Contacts of the helix formed by residues 70 - 86 (chain A) in PDB entry 7CR3
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 ARG 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ASN* 1.3 56.9 + - - +
72A ALA 3.2 2.7 - - - +
73A PHE* 3.0 37.8 + - + +
74A TYR* 2.4 38.8 + - - +
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Residues in contact with ASN 71 (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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70A ARG* 1.3 76.9 - - - +
72A ALA* 1.3 57.2 + - - +
74A TYR* 3.3 21.6 - - - +
75A ARG* 2.9 54.7 + - - +
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Residues in contact with ALA 72 (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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70A ARG* 3.2 0.8 - - - -
71A ASN* 1.3 78.8 - - - +
73A PHE* 1.3 58.5 + - - +
75A ARG* 3.3 8.2 + - - +
76A LYS* 2.9 28.2 + - - +
132F ASP* 5.2 17.3 - - + +
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Residues in contact with PHE 73 (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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70A ARG* 3.0 40.7 + - + +
72A ALA* 1.3 74.3 - - - +
74A TYR* 1.3 62.0 + - - +
76A LYS* 4.0 31.0 - - + -
77A LEU* 2.9 50.9 + - + +
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Residues in contact with TYR 74 (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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70A ARG 2.4 31.4 + - - +
71A ASN* 3.3 23.8 - - - +
73A PHE* 1.3 69.9 - - - +
75A ARG* 1.3 63.0 + - + +
77A LEU* 3.4 4.8 + - - +
78A GLN* 3.0 36.4 + - - +
146A TRP* 3.1 44.5 + + - -
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Residues in contact with ARG 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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71A ASN* 2.9 45.1 + - - +
72A ALA* 3.9 5.4 - - - +
73A PHE 3.3 0.2 - - - -
74A TYR* 1.3 78.4 - - + +
76A LYS* 1.3 59.7 + - - +
78A GLN* 3.6 9.9 - - - +
79A ASN* 2.8 27.9 + - - +
155A ARG* 4.8 21.3 - - - +
131F ILE* 4.3 21.6 - - - +
132F ASP* 4.9 25.2 - - - +
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Residues in contact with LYS 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 ALA 2.9 18.3 + - - +
73A PHE* 3.2 32.4 + - + +
75A ARG* 1.3 74.3 - - - +
77A LEU* 1.3 67.9 + - - +
79A ASN* 3.1 11.7 + - + +
80A PHE* 2.9 42.8 + - - +
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Residues in contact with LEU 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 PHE* 2.9 38.2 + - + +
74A TYR* 3.8 5.2 - - - +
76A LYS* 1.3 80.8 - - - +
78A GLN* 1.3 66.2 + - - +
80A PHE* 3.2 12.5 + - + -
81A LEU* 3.0 49.4 + - + +
146A TRP* 4.7 7.2 - - + -
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Residues in contact with GLN 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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74A TYR* 3.0 26.1 + - - +
75A ARG* 3.6 9.7 - - - +
77A LEU* 1.3 76.1 - - - +
79A ASN* 1.3 61.6 + - - +
81A LEU* 3.8 2.5 - - - +
82A TYR* 3.0 23.7 + - - +
146A TRP* 2.3 66.8 + - + -
147A ALA* 3.8 11.3 - - - +
149A GLY* 3.1 21.4 - - - +
150A CYS* 4.4 8.7 - - + +
160A ARG* 3.0 13.2 + - - +
