Contacts of the helix formed by residues 64 - 77 (chain A) in PDB entry 3T79
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ILE* 4.2 15.5 - - + -
60A ILE* 3.1 14.6 - - + +
61A ALA 3.1 20.2 - - - +
62A LYS 3.5 4.3 - - - +
63A ASP* 1.3 89.8 - - - +
65A LEU* 1.3 68.1 + - + +
66A PRO 3.5 0.4 - - - -
67A THR* 2.9 16.9 + - - -
68A CYS* 3.0 17.5 + - - -
95A LEU* 5.7 0.4 - - + -
96A VAL* 4.0 25.6 - - + -
99A LEU* 4.2 14.1 - - + -
100A GLU* 4.7 13.9 - - + +
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Residues in contact with LEU 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* 3.4 4.0 - - - +
64A PRO* 1.3 81.5 - - + +
66A PRO* 1.3 72.8 - - + +
68A CYS* 2.9 8.7 + - + +
69A ASP* 2.9 45.2 + - - +
93A TYR* 4.1 24.0 - - + +
96A VAL* 4.8 14.6 - - + -
100A GLU* 6.0 2.7 - - - +
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Residues in contact with PRO 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.4 21.8 - - + +
19A TYR* 4.5 1.3 - - + -
22A ILE* 3.5 6.0 - - + +
63A ASP* 3.4 35.9 - - - +
65A LEU* 1.3 93.0 - - + +
67A THR* 1.3 56.9 + - - +
69A ASP* 3.9 9.3 - - + +
70A ALA* 3.0 29.3 + - - +
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Residues in contact with THR 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* 3.6 18.4 - - + +
50A ILE* 5.5 0.4 - - + -
53A TYR* 4.4 10.3 - - + -
54A ILE* 4.2 24.0 - - + -
60A ILE* 3.7 25.0 - - + +
63A ASP 4.4 3.6 + - - -
64A PRO 2.9 12.5 + - - -
66A PRO* 1.3 80.7 - - - +
68A CYS* 1.3 57.7 + - - +
70A ALA* 3.2 5.2 + - - +
71A MET* 2.9 52.7 + - + +
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Residues in contact with CYS 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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54A ILE* 4.0 20.2 - - - -
64A PRO* 3.0 22.8 + - - -
65A LEU* 2.9 15.3 + - + +
67A THR* 1.3 73.6 - - - +
69A ASP* 1.3 68.0 + - - +
71A MET* 3.0 5.1 + - - +
72A ILE* 2.9 29.1 + - + +
92A LEU* 3.8 35.9 - - + -
93A TYR* 4.9 6.3 - - + -
95A LEU* 5.3 1.1 - - - -
96A VAL* 4.3 17.9 - - - -
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.5 14.9 + - + +
65A LEU* 2.9 40.0 + - - +
66A PRO* 3.9 7.0 - - + +
68A CYS* 1.3 75.0 - - - +
70A ALA* 1.3 64.5 + - - +
72A ILE* 3.3 9.3 + - - +
73A TRP* 3.0 23.0 + - - +
93A TYR* 4.0 14.4 + - - -
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Residues in contact with ALA 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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19A TYR* 3.5 19.9 + - + -
22A ILE* 3.2 33.7 - - + -
66A PRO 3.0 6.7 + - - +
67A THR 3.2 9.9 - - - +
68A CYS 3.1 0.2 - - - -
69A ASP* 1.3 76.7 - - - +
71A MET* 1.3 55.1 + - - +
73A TRP* 3.0 5.0 + - - +
74A PHE* 2.7 51.9 + - + -
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Residues in contact with MET 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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22A ILE* 3.2 35.7 - - + -
23A TRP* 5.5 2.7 - - + -
26A TYR* 4.4 30.1 - - + -
45A LEU* 4.5 15.2 - - + +
50A ILE* 3.7 39.9 - - + -
53A TYR* 5.6 1.3 - - + -
67A THR* 2.9 33.1 + - + +
68A CYS* 3.0 6.0 + - - +
70A ALA* 1.3 75.3 - - - +
72A ILE* 1.3 64.0 + - - +
74A PHE* 3.4 13.4 + - + +
75A SER* 2.9 25.9 + - - -
88A LEU* 6.1 1.8 - - + -
92A LEU* 4.5 6.5 - - + -
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Residues in contact with ILE 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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68A CYS 2.9 20.8 + - - +
69A ASP* 3.8 8.1 - - - +
71A MET* 1.3 75.1 - - - +
73A TRP* 1.3 62.8 + - - +
75A SER* 3.4 5.5 - - - -
76A ARG* 2.9 36.6 + - - +
85A VAL* 3.6 22.2 - - + -
88A LEU* 5.5 4.5 - - + -
89A GLN* 3.7 50.7 - - + +
92A LEU* 4.2 13.5 - - + -
93A TYR* 4.2 15.0 - - + +
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Residues in contact with TRP 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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4A LEU* 4.7 6.3 - - + -
7A LEU* 3.5 37.9 - - + -
8A LEU* 3.8 28.7 - - + -
11A LEU* 4.7 20.8 - - + +
19A TYR* 3.5 33.2 - + + +
69A ASP 3.0 10.1 + - - +
70A ALA 3.0 8.9 + - - +
72A ILE* 1.3 76.2 - - - +
74A PHE* 1.3 93.0 + + - +
75A SER 2.9 0.9 + - - -
76A ARG* 3.5 11.4 - - + +
77A ALA* 2.5 57.5 + - + +
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Residues in contact with PHE 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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4A LEU* 4.6 18.5 - - + +
8A LEU* 4.9 6.3 - - + -
19A TYR* 3.5 41.5 - + + -
22A ILE* 4.5 6.3 - - + -
23A TRP* 3.7 37.9 - + + -
45A LEU* 4.0 17.3 - - + +
70A ALA* 2.7 54.9 + - + +
71A MET* 3.9 12.3 - - - +
73A TRP* 1.3 95.1 - + - +
75A SER* 1.3 63.9 + - - +
77A ALA* 3.6 2.9 + - - -
78A LEU* 3.2 26.0 + - + +
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Residues in contact with SER 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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45A LEU* 4.1 14.0 - - - +
71A MET 2.9 18.2 + - - -
72A ILE* 3.4 6.5 - - - -
73A TRP 2.9 0.4 + - - -
74A PHE* 1.3 77.1 - - - +
76A ARG* 1.3 56.8 + - - -
78A LEU 2.8 26.0 + - - +
80A ILE* 3.3 36.3 - - - +
85A VAL* 3.4 20.1 - - - +
88A LEU* 5.8 9.0 - - - +
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Residues in contact with ARG 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 ILE* 2.9 26.1 + - - +
73A TRP* 3.5 13.9 - - + +
75A SER* 1.3 74.0 + - - +
77A ALA* 1.3 60.3 + - + +
78A LEU 2.9 19.3 + - - +
80A ILE* 5.0 6.1 - - - +
82A ASN* 3.1 26.1 + - - -
85A VAL* 3.9 29.9 - - + +
86A LEU* 5.9 2.6 - - - +
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Residues in contact with ALA 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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4A LEU* 5.4 6.6 - - + +
7A LEU* 4.3 20.4 - - + +
73A TRP* 2.5 65.5 + - + +
74A PHE 3.6 4.0 - - - +
76A ARG* 1.3 72.9 - - - +
78A LEU* 1.3 60.0 + - - +
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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