Contacts of the strand formed by residues 44 - 50 (chain E) in PDB entry 6D48
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 VAL 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E PHE* 4.7 4.3 - - + -
42E SER 4.2 2.2 - - - +
43E PRO* 1.3 72.6 - - - +
45E HIS* 1.3 68.6 + - - +
64E ASN* 3.2 19.2 + - - -
84E PRO* 3.6 29.6 - - + +
85E SER* 3.7 33.4 + - - +
108E MET* 4.6 13.5 - - + -
109E GLU 3.7 7.2 - - - +
110E ARG* 3.7 43.3 - - + +
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Residues in contact with HIS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PRO* 4.0 36.2 - - + +
44E VAL* 1.3 78.7 + - - +
46E GLY* 1.3 59.2 + - - +
47E TYR* 3.6 24.8 - - + +
64E ASN* 3.4 10.4 + - - +
65E LYS* 3.8 50.0 - - + +
66E LEU 5.4 0.7 - - - -
84E PRO* 4.5 2.2 - - - -
108E MET* 3.3 7.4 - - - +
109E GLU* 2.9 43.5 + - + +
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E HIS* 1.3 73.2 - - - +
47E TYR* 1.3 62.3 + - - -
63E THR* 2.9 29.6 + - - -
64E ASN* 2.9 13.0 + - - +
80E LEU* 3.7 12.8 - - - -
84E PRO* 4.1 3.6 - - - +
106E PHE* 3.7 17.9 - - - -
107E ARG 3.3 7.9 - - - -
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Residues in contact with TYR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E HIS* 3.6 24.2 - - + +
46E GLY* 1.3 72.5 - - - -
48E TRP* 1.3 60.3 + - - +
49E PHE* 3.5 26.4 - + + -
60E PRO* 4.2 13.2 - - + -
62E ALA 3.4 7.9 - - - +
63E THR* 3.3 25.4 - - - -
65E LYS* 3.3 26.4 + - + +
68E GLN* 4.2 20.4 - - + -
105E PHE 3.8 0.2 - - - +
106E PHE* 3.3 12.2 - - - -
107E ARG* 2.9 51.1 + - + +
109E GLU* 3.3 41.2 + - + -
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Residues in contact with TRP 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 5.3 2.7 - - + -
13E VAL* 4.8 7.9 - - + -
27E VAL* 6.4 0.4 - - + -
29E CYS* 3.8 22.4 - - + -
47E TYR* 1.3 72.6 - - - +
49E PHE* 1.3 54.9 + - - +
60E PRO* 3.2 6.1 - - - +
61E VAL* 2.7 46.2 + - + -
62E ALA* 2.9 14.8 + - + +
80E LEU* 3.8 17.9 - - + +
89E CYS 2.9 28.4 + - - -
91E LEU* 3.8 37.2 - - + +
104E TYR* 3.8 28.9 - - + -
105E PHE* 3.4 30.7 - - - -
106E PHE* 3.6 26.5 - + + -
122E LEU* 4.3 23.1 - - + -
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Residues in contact with PHE 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E TYR* 3.5 31.4 - + + -
48E TRP* 1.3 75.5 - - - +
50E ARG* 1.3 62.2 + - - +
53E ALA* 4.0 17.3 - - + -
55E ILE* 3.8 29.2 - - + -
58E ASP 3.5 21.8 - - - -
59E SER 4.1 3.4 - - - -
60E PRO* 3.6 29.4 - - + -
61E VAL* 4.4 3.1 - - - +
104E TYR* 3.1 10.3 - - - +
105E PHE* 2.8 68.3 + + + -
107E ARG* 4.1 14.1 - - + -
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Residues in contact with ARG 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PHE* 1.3 74.5 - - - +
51E GLU* 1.3 70.1 + - - +
53E ALA* 3.0 26.6 + - + +
59E SER 5.7 1.2 + - - -
61E VAL* 3.7 21.5 - - + +
71E GLN* 3.6 44.0 + - + +
73E GLU* 3.8 28.0 + - - +
74E THR* 4.6 6.7 - - - +
99E ARG 5.7 3.2 + - - -
103E SER 3.7 6.7 - - - +
104E TYR* 3.7 17.6 + - + -
105E PHE* 3.6 4.3 - - - -
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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