Contacts of the helix formed by residues 70 - 84 (chain B) in PDB entry 2Y4T
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 4.2 5.3 - - - +
41B LEU* 3.7 26.5 - - - +
67B ASP* 3.3 33.9 + - + +
69B ASP* 1.3 76.9 - - - +
71B TYR* 1.3 69.0 + - - +
72B ILE* 3.2 30.3 + - - +
73B ALA* 3.2 17.6 - - + +
74B TYR* 3.1 18.0 - - - -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASP 3.4 4.8 + - - -
70B ASN* 1.3 74.4 + - - +
72B ILE* 1.3 96.8 - - + +
74B TYR* 3.1 4.6 + - - -
75B TYR* 3.0 20.1 + - + +
97B VAL* 3.4 33.8 - - + +
100B LEU* 3.7 34.3 - - + -
101B LYS* 3.8 45.1 + - + -
104B PHE* 4.2 20.9 - + - -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.5 8.7 - - + -
45B LYS* 4.2 9.0 - - - +
70B ASN* 3.2 21.5 + - - +
71B TYR* 1.3 110.3 - - + +
73B ALA* 1.3 56.2 + - - +
75B TYR* 3.2 4.9 + - - -
76B ARG* 2.8 68.4 + - + +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.9 15.9 - - + +
60B PHE* 4.5 2.8 - - - +
63B ALA* 4.1 18.6 - - + +
64B VAL* 3.6 25.7 - - + +
67B ASP 4.4 1.1 - - - +
70B ASN* 3.2 27.4 + - + +
71B TYR 3.2 0.6 - - - -
72B ILE* 1.3 78.0 - - - +
74B TYR* 1.3 61.5 + - + +
76B ARG* 3.8 2.8 - - - +
77B ARG* 3.2 22.3 + - - +
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.0 24.4 - - + +
68B PRO* 2.9 33.2 + - + +
70B ASN 3.1 26.9 - - - -
71B TYR* 3.1 3.4 + - - +
73B ALA* 1.3 76.6 - - + +
75B TYR* 1.3 54.5 + - - +
77B ARG* 3.1 12.2 + - - +
78B ALA* 2.7 36.8 + - - +
93B ASP* 3.7 29.3 - - + +
96B LYS* 3.4 32.1 + - + -
97B VAL* 3.3 18.4 - - + -
100B LEU* 3.6 26.9 - - + -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.0 16.9 + - + +
72B ILE* 3.2 8.0 + - - +
74B TYR* 1.3 76.6 - - - +
76B ARG* 1.3 71.6 + - - +
78B ALA* 3.9 3.6 - - + +
79B THR* 2.8 56.2 + - + +
94B LEU* 4.2 16.2 - - + -
97B VAL* 3.4 12.5 - - + +
104B PHE* 3.7 36.7 - + + -
106B ALA* 4.1 7.8 + - - +
107B ALA* 3.7 25.4 - - + -
110B GLN* 3.9 22.0 + - + +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.0 6.5 - - + -
45B LYS* 3.0 36.1 - - - +
48B LEU* 5.8 3.8 - - - -
60B PHE* 3.3 54.1 - - + -
72B ILE* 2.8 40.3 + - + +
73B ALA 3.8 2.7 - - - +
75B TYR* 1.3 100.3 - - - +
77B ARG* 1.3 61.2 + - - +
79B THR* 2.7 19.7 + - - -
80B VAL 3.3 7.4 + - - -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 3.9 12.3 - - + +
60B PHE* 4.0 20.4 - - + -
61B HIS* 3.2 39.1 + - - +
64B VAL* 3.5 41.5 - - - +
65B ASP* 5.0 3.2 + - - -
73B ALA 3.2 13.5 + - - +
74B TYR* 3.1 10.6 + - - +
76B ARG* 1.3 77.1 - - - +
78B ALA* 1.3 54.9 + - - +
80B VAL* 3.1 5.8 + - - +
81B PHE* 2.8 50.5 + - + -
93B ASP* 2.7 36.1 + - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR 2.7 19.9 + - - +
75B TYR* 3.9 8.3 - - - +
77B ARG* 1.3 73.7 - - - +
79B THR* 1.3 52.5 + - + +
81B PHE* 3.1 13.8 + - - +
82B LEU* 2.7 40.3 + - + +
90B ALA* 3.9 11.0 - - - +
93B ASP* 3.8 16.7 + - + -
94B LEU* 4.0 22.0 - - + +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.5 13.7 - - - +
75B TYR* 2.8 48.4 + - + +
76B ARG* 2.7 28.3 + - - +
78B ALA* 1.3 74.3 - - - +
80B VAL* 1.3 51.5 + - - +
82B LEU* 3.7 12.9 - - + +
83B ALA* 2.8 34.4 + - - +
110B GLN* 5.3 6.1 - - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 24.9 - - + -
53B LEU* 3.4 29.6 - - + +
56B ALA* 3.9 4.7 - - + -
57B LEU* 3.7 21.1 - - + +
60B PHE* 3.6 24.5 - - + -
76B ARG 3.3 12.7 + - - +
77B ARG 3.1 7.6 + - - +
79B THR* 1.3 72.3 - - - +
81B PHE* 1.3 57.5 + - - +
83B ALA* 3.1 5.9 + - - -
84B MET* 2.7 47.2 + - + +
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.4 26.2 - - + -
61B HIS* 3.7 25.1 - + - -
77B ARG* 2.8 32.9 + - + -
78B ALA 3.3 7.2 - - - +
80B VAL* 1.3 72.2 - - - +
82B LEU* 1.3 60.6 + - - +
84B MET* 3.1 10.5 + - - +
86B LYS* 2.9 47.4 + - + +
89B ALA* 3.4 42.8 - - + -
90B ALA* 3.7 15.9 - - + +
93B ASP* 3.3 25.1 - - - -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 2.7 25.2 + - + +
79B THR* 3.7 8.5 - - + +
81B PHE* 1.3 68.4 - - - +
83B ALA* 1.3 55.4 + - - +
84B MET 3.0 4.3 - - - -
85B GLY* 2.7 25.2 + - - +
86B LYS 4.8 1.1 - - - +
90B ALA* 3.8 10.7 - - + +
94B LEU* 4.4 11.2 - - + -
110B GLN* 3.8 38.6 - - + +
114B LEU* 3.6 39.5 - - + -
117B LYS* 4.7 6.9 + - - +
186B TRP* 3.9 22.3 - - + -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.8 5.6 - - + -
53B LEU* 3.8 32.3 - - + +
79B THR 2.8 23.0 + - - +
80B VAL* 3.1 7.6 + - - +
82B LEU* 1.3 71.5 - - - +
84B MET* 1.3 60.0 + - - +
85B GLY 3.8 0.2 + - - -
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.7 22.7 - - + +
54B ALA* 3.4 39.0 - - + +
57B LEU* 3.7 28.0 - - + -
80B VAL* 2.7 30.1 + - + +
81B PHE* 3.4 6.5 - - - +
83B ALA* 1.3 73.3 - - - +
85B GLY* 1.3 59.1 + - - +
86B LYS* 3.2 25.9 + - + +
216B LYS* 5.5 0.7 + - - -
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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