Contacts of the helix formed by residues 49 - 61 (chain A) in PDB entry 1D5R
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 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.9 3.5 - - - +
39A ALA 3.9 4.5 - - - -
42A LEU* 3.9 23.3 - - - +
47A ARG 3.5 11.8 - - - +
48A ASN* 1.3 70.8 - - - +
50A ILE* 1.3 67.3 + - - +
51A ASP* 3.0 10.3 + - + +
52A ASP* 3.1 35.6 + - - +
53A VAL* 3.3 13.1 + - - +
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Residues in contact with ILE 50 (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 PRO* 3.8 24.9 - - - +
39A ALA 3.1 19.9 + - - +
40A GLU* 4.2 21.3 - - + +
48A ASN 3.5 1.0 + - - -
49A ASN* 1.3 71.8 - - - +
51A ASP* 1.3 67.1 + - - +
53A VAL* 3.6 2.2 + - - +
54A VAL* 2.7 31.2 + - - +
76A TYR* 4.4 15.5 - - + -
77A ASP 5.0 3.8 - - - +
80A LYS* 4.0 40.2 - - + +
81A PHE* 3.4 34.5 - - + -
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Residues in contact with ASP 51 (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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49A ASN* 3.0 7.9 + - + +
50A ILE* 1.3 84.5 + - - +
52A ASP* 1.3 58.5 + - - +
54A VAL* 3.2 8.8 + - - +
55A ARG* 2.9 53.7 + - - +
80A LYS* 3.7 27.6 + - - +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.6 9.8 - - + -
23A LEU* 3.9 24.0 - - + +
49A ASN* 3.1 33.6 + - - +
51A ASP* 1.3 74.4 - - - +
53A VAL* 1.3 56.4 + - - +
55A ARG* 3.2 23.1 + - - +
56A PHE* 2.7 35.9 + - - +
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Residues in contact with VAL 53 (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 LEU* 4.0 20.0 - - + -
25A LEU* 5.3 3.8 - - + -
35A MET* 3.5 34.5 - - + -
38A PRO* 4.4 6.1 - - + -
48A ASN* 4.2 16.6 - - + +
49A ASN 3.3 15.2 + - - +
50A ILE 3.8 7.0 - - - +
51A ASP 3.3 0.2 - - - -
52A ASP* 1.3 73.5 - - - +
54A VAL* 1.3 60.6 + - - +
56A PHE* 3.4 0.7 - - - +
57A LEU* 2.8 57.7 + - + +
81A PHE* 4.1 13.2 - - + -
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Residues in contact with VAL 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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50A ILE* 2.7 28.3 - - + +
51A ASP* 3.3 9.0 - - - +
52A ASP 3.2 0.2 - - - -
53A VAL* 1.3 74.4 - - - +
55A ARG* 1.3 67.6 + - - +
57A LEU* 3.2 6.1 + - - +
58A ASP* 2.8 50.3 + - - +
65A TYR* 4.6 4.7 - - - +
80A LYS* 3.1 48.2 - - + +
81A PHE* 4.4 9.2 - - + -
82A ASN* 6.2 0.2 - - + -
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Residues in contact with ARG 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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21A PHE* 4.6 12.3 - - + -
51A ASP* 2.9 48.1 + - - +
52A ASP* 3.4 23.0 + - - +
54A VAL* 1.3 76.0 - - + +
56A PHE* 1.3 53.7 + - - +
58A ASP* 3.2 4.3 + - - +
59A SER* 2.7 41.4 + - - -
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Residues in contact with PHE 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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18A GLU* 3.8 18.2 - - + -
21A PHE* 3.7 29.3 - + + -
23A LEU* 4.0 13.0 - - + -
25A LEU* 3.7 22.7 - - + -
27A TYR* 2.8 41.1 - + - -
33A ILE* 4.2 2.7 - - + -
52A ASP 2.7 20.7 + - - +
53A VAL* 3.4 4.9 - - - +
55A ARG* 1.3 72.2 - - - +
57A LEU* 1.3 84.4 + - + +
59A SER* 3.0 18.6 + - - -
60A LYS* 3.0 48.0 + - + +
61A HIS* 5.0 1.8 - + - -
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Residues in contact with LEU 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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25A LEU* 5.4 2.2 - - + -
33A ILE* 4.3 14.8 - - + -
35A MET* 5.2 0.9 - - - -
53A VAL* 2.8 41.7 + - + +
54A VAL* 3.9 2.0 - - - +
56A PHE* 1.3 98.7 - - + +
58A ASP* 1.3 51.3 + - - +
61A HIS* 2.5 50.8 + - + +
65A TYR* 3.7 29.8 - - + -
67A ILE* 3.7 28.0 - - + -
81A PHE* 3.9 9.2 - - + -
119A VAL* 6.0 0.7 - - + -
121A ALA* 4.7 9.6 - - + -
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Residues in contact with ASP 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 VAL* 2.8 50.7 + - - +
55A ARG* 3.8 4.2 - - - +
57A LEU* 1.3 70.8 - - - +
59A SER* 1.3 64.9 + - - +
61A HIS 3.7 3.8 - - - -
62A LYS* 3.5 32.7 + - - +
65A TYR* 3.3 21.6 + - - -
82A ASN* 4.3 12.6 + - - +
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Residues in contact with SER 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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21A PHE* 3.9 11.3 - - - -
55A ARG* 2.7 26.6 + - - -
56A PHE* 3.0 14.2 + - - -
58A ASP* 1.3 73.1 - - - +
60A LYS* 1.3 65.9 + - - +
62A LYS* 5.3 1.3 - - - +
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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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18A GLU* 3.3 27.3 + - - -
20A GLY* 5.0 3.2 - - - -
21A PHE* 3.9 18.8 - - - -
27A TYR* 4.0 5.3 + - + +
56A PHE* 3.0 40.1 + - + +
59A SER* 1.3 83.9 - - - +
61A HIS* 1.3 85.7 + - + +
62A LYS* 4.1 1.1 - - - -
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Residues in contact with HIS 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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27A TYR* 3.2 37.2 - + - -
30A PRO 4.7 2.2 + - - -
33A ILE* 4.7 3.1 - - + -
57A LEU* 2.5 37.4 + - + +
58A ASP 3.6 1.3 - - - -
60A LYS* 1.3 101.7 + - + +
62A LYS* 1.3 70.8 + - - +
63A ASN 3.8 0.2 - - - -
64A HIS* 4.4 10.1 - - + -
65A TYR* 3.1 25.4 - - + -
118A HIS* 5.0 6.7 - + - -
119A VAL* 3.3 44.6 - - + +
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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