Contacts of the helix formed by residues 75 - 94 (chain B) in PDB entry 2Y43
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 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.7 9.2 - - - +
42A SER* 3.6 1.1 - - - -
44A ASN* 4.7 0.2 + - - -
75A ASN* 3.0 42.2 + - - -
77A ILE* 4.2 0.6 - - - +
35B ALA* 2.7 23.0 + - + +
37B ILE* 3.8 12.5 - - + +
44B ASN* 2.8 32.6 + - - +
73B LYS 3.5 0.8 + - - -
74B ASN* 1.3 71.0 - - - +
76B ARG* 1.3 65.1 + - - +
77B ILE* 3.5 10.2 - - - +
78B LEU* 3.1 34.3 + - + +
79B ASP* 3.9 1.3 + - - +
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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
----------------------------------------------------------
41A CYS 4.5 7.4 + - - -
42A SER* 2.9 33.5 + - - +
74B ASN* 3.6 42.2 + - + +
75B ASN* 1.3 71.4 + - - +
77B ILE* 1.3 63.5 + - - +
79B ASP* 3.0 30.7 + - + +
80B GLU* 3.2 16.1 + - + +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.1 37.0 - - + +
32A PHE* 3.8 13.5 - - + -
42A SER* 4.7 3.2 + - - +
44A ASN* 3.7 23.8 - - - +
75A ASN* 4.3 0.7 - - - +
78A LEU* 3.7 35.7 - - + -
75B ASN* 3.5 17.0 - - - +
76B ARG* 1.3 77.8 - - - +
78B LEU* 1.3 63.5 + - + +
80B GLU* 3.3 8.7 + - + +
81B LEU* 2.9 36.0 + - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.8 28.3 - - + -
81A LEU* 4.1 9.0 - - + -
23B LEU* 4.1 17.2 - - + +
32B PHE* 3.9 18.2 - - + -
35B ALA* 3.6 21.1 - - + -
44B ASN* 3.7 24.9 - - + +
75B ASN* 3.1 35.9 + - - +
77B ILE* 1.3 78.9 - - + +
79B ASP* 1.3 60.4 + - - +
81B LEU* 3.8 7.3 - - + +
82B VAL* 2.9 35.6 + - - +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE 4.3 6.4 - - - +
34B ILE* 3.3 19.0 + - - +
35B ALA* 3.0 33.5 + - - +
74B ASN* 5.3 1.9 + - - -
75B ASN 4.5 0.7 - - - -
76B ARG* 3.0 28.8 + - - +
78B LEU* 1.3 78.6 - - - +
80B GLU* 1.3 61.9 + - + +
82B VAL* 3.5 6.8 + - - +
83B LYS* 3.1 23.9 + - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 28.7 - - + +
76B ARG* 3.2 14.5 + - + +
77B ILE* 3.3 12.1 + - + +
79B ASP* 1.3 78.0 - - + +
81B LEU* 1.3 59.3 + - - +
83B LYS* 3.4 7.4 + - - +
84B SER* 2.9 35.0 + - - -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.9 27.0 - - + +
22A LEU* 3.8 30.1 - - + -
23A LEU* 4.2 17.9 - - + -
78A LEU* 4.2 2.2 - - + -
81A LEU* 3.8 31.4 - - + -
23B LEU* 3.9 18.5 - - + +
77B ILE* 2.9 32.2 + - + +
78B LEU* 3.3 11.6 + - + +
79B ASP 3.3 0.2 - - - -
80B GLU* 1.3 75.1 - - - +
82B VAL* 1.3 56.8 + - - +
84B SER* 3.7 0.7 - - - -
85B LEU* 2.8 37.8 + - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.9 37.0 - - + +
31B TYR* 3.6 31.0 - - + -
32B PHE* 3.9 24.7 - - + +
78B LEU 2.9 22.5 + - - +
79B ASP* 3.8 5.6 - - - +
81B LEU* 1.3 76.6 - - - +
83B LYS* 1.3 63.8 - - - +
85B LEU* 4.0 1.4 - - - +
86B ASN* 3.0 26.5 + - + +
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP 3.1 18.1 + - - +
80B GLU* 3.7 8.3 - - - +
82B VAL* 1.3 78.8 - - - +
84B SER* 1.3 60.8 + - - +
86B ASN* 3.5 10.1 + - - +
87B PHE* 3.0 32.5 + - + +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 4.2 17.7 + - - -
19A ILE* 3.5 20.5 - - - +
22A LEU* 3.6 16.8 - - - +
80B GLU* 2.9 20.3 + - - -
81B LEU 3.9 0.7 - - - -
83B LYS* 1.3 77.8 - - - +
85B LEU* 1.3 58.2 + - - +
87B PHE* 3.3 7.5 + - - +
88B ALA* 2.8 29.3 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 4.6 1.3 - - + -
19A ILE* 3.6 23.4 - - + +
9B TRP* 3.7 26.7 - - + -
