Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 1TAR
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 ALA 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PRO* 5.6 2.5 - - + +
75A GLY 3.4 6.2 + - - +
76A LEU* 1.3 74.8 - - - +
78A ASP* 1.3 66.9 + - - +
80A THR* 3.4 8.5 + - - -
81A ARG* 3.1 26.9 + - - +
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Residues in contact with ASP 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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76A LEU* 3.3 10.4 - - + +
77A ALA* 1.3 80.1 - - - +
79A PHE* 1.3 62.0 - - - +
81A ARG* 4.1 18.2 + - - +
82A ALA* 3.3 16.1 + - - +
307A SER* 3.5 15.3 - - - +
311A ASN* 3.3 25.5 + - - +
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Residues in contact with PHE 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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76A LEU* 3.1 20.2 + - + +
77A ALA 3.1 0.6 - - - -
78A ASP* 1.3 78.5 - - - +
80A THR* 1.3 69.5 + - + +
82A ALA* 3.4 4.9 + - - +
83A SER* 3.0 32.6 + - - -
104A GLN* 3.7 35.4 - - + -
256A TYR* 3.7 33.0 - + - -
267A ALA* 4.4 5.4 - - + -
268A GLY 3.4 34.3 - - - -
269A ALA* 4.8 1.1 - - + -
303A ALA* 3.8 30.3 - - + +
306A ALA* 3.9 20.9 - - + -
307A SER* 3.6 8.5 + - - -
310A LEU* 5.2 2.7 - - + -
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Residues in contact with THR 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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74A ALA 3.7 8.5 - - - +
75A GLY 4.9 0.4 + - - -
76A LEU 2.9 21.0 + - - +
77A ALA* 3.4 13.0 + - - -
79A PHE* 1.3 76.9 - - + +
81A ARG* 1.3 61.1 + - - +
83A SER* 3.3 7.0 + - - -
84A ALA* 3.2 19.2 + - - +
100A TYR* 5.8 0.7 - - - -
102A THR* 3.6 36.3 + - + +
103A VAL 4.0 1.3 - - - -
104A GLN* 3.5 36.8 - - + +
269A ALA* 5.5 0.2 - - + -
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Residues in contact with ARG 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 ALA 3.1 17.4 + - - +
78A ASP* 4.1 23.0 + - - +
80A THR* 1.3 72.4 + - - +
82A ALA* 1.3 73.8 + - - +
83A SER 3.2 0.2 + - - -
84A ALA* 3.2 4.1 + - - +
85A GLU* 2.9 43.4 + - - +
95A PHE* 4.0 13.7 - - + -
100A TYR* 3.8 24.0 - - - +
311A ASN* 2.7 31.9 + - - +
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Residues in contact with ALA 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 ASP 3.3 18.9 + - - +
79A PHE* 3.7 3.8 - - - +
81A ARG* 1.3 84.8 - - - +
83A SER* 1.4 51.2 + - - +
85A GLU* 3.3 10.0 + - - +
86A LEU* 2.8 34.7 + - - +
307A SER* 5.4 0.4 - - - +
310A LEU* 3.7 35.0 - - + +
311A ASN* 4.0 14.8 - - - +
316A ARG* 5.6 2.6 + - - +
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Residues in contact with SER 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 PHE* 3.0 25.2 + - - -
80A THR* 3.3 10.1 - - - -
81A ARG 3.1 0.2 - - - -
82A ALA* 1.4 74.5 - - - +
84A ALA* 1.3 64.8 + - - +
86A LEU* 3.4 1.1 + - - +
87A ALA* 3.1 10.9 + - - +
102A THR* 4.5 1.3 - - - -
254A GLN* 3.0 34.7 + - - +
256A TYR* 2.8 34.4 + - - -
269A ALA* 4.2 10.6 - - - +
310A LEU* 4.5 0.2 - - - +
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Residues in contact with ALA 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 THR 3.2 4.9 + - - +
81A ARG 3.8 5.8 - - - +
83A SER* 1.3 79.4 - - - +
85A GLU* 1.3 58.4 + - - +
87A ALA* 3.1 4.1 + - - +
88A LEU* 2.8 46.9 + - + +
95A PHE* 4.4 1.8 - - + -
100A TYR* 3.6 36.6 - - + -
102A THR* 3.7 15.9 + - - +
254A GLN* 5.0 1.6 - - - -
271A THR* 4.9 3.1 - - + +
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Residues in contact with GLU 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 ARG* 2.9 34.7 + - - +
82A ALA* 3.5 7.6 - - - +
84A ALA* 1.3 76.9 - - - +
86A LEU* 1.3 57.4 + - - +
89A GLY* 3.0 29.9 + - - +
90A GLU* 3.4 44.2 + - + +
95A PHE* 3.7 30.2 - - + -
241A ARG* 4.5 0.2 + - - -
316A ARG* 4.5 15.9 + - - +
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Residues in contact with LEU 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 ALA 2.8 17.5 + - - +
83A SER* 3.7 4.9 - - - +
85A GLU* 1.3 77.3 - - - +
87A ALA* 1.3 57.3 + - - +
226A GLN* 2.7 42.7 + - - +
233A ILE* 3.7 31.3 - - + +
241A ARG* 3.0 12.5 + - - -
254A GLN* 4.1 5.2 - - - +
256A TYR* 3.9 30.3 - - + +
259A ASN* 4.9 5.6 - - - +
310A LEU* 4.4 7.4 - - + -
316A ARG* 4.0 15.2 - - - +
319A TRP* 3.9 27.1 - - + -
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Residues in contact with ALA 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 SER 3.1 16.6 + - - +
84A ALA* 3.1 3.8 + - - +
86A LEU* 1.3 78.4 - - - +
88A LEU* 1.3 56.7 + - + +
223A MET* 3.7 28.5 - - + -
226A GLN* 4.2 0.4 - - - +
237A ALA* 3.8 6.2 - - - +
240A LEU* 4.0 6.3 - - + +
241A ARG* 2.6 33.8 + - - +
252A LEU* 3.9 17.9 - - + -
254A GLN* 3.9 7.6 - - - +
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Residues in contact with LEU 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 ALA* 2.8 39.1 + - + +
87A ALA* 1.3 75.8 - - + +
89A GLY* 1.3 60.7 + - - +
92A SER* 3.1 26.8 + - - +
94A ALA* 4.3 7.6 - - + -
95A PHE* 4.3 14.6 - - + +
100A TYR* 4.5 13.9 - - + -
240A LEU* 5.2 6.5 - - + -
241A ARG* 3.4 19.6 + - + +
244A ILE* 3.1 36.3 - - + -
252A LEU* 6.2 2.2 - - + -
271A THR* 5.3 3.6 - - + -
273A ILE* 4.0 18.8 - - + -
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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