Contacts of the helix formed by residues 49 - 55 (chain A) in PDB entry 3U7U
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 LEU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 4.0 9.6 - - + -
24A LEU* 3.8 28.0 - - + -
40A ILE* 4.9 1.1 - - + -
43A ILE* 4.2 9.4 - - + -
47A ARG* 3.8 8.6 + - + +
48A ASP* 1.3 82.1 + - - +
50A SER* 1.3 64.3 + - - +
51A PHE* 3.1 12.6 - - + -
52A LEU* 2.9 30.2 + - + +
69A PHE* 3.5 52.3 - - + -
71A TYR 4.5 0.9 - - - +
73A PRO* 3.3 28.4 - - + +
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Residues in contact with SER 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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25A ARG* 4.5 1.7 + - - -
48A ASP* 3.0 27.7 + - - -
49A LEU* 1.3 76.5 - - - +
51A PHE* 1.4 57.0 + - - +
53A ARG* 3.0 57.5 + - - +
73A PRO* 4.1 5.5 - - - +
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Residues in contact with PHE 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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21A TYR* 4.1 9.0 - + - -
24A LEU* 3.7 33.7 - - + -
25A ARG* 3.7 48.9 - - + +
28A TYR* 4.3 5.5 - - + +
29A GLU* 3.8 35.9 - - + +
30A ASN 4.6 1.8 + - - +
48A ASP 3.3 26.7 - - - -
49A LEU* 3.0 13.1 + - + -
50A SER* 1.4 79.5 + - - +
52A LEU* 1.4 76.4 + - + +
53A ARG 3.1 2.0 + - - -
54A SER* 2.9 28.2 + - - -
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Residues in contact with LEU 52 (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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24A LEU* 5.0 3.1 - - + -
28A TYR* 4.5 8.7 - - + -
38A LEU* 4.2 24.7 - - + -
40A ILE* 4.0 24.9 - - + -
49A LEU* 2.9 42.7 + - + +
51A PHE* 1.4 93.7 - - + +
53A ARG* 1.3 60.4 + - - +
54A SER* 3.0 8.3 + - - -
55A VAL* 3.2 17.8 + - + +
72A LEU* 4.3 4.9 - - + -
73A PRO* 3.6 18.2 - - + +
74A LEU* 3.7 27.2 - - + +
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Residues in contact with ARG 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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50A SER* 3.0 38.4 + - - +
52A LEU* 1.3 77.0 - - - +
54A SER* 1.3 60.3 + - - +
55A VAL 3.3 0.2 - - - -
71A TYR* 4.6 5.3 - - - -
73A PRO* 3.3 27.8 - - + +
75A GLU* 3.0 46.7 + - + +
76A ASN* 2.7 38.6 + - - +
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Residues in contact with SER 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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28A TYR 3.6 5.7 + - - -
30A ASN* 3.7 11.8 + - - -
31A CYS 2.7 40.4 + - - +
32A GLU* 3.4 21.4 - - - +
51A PHE 2.9 20.6 + - - -
53A ARG* 1.3 80.1 - - - +
55A VAL* 1.4 61.5 + - - +
56A ARG* 3.5 3.8 + - - +
76A ASN* 5.2 0.5 - - - +
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Residues in contact with VAL 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 TYR* 4.7 8.5 - - + +
31A CYS 3.6 15.5 - - - +
32A GLU 3.7 2.2 - - - +
34A VAL* 4.1 17.0 - - + -
38A LEU* 4.8 12.6 - - + -
52A LEU* 3.2 22.0 + - + +
53A ARG 4.1 0.5 - - - +
54A SER* 1.4 77.7 - - - +
56A ARG* 1.4 56.3 + - - +
57A GLU 3.7 20.9 - - - +
58A VAL* 3.9 18.4 - - + -
74A LEU* 4.3 11.2 - - + +
76A ASN* 3.1 8.6 + - - +
77A LEU* 2.9 35.2 + - + +
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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