Contacts of the helix formed by residues 53 - 63 (chain A) in PDB entry 3BMW
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 ASP 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 3.6 15.0 + - - +
26A VAL 3.0 5.4 + - - +
27A ASP* 3.2 0.5 - - - +
28A GLY* 2.8 23.3 + - - -
29A ASN 3.0 19.4 + - - +
32A ASN* 3.2 8.0 + - - +
51A GLY 3.7 0.2 - - - -
52A GLY* 1.3 75.6 - - - +
54A TRP* 1.3 64.1 + - - +
55A GLN* 3.4 5.2 + - - +
56A GLY* 2.9 24.1 + - - -
57A ILE* 3.3 15.2 + - - +
112A TYR 3.6 12.1 - - - +
113A PHE* 3.4 14.4 - - - +
699A CA 2.3 28.1 - - - -
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Residues in contact with TRP 54 (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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22A THR* 3.9 19.0 + - + -
53A ASP* 1.3 73.2 - - - +
55A GLN* 1.3 59.8 + - - +
57A ILE* 3.1 11.4 + - + +
58A ILE* 2.9 32.7 + - - +
76A ILE* 3.8 12.9 - - + +
77A PRO 5.5 0.8 + - - -
79A PRO* 3.4 43.0 - - + +
109A THR* 4.0 12.8 - - + -
110A ASN 4.5 0.2 - - - -
113A PHE* 3.1 41.1 + + + +
114A GLY* 3.5 24.0 - - - -
115A SER 3.5 11.0 - - - -
118A ASP* 4.0 13.5 - - + +
119A PHE* 3.8 39.7 - + + -
122A LEU* 3.9 24.2 - - + +
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Residues in contact with GLN 55 (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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28A GLY* 3.6 25.8 - - - +
29A ASN* 4.4 9.6 - - + +
32A ASN* 5.7 0.9 - - - +
53A ASP* 3.3 10.3 + - - +
54A TRP* 1.3 77.0 - - - +
56A GLY* 1.3 57.6 + - - +
58A ILE* 3.2 30.2 + - - +
59A ASN* 2.9 52.5 + - - +
113A PHE 4.6 1.0 + - - -
118A ASP* 4.8 15.7 - - - +
121A ASN* 5.1 5.2 + - - -
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Residues in contact with GLY 56 (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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25A PHE* 4.8 0.2 - - - -
26A VAL* 3.4 41.9 - - - +
28A GLY* 3.6 6.0 - - - -
53A ASP* 2.9 12.4 + - - -
55A GLN* 1.3 77.0 - - - +
57A ILE* 1.3 60.5 + - - +
59A ASN* 3.3 13.0 + - - +
60A LYS* 3.3 18.5 + - - +
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Residues in contact with ILE 57 (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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20A ILE* 3.8 27.6 - - + -
22A THR* 3.9 16.8 - - + +
25A PHE* 4.1 23.3 - - + -
53A ASP 3.3 9.5 + - - +
54A TRP* 3.1 20.9 + - + +
56A GLY* 1.3 71.9 - - - +
58A ILE* 1.3 67.7 + - - +
60A LYS* 3.0 4.9 + - - +
61A ILE* 3.0 26.8 + - + +
66A LEU* 4.8 3.3 - - + +
74A ILE* 3.8 9.2 - - + -
76A ILE* 3.7 27.4 - - + -
122A LEU* 3.7 19.7 - - + -
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Residues in contact with ILE 58 (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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54A TRP 2.9 19.4 + - - +
55A GLN* 3.3 35.9 - - - +
57A ILE* 1.3 76.4 - - - +
59A ASN* 1.3 57.0 + - - +
61A ILE* 3.1 10.9 + - - +
62A ASN* 2.9 47.9 + - - +
118A ASP* 4.1 6.7 - - + +
121A ASN* 3.6 18.2 - - + -
122A LEU* 3.6 39.9 - - + +
125A THR* 3.9 15.7 - - + +
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Residues in contact with ASN 59 (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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26A VAL* 4.7 5.9 - - + +
28A GLY* 4.0 21.8 + - - -
55A GLN* 2.9 41.0 + - - +
56A GLY* 3.4 9.0 - - - +
57A ILE 3.2 0.4 - - - -
58A ILE* 1.3 76.3 - - - +
60A LYS* 1.3 65.6 + - + +
62A ASN* 3.5 6.3 + - - +
63A ASP* 3.0 34.3 + - - +
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Residues in contact with LYS 60 (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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25A PHE* 3.6 29.2 - - + -
26A VAL* 3.8 13.5 - - + -
56A GLY 3.3 12.3 + - - +
57A ILE 3.0 8.2 + - - +
59A ASN* 1.3 77.8 - - + +
61A ILE* 1.3 62.4 + - - +
63A ASP* 2.7 34.0 + - - +
65A TYR* 3.4 27.4 + - + +
66A LEU* 3.4 30.7 + - + +
381A PHE* 3.7 39.9 - - + +
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Residues in contact with ILE 61 (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 ILE* 3.0 20.3 + - + +
58A ILE* 3.5 8.3 - - - +
60A LYS* 1.3 77.7 - - - +
62A ASN* 1.3 65.2 + - - +
63A ASP 3.3 0.7 + - - -
64A GLY* 3.4 12.1 + - - -
66A LEU* 4.0 20.2 - - + -
67A THR* 4.6 4.9 + - + +
74A ILE* 4.7 4.9 - - + -
122A LEU* 4.0 24.7 - - + -
125A THR* 3.8 10.8 - - + +
126A ALA* 4.0 22.7 - - + +
129A HIS* 3.5 46.0 - - + +
131A ILE* 4.1 14.4 - - + -
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Residues in contact with ASN 62 (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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58A ILE* 2.9 37.2 + - - +
59A ASN* 4.0 6.1 + - - +
61A ILE* 1.3 77.2 - - - +
63A ASP* 1.3 59.6 + - + +
64A GLY* 3.3 1.9 + - - -
125A THR* 3.5 10.4 + - - +
129A HIS* 3.2 29.9 + - - -
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Residues in contact with ASP 63 (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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59A ASN* 3.0 25.5 + - - +
60A LYS* 2.7 40.3 + - - +
61A ILE 3.3 0.2 - - - -
62A ASN* 1.3 75.5 - - + +
64A GLY* 1.3 61.5 + - - +
65A TYR* 3.2 12.0 + - - +
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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