Contacts of the helix formed by residues 70 - 84 (chain A) in PDB entry 2Y4U
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 ASN 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A MSE 5.6 4.9 - - - +
37A VAL* 5.4 3.8 - - + +
38A GLU* 5.9 0.4 + - - -
41A LEU* 4.6 14.1 - - - +
63A ALA 5.6 0.2 - - - +
67A ASP* 2.7 37.3 + - + +
69A ASP* 1.3 74.5 - - - +
71A TYR* 1.3 60.9 + - - +
72A ILE* 2.3 57.4 + - - +
73A ALA* 3.0 16.6 + - + +
74A TYR* 2.9 28.4 + - - -
100A LEU* 3.6 0.3 - - - +
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Residues in contact with TYR 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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69A ASP 3.6 1.4 + - - +
70A ASN* 1.3 76.4 + - - +
72A ILE* 1.3 96.5 + - + +
73A ALA 3.3 1.6 - - - -
74A TYR* 3.5 4.3 + - - -
75A TYR* 3.2 18.7 + - + +
97A VAL* 3.8 24.8 - - + +
100A LEU* 3.9 27.6 - - + -
101A LYS* 3.4 54.6 + - + -
104A PHE* 4.4 14.8 - + - -
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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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41A LEU* 4.7 7.9 - - + -
45A LYS* 3.9 26.5 - - - +
70A ASN* 2.3 45.2 + - - +
71A TYR* 1.3 104.7 - - + +
73A ALA* 1.3 62.8 + - - +
75A TYR* 3.0 10.4 + - + +
76A ARG* 2.9 33.7 + - + +
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Residues in contact with ALA 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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37A VAL* 6.4 0.4 - - + -
41A LEU* 3.9 14.9 - - + +
60A PHE* 4.8 1.8 - - - +
63A ALA* 4.1 24.5 - - + +
64A VAL* 3.7 25.6 - - + +
67A ASP 5.2 0.7 - - - +
70A ASN* 3.0 20.6 + - + +
72A ILE* 1.3 75.8 - - - +
74A TYR* 1.3 57.2 + - + +
76A ARG* 2.7 25.7 + - - +
77A ARG* 2.9 12.8 + - - +
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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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64A VAL* 3.6 29.4 - - + +
67A ASP 4.5 1.3 - - - -
68A PRO* 2.8 45.9 + - + +
70A ASN 2.9 23.1 - - - -
71A TYR* 3.5 2.2 + - - +
72A ILE 3.4 0.4 - - - -
73A ALA* 1.3 78.1 - - + +
75A TYR* 1.3 62.0 + - - +
77A ARG* 3.9 18.8 - - - -
78A ALA* 3.1 24.8 + - - +
93A ASP* 3.7 17.8 - - - +
96A LYS* 3.7 41.8 + - + -
97A VAL* 3.6 19.5 - - + +
100A LEU* 4.3 3.6 - - + -
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Residues in contact with TYR 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 TYR* 3.2 13.1 + - + +
72A ILE* 3.0 13.8 + - + +
73A ALA 2.9 0.8 + - - -
74A TYR* 1.3 78.2 - - - +
76A ARG* 1.3 79.9 + - - +
78A ALA* 3.2 5.8 + - - +
79A THR* 3.0 50.4 + - + +
94A LEU* 4.6 10.8 - - + -
97A VAL* 3.5 18.3 - - + +
104A PHE* 3.9 35.1 - + + -
106A ALA* 5.1 3.6 + - - +
107A ALA* 4.5 9.2 - - + -
110A GLN* 3.9 26.2 + - + +
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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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41A LEU* 4.5 2.2 - - + -
45A LYS* 3.2 54.2 - - - +
48A LEU* 5.8 4.4 - - - +
60A PHE* 3.5 31.1 - - + -
72A ILE* 2.9 25.8 + - + +
73A ALA 2.7 11.4 + - - +
75A TYR* 1.3 88.2 - - - +
77A ARG* 1.3 68.7 + - - +
79A THR* 2.7 23.3 + - - +
80A VAL* 3.2 11.8 + - - +
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Residues in contact with ARG 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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57A LEU* 3.9 12.1 - - + -
60A PHE* 3.8 18.2 - - + +
