Contacts of the helix formed by residues 81 - 97 (chain A) in PDB entry 5Y39
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 TYR 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 3.3 34.8 + + + +
80A GLU* 1.3 83.7 - - - +
82A MET* 1.3 61.5 + - - +
83A ASP 3.3 1.1 - - - -
84A ARG* 3.4 36.1 + - + +
85A ALA* 2.9 31.4 + - - +
28C ASP* 3.6 34.2 + - + +
30C VAL* 3.7 18.4 - - + +
47C PRO* 4.3 24.5 - - + -
48C GLY 6.0 0.4 - - - -
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.4 25.1 - - + +
80A GLU* 5.2 0.2 - - - -
81A TYR* 1.3 81.2 - - - +
83A ASP* 1.3 61.1 + - - +
85A ALA* 3.5 8.5 + - + +
86A ARG* 3.0 30.0 + - - +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 4.3 31.3 - - + +
81A TYR 3.3 0.4 - - - -
82A MET* 1.3 81.9 - - - +
84A ARG* 1.3 56.7 - - - +
86A ARG* 3.4 31.2 + - - +
87A GLN* 3.0 28.8 + - - +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU 4.5 3.7 + - - +
81A TYR* 3.4 35.8 + - - +
82A MET 3.3 0.4 - - - -
83A ASP* 1.3 75.1 - - - +
85A ALA* 1.3 65.1 + - - +
87A GLN* 3.2 20.9 - - - +
88A TYR* 3.1 49.5 + - + -
26C ASP* 3.3 16.5 + - - -
28C ASP* 3.2 43.2 + - - +
30C VAL* 3.9 9.8 - - + +
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Residues in contact with ALA 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 TYR 2.9 19.0 + - - +
82A MET* 3.8 10.5 - - + +
84A ARG* 1.3 75.4 - - - +
86A ARG* 1.3 52.7 + - - +
88A TYR* 3.5 6.0 + - - +
89A SER* 2.6 37.2 + - - +
30C VAL* 3.7 16.7 - - + +
31C PRO* 4.4 17.0 - - + +
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Residues in contact with ARG 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 MET 3.0 19.4 + - - +
83A ASP* 3.4 32.6 + - - +
85A ALA* 1.3 75.1 - - - +
87A GLN* 1.3 84.3 + - - +
89A SER* 3.2 10.4 + - - -
90A THR* 3.0 35.6 + - - +
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Residues in contact with GLN 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 ASP 3.0 17.0 + - - +
84A ARG* 3.2 27.8 - - - +
86A ARG* 1.3 90.3 - - - +
88A TYR* 1.3 83.4 + - - +
90A THR* 3.3 8.1 + - - -
91A ARG* 3.1 60.6 + - + +
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Residues in contact with TYR 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 ARG* 3.1 29.8 + - + +
85A ALA 3.6 5.4 - - - +
86A ARG 3.3 0.2 - - - -
87A GLN* 1.3 94.3 - - - +
89A SER* 1.3 59.0 + - - +
91A ARG* 3.2 1.7 + - - -
92A LEU* 2.9 32.6 + - - +
26C ASP* 2.6 38.7 + - - +
30C VAL* 3.6 21.3 - - + -
31C PRO 3.3 26.5 - - - +
32C VAL* 4.0 9.4 - - + -
120C VAL* 3.6 39.1 - - + +
121C VAL* 3.8 25.3 + - + +
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Residues in contact with SER 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 ALA 2.6 21.8 + - - -
86A ARG* 3.2 12.2 + - - -
88A TYR* 1.3 76.1 - - - +
90A THR* 1.3 55.6 + - - +
92A LEU* 3.7 10.5 + - - +
93A ALA* 3.0 29.3 + - - +
31C PRO 5.6 0.2 + - - -
32C VAL 5.6 1.6 - - - -
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Residues in contact with THR 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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86A ARG* 3.0 22.3 + - - +
87A GLN* 3.5 10.4 - - - -
88A TYR 3.2 0.2 - - - -
89A SER* 1.3 76.1 - - - +
91A ARG* 1.3 59.1 + - + +
93A ALA* 3.2 9.5 + - + +
94A VAL* 3.0 34.6 + - + +
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Residues in contact with ARG 91 (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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87A GLN* 3.1 42.2 + - - +
88A TYR* 3.2 3.7 + - - +
90A THR* 1.3 74.4 - - + +
92A LEU* 1.3 64.8 + - - +
94A VAL* 3.2 11.2 + - - +
95A LEU* 3.1 30.9 + - + +
119C GLN 4.3 11.2 + - - -
120C VAL* 2.9 41.6 + - + -
121C VAL 4.1 1.6 + - - -
122C GLU* 2.8 29.7 + - - +
123C VAL* 4.4 14.6 - - - +
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Residues in contact with LEU 92 (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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88A TYR 2.9 18.1 + - - +
89A SER* 3.9 7.2 - - - +
91A ARG* 1.3 75.7 - - - +
93A ALA* 1.3 54.8 + - - +
95A LEU* 3.2 5.8 + - + +
96A SER* 2.8 58.7 + - - +
3C ASP* 4.7 11.9 - - - +
5C LEU* 4.4 4.9 - - + -
6C LYS* 5.5 2.7 - - + -
32C VAL* 3.4 24.5 - - + +
33C ILE* 3.6 33.2 - - + -
117C LEU* 3.8 18.4 - - + -
120C VAL* 4.2 12.6 - - + +
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Residues in contact with ALA 93 (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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89A SER 3.0 20.3 + - - +
90A THR* 3.2 8.5 + - - +
92A LEU* 1.3 77.8 - - - +
94A VAL* 1.3 63.8 + - + +
96A SER* 3.8 10.5 + - - -
97A SER* 4.2 12.1 + - - -
3C ASP* 6.3 1.3 - - - -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.0 27.6 + - + +
91A ARG* 3.2 11.4 + - - +
93A ALA* 1.3 79.0 - - + +
95A LEU* 1.3 71.7 + - + +
96A SER 3.7 0.2 + - - -
97A SER* 4.1 4.7 + - - -
98A SER* 4.1 12.1 + - - -
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Residues in contact with LEU 95 (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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91A ARG* 3.1 14.6 + - + +
92A LEU* 3.2 6.5 + - + +
94A VAL* 1.3 83.0 - - + +
96A SER* 1.3 60.6 + - - +
97A SER 3.3 2.9 - - - -
98A SER* 2.9 30.9 + - - -
99A LEU* 3.2 20.0 + - + +
116C GLU 4.2 10.3 - - - +
117C LEU* 5.2 4.7 - - + -
119C GLN* 3.7 42.2 - - + +
120C VAL* 3.9 24.0 - - + +
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Residues in contact with SER 96 (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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92A LEU* 2.8 41.1 + - - +
93A ALA* 3.8 6.5 + - - -
94A VAL 3.5 0.6 - - - -
95A LEU* 1.3 72.2 - - - +
97A SER* 1.3 59.5 + - - +
99A LEU 4.3 4.0 - - - +
100A THR* 3.5 21.8 + - - -
3C ASP* 2.6 38.0 + - - -
5C LEU* 4.6 4.0 - - - +
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Residues in contact with SER 97 (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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93A ALA 4.2 8.7 + - - -
94A VAL 4.1 6.8 + - - -
95A LEU 3.3 0.4 - - - -
96A SER* 1.3 76.2 - - - +
98A SER* 1.3 64.8 + - - +
100A THR* 3.3 19.3 - - - +
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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