Contacts of the helix formed by residues 37 - 46 (chain A) in PDB entry 2W7U
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 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 1.3 89.7 + - - +
38A LYS* 1.3 65.2 + - - +
39A HIS* 3.5 9.2 - - - +
40A ILE* 3.6 16.6 + - + +
41A ALA* 3.3 17.2 + - - +
78A ASP* 3.2 28.6 + - - +
80A ALA* 3.8 1.6 - - - +
154A SER* 3.4 15.8 + - - -
155A GLY* 3.1 23.0 - - - +
168A ILE* 3.5 6.8 - - - +
169A LEU 3.1 20.9 + - - +
170A TYR* 3.4 17.1 + - - +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 1.3 72.4 - - - +
39A HIS* 1.3 58.9 + - - +
41A ALA* 3.2 4.0 + - - +
42A LYS* 2.9 47.1 + - + +
72A GLU* 3.9 23.5 - - + +
73A TYR 2.8 28.6 + - - -
74A PRO 4.8 0.2 - - - -
75A GLY 3.0 17.6 + - - -
76A LYS 4.5 2.6 + - - +
77A GLU 3.3 20.9 + - - +
78A ASP* 3.0 21.8 + - - +
79A LEU 3.7 21.1 - - - +
80A ALA* 3.9 10.5 - - + +
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Residues in contact with HIS 39 (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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23A GLY 5.4 0.6 + - - -
37A ASN* 4.0 12.5 - - - +
38A LYS* 1.3 75.8 - - - +
40A ILE* 1.3 88.8 + - + +
41A ALA 3.4 0.2 - - - -
42A LYS* 3.9 9.4 - - - -
43A SER* 2.8 32.3 + - - -
78A ASP* 4.4 8.3 + - - -
154A SER* 3.6 24.2 + - - -
170A TYR 5.2 2.7 - - - -
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Residues in contact with ILE 40 (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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21A PHE* 3.5 34.7 - - + -
23A GLY* 3.6 33.7 - - - +
24A GLY* 3.8 3.4 - - - +
25A THR 4.7 1.6 - - - +
36A THR* 3.5 22.9 - - + +
37A ASN* 3.6 23.6 - - + +
39A HIS* 1.3 101.9 - - + +
41A ALA* 1.3 60.5 + - - +
43A SER* 3.8 3.4 + - - -
44A ASN* 3.3 24.1 + - - +
154A SER* 3.8 14.8 - - - +
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Residues in contact with ALA 41 (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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21A PHE* 5.0 2.9 - - - -
36A THR* 4.3 2.4 - - + +
37A ASN 3.3 9.9 + - - +
38A LYS 3.2 7.4 + - - +
40A ILE* 1.3 77.1 - - - +
42A LYS* 1.3 65.1 + - + +
44A ASN* 3.7 4.8 + - - +
45A ASP* 3.2 22.9 + - - +
70A ILE* 3.9 20.0 - - + +
80A ALA* 4.0 14.4 - - + -
82A VAL* 3.8 28.9 - - + -
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Residues in contact with LYS 42 (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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38A LYS* 2.9 32.2 + - + +
39A HIS* 4.3 6.1 - - - +
41A ALA* 1.3 78.9 - - + +
43A SER* 1.3 61.7 + - - +
45A ASP* 3.2 18.7 + - - +
46A ILE* 3.6 14.0 + - - +
70A ILE* 5.7 3.1 - - + -
72A GLU* 3.2 42.3 + - + +
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Residues in contact with SER 43 (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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23A GLY* 6.0 1.7 - - - -
39A HIS* 2.8 22.0 + - - -
40A ILE* 3.8 4.7 + - - -
42A LYS* 1.3 77.4 - - - +
44A ASN* 1.3 64.9 + - - +
46A ILE* 3.4 26.4 - - - +
47A PHE* 3.7 15.2 + - - +
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Residues in contact with ASN 44 (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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21A PHE* 4.2 20.7 - - + -
22A VAL* 4.3 18.6 - - - +
40A ILE 3.3 17.6 + - - +
41A ALA* 3.9 5.6 - - - +
42A LYS 3.3 0.6 - - - -
43A SER* 1.3 82.6 + - - +
45A ASP* 1.3 56.9 + - - +
46A ILE 3.3 0.2 - - - -
47A PHE* 3.5 2.7 + - - +
48A LYS* 2.8 23.4 + - - -
49A ASN* 3.0 46.6 + - - +
50A ARG 4.5 4.2 + - - -
51A VAL* 4.6 0.7 - - - +
67A VAL* 3.7 16.8 - - - +
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Residues in contact with ASP 45 (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 ALA 3.2 13.7 + - - +
42A LYS* 3.2 14.4 + - - +
44A ASN* 1.3 77.7 - - - +
46A ILE* 1.3 61.2 + - + +
47A PHE 3.4 0.2 - - - -
48A LYS* 3.0 51.7 + - - +
67A VAL* 5.2 4.2 - - - +
69A ASP* 5.8 0.7 - - - -
70A ILE* 3.5 25.6 - - + +
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Residues in contact with ILE 46 (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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42A LYS 3.8 9.6 - - - +
43A SER* 3.4 26.2 - - - +
45A ASP* 1.3 81.5 - - + +
47A PHE* 1.3 71.1 + - + +
48A LYS* 5.0 4.5 - - - +
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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