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Residues in contact with ASN 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 ARG 2.8 14.9 + - - +
76A LYS* 3.1 15.1 + - - +
78A GLN* 1.3 76.1 - - - +
80A PHE* 1.3 54.5 + - - +
82A TYR* 3.2 2.9 + - - +
83A ASN* 2.7 53.1 + - - +
150A CYS* 3.8 27.1 - - + +
100F TYR* 2.2 38.1 + - - -
138F ASN* 4.1 7.8 + - - +
140F GLU* 4.8 0.2 - - - +
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Residues in contact with PHE 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 LYS* 2.9 29.7 + - - +
77A LEU* 3.7 17.3 - - + +
79A ASN* 1.3 75.3 - - - +
81A LEU* 1.3 73.3 + - + +
83A ASN* 3.1 12.9 + - + +
84A VAL* 3.0 44.7 + - + +
89A ARG* 5.2 11.0 - - - -
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Residues in contact with LEU 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 LEU* 3.0 48.9 + - + +
78A GLN* 3.8 2.7 - - - +
80A PHE* 1.3 84.7 - - + +
82A TYR* 1.3 57.6 + - - +
83A ASN 3.2 0.2 + - - -
84A VAL* 5.2 0.9 - - - -
85A LEU* 2.9 56.1 + - + +
143A VAL* 4.6 18.6 - - + -
146A TRP* 5.3 8.1 - - + -
147A ALA* 3.7 19.5 - - + -
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Residues in contact with TYR 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 GLN 3.0 13.3 + - - +
79A ASN* 3.7 4.9 - - - +
81A LEU* 1.3 77.3 - - - +
83A ASN* 1.3 68.0 + - - +
85A LEU* 4.8 1.6 - - - -
86A GLU* 3.1 54.8 + - + +
87A ARG* 4.5 11.7 + - + +
147A ALA* 3.2 34.2 - - + +
148A ALA* 4.7 5.6 - - - -
150A CYS* 3.5 24.7 - - + -
151A CYS* 4.7 20.7 - - + +
154A TYR* 6.5 0.2 - + - -
163A PHE* 6.3 1.6 - + - -
140F GLU* 3.5 29.1 + - - -
144F GLN* 5.5 2.6 + - - -
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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 ASN* 2.7 42.9 + - - +
80A PHE* 3.1 13.9 + - + +
82A TYR* 1.3 87.8 - - - +
84A VAL* 1.3 60.7 + - + +
86A GLU 2.9 18.2 - - - +
87A ARG 3.0 17.4 + - - +
88A PRO* 3.9 3.1 - - - +
89A ARG* 3.2 36.6 + - - +
98F ASN 4.7 6.5 + - - -
100F TYR* 3.6 8.6 + - - -
140F GLU* 5.1 3.6 + - - -
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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
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80A PHE* 3.0 43.9 + - + +
81A LEU* 4.3 2.0 - - - +
83A ASN* 1.3 75.1 - - + +
85A LEU* 1.3 73.6 + - + +
86A GLU 3.0 7.4 - - - +
88A PRO* 5.2 0.2 - - - -
89A ARG* 5.8 3.4 - - - +
92A ALA* 3.7 32.9 - - + +
95A TYR* 4.2 23.6 - - + -
96A HIS* 3.2 18.4 + - - -
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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 LEU* 2.9 44.0 + - + +
82A TYR* 4.8 2.0 - - - +
84A VAL* 1.3 88.9 - - + +
86A GLU* 1.3 64.4 + - + +
95A TYR* 3.6 30.1 - - + +
96A HIS* 3.8 17.2 - - + -
140A GLU* 3.8 26.5 - - + +
143A VAL* 4.5 13.0 - - + +
144A ARG* 4.1 32.9 + - + +
147A ALA* 5.7 0.9 - - + -
213A ARG* 4.7 5.0 + - - -
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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 TYR* 3.1 49.4 + - + +
83A ASN 2.9 10.4 - - - +
84A VAL 3.0 10.4 - - - +
85A LEU* 1.3 79.1 - - + +
87A ARG* 1.3 72.5 + - + +
88A PRO* 3.0 5.0 - - - +
144A ARG* 2.9 39.9 + - + +
163A PHE* 4.2 13.2 - - + -
213A ARG* 2.8 25.0 + - - +
214A ARG* 4.6 4.9 + - - -
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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