Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 1P7L
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 ASP 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A VAL* 1.3 73.7 - - - +
64A ILE* 1.3 62.5 + - - +
65A GLU* 3.2 19.2 + - - +
66A GLU* 3.3 23.0 + - + +
67A ILE* 3.0 31.1 + - + +
61C TRP* 4.3 9.6 - - + -
97C LYS* 2.5 33.4 + - - -
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Residues in contact with ILE 64 (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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26A VAL* 4.3 22.9 - - + -
52A VAL* 3.7 26.2 - - + -
56A ILE* 5.8 1.6 - - + -
62A VAL* 3.8 25.5 + - + +
63A ASP* 1.3 72.7 + - - +
65A GLU* 1.3 52.8 + - - +
67A ILE* 3.3 4.8 + - + +
68A THR* 2.6 52.7 + - - +
91A VAL* 4.6 3.6 - - + -
93A SER* 3.7 19.3 - - - +
95A ILE* 4.2 22.9 - - + -
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Residues in contact with GLU 65 (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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63A ASP* 3.2 9.3 + - - +
64A ILE* 1.3 77.0 - - - +
66A GLU* 1.3 71.6 + - - +
68A THR* 3.6 0.2 - - - -
69A ARG* 2.5 83.4 + - - +
91A VAL* 4.0 21.6 - - + +
95C ILE 4.2 8.4 - - - +
96C GLY* 3.4 28.5 - - - -
97C LYS* 4.0 15.8 + - - +
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Residues in contact with GLU 66 (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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63A ASP* 3.3 21.6 + - + +
64A ILE 3.3 0.2 - - - -
65A GLU* 1.3 92.2 - - - +
67A ILE* 1.3 64.0 + - + +
69A ARG* 4.7 8.2 - - - +
70A ASN* 2.9 47.2 + - - +
73A ARG* 5.7 0.5 + - - -
97C LYS* 2.6 33.6 + - - +
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Residues in contact with ILE 67 (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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22A ILE* 4.9 0.7 - - + +
25A ALA* 3.8 35.2 - - + +
26A VAL* 4.0 17.3 - - + +
29A ALA* 3.5 30.1 - - + -
62A VAL* 3.9 16.8 - - + -
63A ASP* 3.0 31.5 + - + +
64A ILE* 3.8 4.7 - - - +
66A GLU* 1.3 75.5 - - + +
68A THR* 1.3 58.1 + - - +
70A ASN* 3.9 4.4 - - - +
71A THR* 2.7 37.7 + - - +
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Residues in contact with THR 68 (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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22A ILE* 3.5 32.0 - - + +
26A VAL* 5.1 0.7 - - - +
50A VAL* 3.6 23.8 - - + -
52A VAL* 3.9 6.4 - - - +
64A ILE* 2.6 43.0 + - - +
65A GLU 3.6 2.2 - - - -
67A ILE* 1.3 72.6 - - - +
69A ARG* 1.3 68.8 + - - +
71A THR* 3.0 6.5 + - - -
72A VAL* 2.9 24.8 + - + +
89A CYS* 5.9 1.6 - - - -
91A VAL* 4.0 16.6 - - + +
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Residues in contact with ARG 69 (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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65A GLU* 2.5 58.0 + - + +
66A GLU* 4.1 8.3 - - - +
68A THR* 1.3 72.5 - - - +
70A ASN* 1.3 53.7 + - - +
72A VAL* 3.3 1.1 + - - -
73A ARG* 2.7 50.6 + - - +
86A ALA* 2.9 37.6 + - - +
87A ASN* 3.8 14.4 + - - +
89A CYS* 2.5 48.9 + - - +
91A VAL* 3.6 17.3 - - + +
47D THR* 4.0 21.4 + - - +
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Residues in contact with ASN 70 (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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66A GLU* 2.9 39.7 + - - +
67A ILE* 4.0 4.6 - - - +
69A ARG* 1.3 77.0 - - - +
71A THR* 1.3 57.6 + - - +
73A ARG* 2.6 37.4 + - - +
74A GLU* 2.9 47.4 + - - +
352A LYS* 6.2 0.2 - - - +
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Residues in contact with THR 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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21A GLN* 4.0 15.9 - - + -
22A ILE* 3.9 33.4 - - + +
25A ALA* 3.3 12.9 - - - +
67A ILE* 2.7 25.6 + - - +
68A THR* 3.0 6.5 + - - -
70A ASN* 1.3 77.5 - - - +
72A VAL* 1.3 63.8 + - - +
74A GLU* 3.5 4.0 + - - +
75A ILE* 3.2 24.8 + - + +
352A LYS* 3.2 29.6 + - + +
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Residues in contact with VAL 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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18A ILE* 4.0 27.6 - - + -
22A ILE* 4.1 15.5 - - + -
50A VAL* 4.8 3.4 - - + -
68A THR* 2.9 12.7 + - + +
69A ARG* 3.8 2.7 - - - +
71A THR* 1.3 73.8 - - - +
73A ARG* 1.3 70.8 + - - +
75A ILE* 2.8 20.4 + - + +
76A GLY 3.1 9.9 + - - -
77A TYR* 3.8 14.2 + - + +
84A PHE* 4.3 25.6 - - + -
86A ALA* 3.2 30.3 - - + +
89A CYS* 5.8 0.9 - - - -
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Residues in contact with ARG 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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66A GLU* 5.7 1.0 + - - -
69A ARG* 2.7 35.4 + - - +
70A ASN* 2.6 45.2 + - - +
72A VAL* 1.3 74.5 - - - +
74A GLU* 1.3 66.8 + - - +
76A GLY* 3.0 15.9 + - - -
78A VAL* 3.9 24.6 - - + +
86A ALA* 3.5 10.0 - - + +
87A ASN* 3.1 41.0 + - - +
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Residues in contact with GLU 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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12A GLU* 5.0 1.1 - - - -
70A ASN* 2.9 34.4 + - - +
71A THR 3.8 4.7 - - - +
73A ARG* 1.3 80.2 - - - +
75A ILE* 1.3 65.0 + - - +
76A GLY* 3.2 1.4 + - - -
153A LYS* 3.9 15.6 + - - +
352A LYS* 3.8 21.7 + - - +
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Residues in contact with ILE 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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12A GLU* 3.6 38.2 - - - +
13A GLY* 3.9 14.6 - - - -
18A ILE* 4.2 24.5 - - + -
21A GLN* 3.8 23.6 - - + +
71A THR* 3.2 34.3 + - + +
72A VAL* 2.8 17.1 + - + +
74A GLU* 1.3 77.2 - - - +
76A GLY* 1.3 58.0 + - - +
77A TYR* 4.2 17.3 - - + -
152A ARG* 2.7 27.0 + - - -
162A PRO* 4.2 1.6 - - + +
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Residues in contact with GLY 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 VAL 3.1 2.0 + - - -
73A ARG 3.0 14.5 + - - -
74A GLU 4.0 1.6 - - - -
75A ILE* 1.3 80.4 - - - +
77A TYR* 1.3 61.6 + - - +
78A VAL* 3.0 15.6 + - - +
82A MET* 3.2 15.8 - - - +
152A ARG* 4.5 3.6 - - - -
162A PRO* 3.9 13.8 - - - +
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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