61A HIS* 3.3 49.8 + - - +
64A VAL* 3.6 44.2 - - + +
65A ASP* 4.7 4.9 + - - -
73A ALA 2.9 14.2 + - - +
74A TYR* 3.9 10.6 - - - +
76A ARG* 1.3 74.0 - - - +
78A ALA* 1.3 64.6 + - - +
80A VAL* 2.8 17.4 + - - +
81A PHE* 3.0 25.8 + - + +
93A ASP* 2.6 36.6 + - - +
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Residues in contact with ALA 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 3.1 19.1 + - - +
75A TYR 3.3 5.2 - - - +
76A ARG 3.2 0.4 - - - -
77A ARG* 1.3 79.9 - - - +
79A THR* 1.3 60.4 + - + +
81A PHE* 3.6 9.4 + - - +
82A LEU* 3.0 30.9 + - - +
90A ALA* 4.1 4.3 - - - +
93A ASP* 3.7 19.7 + - + -
94A LEU* 4.0 28.7 - - + -
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Residues in contact with THR 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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48A LEU* 4.0 17.0 - - - +
75A TYR* 3.0 43.2 + - + +
76A ARG* 2.7 30.6 + - - +
78A ALA* 1.3 77.9 - - + +
80A VAL* 1.3 57.7 + - - +
82A LEU* 3.4 16.4 - - + +
83A ALA* 2.9 26.9 + - - +
94A LEU* 6.2 0.9 - - + -
110A GLN* 5.6 3.4 - - + +
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Residues in contact with VAL 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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48A LEU* 3.7 15.7 - - + -
53A LEU* 3.3 40.8 - - + +
56A ALA* 4.3 2.7 - - + -
57A LEU* 3.9 9.0 - - + +
60A PHE* 3.5 29.4 - - + -
76A ARG 3.2 15.0 - - - +
77A ARG 2.8 5.1 + - - +
79A THR* 1.3 76.1 - - - +
81A PHE* 1.3 69.3 + - - +
83A ALA* 4.2 4.5 - - - -
84A MSE 3.0 40.6 + - + +
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Residues in contact with PHE 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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57A LEU* 3.5 30.5 - - + -
61A HIS* 4.0 15.7 - + - -
77A ARG* 3.0 23.5 + - + -
78A ALA* 3.6 8.1 - - - +
80A VAL* 1.3 77.1 - - - +
82A LEU* 1.3 51.1 - - - +
84A MSE 2.2 42.5 - - + +
86A LYS* 3.3 25.2 + - + +
89A ALA* 3.2 47.3 - - + -
90A ALA* 3.7 16.6 - - + -
93A ASP* 3.6 21.3 - - - -
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Residues in contact with LEU 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 ALA* 3.0 21.7 + - + +
79A THR* 3.4 20.4 - - + +
80A VAL 3.2 0.2 - - - -
81A PHE* 1.3 77.7 - - - +
83A ALA* 1.3 60.1 + - - +
84A MSE 2.7 12.9 - - - +
85A GLY* 4.5 0.2 - - - -
86A LYS 4.7 0.9 - - - -
90A ALA* 3.7 21.1 - - + -
94A LEU* 4.9 13.7 - - + -
110A GLN* 4.2 21.8 - - - +
114A LEU* 4.1 26.0 - - + -
117A LYS* 5.3 8.1 + - - +
186A TRP* 4.0 27.4 - - + -
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Residues in contact with ALA 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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48A LEU* 6.1 4.0 - - + -
53A LEU* 4.0 27.4 - - + +
79A THR 2.9 17.7 + - - +
80A VAL* 3.2 7.4 + - - +
82A LEU* 1.3 77.0 - - - +
84A MSE 1.3 60.5 + - - +
85A GLY* 3.8 1.2 + - - -
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Residues in contact with MSE 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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53A LEU* 3.5 26.4 - - + +
54A ALA* 4.3 23.6 - - - -
57A LEU* 3.7 30.3 - - + -
80A VAL* 3.0 35.3 + - + +
81A PHE* 2.2 31.7 - - + +
82A LEU 2.7 8.0 - - - +
83A ALA* 1.3 72.8 - - - +
85A GLY* 1.3 53.1 + - - +
86A LYS* 2.6 41.6 + - + -
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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