16B MET* 3.9 14.4 - - + -
19B ILE* 4.1 13.0 - - + -
20B ASP* 3.8 35.7 - - - +
23B LEU* 3.7 23.3 - - + -
31B TYR* 4.8 6.7 - - + +
81B LEU 2.8 20.8 + - - +
82B VAL* 4.0 3.4 - - - +
84B SER* 1.3 70.0 - - - +
86B ASN* 1.3 60.3 + - - +
88B ALA* 3.6 2.7 - - + +
89B ARG* 2.9 33.9 + - - +
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 5.8 7.0 - - + -
82B VAL* 3.0 21.6 + - + +
83B LYS* 3.7 9.6 + - - +
85B LEU* 1.3 74.9 - - - +
87B PHE* 1.3 65.3 + - - +
89B ARG* 3.3 29.1 + - - +
90B ASN* 2.8 55.1 + - - +
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.6 25.8 - - + -
18A THR* 5.6 5.2 - - + -
83B LYS* 3.0 20.4 + - + +
84B SER* 3.6 10.5 - - - +
86B ASN* 1.3 80.8 - - - +
88B ALA* 1.3 66.9 + - - +
90B ASN* 3.3 4.3 + - + +
91B HIS* 2.9 45.4 + + + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.9 27.3 - - + +
16A MET* 4.0 26.2 - - - -
18A THR* 5.0 0.2 - - - +
19A ILE* 4.9 3.6 - - + -
9B TRP* 4.5 3.8 - - + -
84B SER 2.8 17.4 + - - +
85B LEU* 3.3 8.3 + - - +
87B PHE* 1.3 78.5 - - - +
89B ARG* 1.3 62.5 + - - +
91B HIS* 3.3 2.1 + - - +
92B LEU* 3.1 29.4 + - - +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.6 27.6 + - - +
8B ARG 3.7 20.2 + - - +
9B TRP* 3.6 49.2 - - + +
20B ASP* 4.1 2.4 + - - -
31B TYR* 3.0 31.3 + - - -
85B LEU* 2.9 19.8 + - - +
86B ASN* 3.3 34.7 + - - +
88B ALA* 1.3 75.8 - - - +
90B ASN* 1.3 68.3 + - - +
92B LEU* 3.4 3.3 + - - +
93B LEU* 3.1 34.6 + - + +
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Residues in contact with ASN 90 (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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86B ASN* 2.8 52.5 + - - +
87B PHE* 3.8 4.8 - - + +
89B ARG* 1.3 85.4 + - - +
91B HIS* 1.3 65.0 + - - +
93B LEU* 3.5 12.3 + - - +
94B GLN* 3.2 23.9 + - - +
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.1 20.5 - - + +
87B PHE* 2.9 47.5 + + + +
88B ALA* 3.6 6.1 - - - +
90B ASN* 1.3 76.3 - - - +
92B LEU* 1.3 64.2 + - + +
94B GLN* 3.5 32.4 + - - +
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Residues in contact with LEU 92 (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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12A GLY 3.1 27.6 - - - +
13A LEU* 3.8 16.8 - - + -
15A VAL* 3.9 19.7 - - + -
16A MET* 4.8 4.5 - - - -
95A PHE* 5.8 1.1 - - + -
9B TRP* 3.6 31.4 - - + -
10B PRO* 3.9 22.5 - - + +
13B LEU* 3.8 12.3 - - + -
88B ALA 3.1 18.7 + - - +
89B ARG 3.8 3.4 - - - +
90B ASN 3.2 0.2 - - - -
91B HIS* 1.3 79.4 - - - +
93B LEU* 1.3 62.8 + - - +
94B GLN 3.0 14.6 + - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 3.5 30.7 - - + +
9B TRP 4.3 1.8 - - - +
10B PRO* 4.0 26.2 - - + -
89B ARG* 3.1 31.8 + - + +
90B ASN* 3.9 11.9 - - - +
92B LEU* 1.3 75.7 - - - +
94B GLN* 1.3 59.6 + - - +
95B PHE 3.4 3.1 + - - -
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Residues in contact with GLN 94 (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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90B ASN 3.2 11.3 + - - +
91B HIS* 3.5 34.9 + - - +
92B LEU 3.0 10.1 - - - +
93B LEU* 1.3 75.1 - - - +
95B PHE 1.3 49.4 + - - +
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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
------------------------------------------------------------
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