5 + - + +
93A VAL* 4.2 15.0 - - - +
127A ASP* 2.8 40.7 - - - +
128A LYS 5.3 0.3 + - - -
129A GLU* 3.8 23.3 - - + +
130A LEU* 3.5 21.3 - - + -
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Residues in contact with PHE 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 PHE 3.0 13.4 + - - +
82A ARG* 3.4 10.8 - - - +
84A GLU* 1.3 75.0 - - - +
86A GLU* 1.3 58.9 + - + +
88A ILE* 3.0 15.7 + - + +
89A CYS* 2.7 58.5 + - - -
118A ILE* 4.0 21.1 - - + -
121A VAL* 4.5 17.7 - - + -
130A LEU* 4.4 2.5 - - + +
158A LEU* 3.8 39.0 - - + -
160A ASN* 3.6 33.0 - - + -
196A MET* 5.4 0.2 - - + -
276A LYS* 3.9 28.9 - - - -
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Residues in contact with GLU 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 ARG* 3.0 15.0 + - + +
83A ASN* 3.8 6.3 - - - +
84A GLU 3.3 0.2 - - - -
85A PHE* 1.3 83.7 - - + +
87A LYS* 1.3 60.7 + - - +
89A CYS* 3.1 23.1 + - - +
90A ARG* 2.8 68.2 + - - +
276A LYS* 5.3 8.5 + - - -
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Residues in contact with LYS 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 ASN* 3.2 28.1 + - + +
84A GLU* 3.3 24.4 + - - +
86A GLU* 1.3 71.4 - - - +
88A ILE* 1.3 67.4 + - - +
90A ARG* 3.1 26.8 + - - +
92A GLU* 3.0 35.4 + - + -
93A VAL* 4.1 18.4 - - + +
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Residues in contact with ILE 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 GLU 3.0 23.1 + - - +
85A PHE* 3.3 10.1 - - + +
87A LYS* 1.3 73.3 - - - +
89A CYS* 1.3 56.8 + - - +
91A LYS* 2.8 25.3 + - - +
93A VAL* 3.7 23.9 - - + +
95A PRO* 4.2 14.4 - - + -
98A LEU* 4.0 23.8 - - + -
100A VAL* 4.8 4.7 - - + -
102A ARG* 5.4 2.1 + - - -
118A ILE* 4.2 17.3 - - + +
121A VAL* 4.5 11.7 - - + -
127A ASP* 3.7 20.0 - - - +
130A LEU* 3.9 22.7 - - + -
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Residues in contact with CYS 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 PHE* 2.7 60.3 + - - +
86A GLU* 3.1 26.9 + - - +
88A ILE* 1.3 72.9 - - - +
90A ARG* 1.3 57.7 + - + +
91A LYS* 3.3 1.8 + - - +
102A ARG* 5.1 5.4 + - - -
118A ILE* 3.7 28.6 - - + +
160A ASN* 5.4 0.4 - - - -
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Residues in contact with ARG 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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83A ASN 5.6 0.6 + - - -
86A GLU* 2.8 56.9 + - - +
87A LYS* 3.1 28.2 + - - +
89A CYS* 1.3 73.1 - - - +
91A LYS* 1.3 70.3 + - - +
92A GLU* 3.1 10.4 + - + +
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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