Contacts of the strand formed by residues 104 - 109 (chain E) in PDB entry 3PB1
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 ALA 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E ILE* 3.4 8.7 - - - +
54E SER 2.8 32.3 + - - +
55E ALA 3.7 7.4 - - - +
56E THR* 3.6 22.7 - - - +
59E PHE* 4.0 18.8 - - + -
88E LEU* 5.1 0.2 - - + -
89E ILE 3.3 12.8 - - - +
90E LEU* 4.1 2.9 - - + -
103E ILE* 1.3 76.2 - - - +
105E LEU* 1.3 65.0 + - - +
106E LEU* 4.5 2.5 - - + -
237E TRP* 4.0 3.4 - - - -
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Residues in contact with LEU 105 (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 ILE* 4.0 19.3 - - + -
51E TRP* 3.7 20.6 - - + -
52E VAL 3.5 8.7 - - - +
53E ILE* 3.8 26.7 - - + -
87E ASN 3.6 1.2 - - - +
88E LEU* 3.6 3.1 - - - +
89E ILE* 2.8 45.9 + - + +
104E ALA* 1.3 73.6 - - - +
106E LEU* 1.3 63.3 - - - +
237E TRP* 3.5 28.0 - - + -
238E ILE* 4.1 15.5 - - + +
241E HIS* 3.7 28.5 - - + +
242E THR* 4.2 7.9 - - + -
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ILE* 4.2 11.9 - - + -
50E CYS 3.6 0.2 - - - +
51E TRP* 3.5 6.4 - - - -
52E VAL* 2.8 54.0 + - + +
54E SER* 3.9 16.8 - - - -
59E PHE* 3.8 40.6 - - + -
64E TYR* 5.4 1.1 - - + -
66E VAL* 3.8 25.1 - - + -
85E VAL* 3.9 18.6 - - + -
87E ASN 3.5 3.6 - - - -
88E LEU* 3.8 14.4 - - + -
105E LEU* 1.3 82.1 - - - +
107E LYS* 1.3 60.9 + - - +
108E ILE* 3.8 4.8 + - + +
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Residues in contact with LYS 107 (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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50E CYS* 3.2 30.3 - - + +
51E TRP* 3.7 36.0 - - + +
85E VAL* 3.3 6.1 - - - -
86E GLU* 2.7 66.2 + - + +
87E ASN* 2.9 25.6 + - + +
106E LEU* 1.3 72.5 - - - +
108E ILE* 1.3 59.1 + - - +
244E GLU* 2.9 32.6 + - + +
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Residues in contact with ILE 108 (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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46E LEU* 4.3 6.7 - - + -
49E PRO 3.9 15.3 - - - +
50E CYS* 3.0 21.6 + - - +
51E TRP 4.4 0.2 - - - +
52E VAL* 4.1 13.2 - - + -
66E VAL* 4.0 27.8 - - + -
68E LEU* 4.0 17.7 - - + -
83E PHE* 3.7 48.7 - - + -
84E GLU 3.4 4.0 - - - +
85E VAL* 5.0 0.7 - - + -
86E GLU* 4.6 3.4 - - - +
106E LEU* 4.3 6.3 - - + +
107E LYS* 1.3 79.3 - - - +
109E ARG* 1.3 63.0 + - - +
110E ARG 4.4 0.9 - - - +
111E CYS* 4.0 18.9 - - - -
112E ALA 4.3 0.9 - - - +
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Residues in contact with ARG 109 (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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83E PHE* 3.7 4.7 - - - -
84E GLU* 2.9 54.3 + - + +
86E GLU* 3.3 35.2 + - + +
108E ILE* 1.3 77.7 - - - +
110E SER* 1.3 117.5 + - + +
111E CYS* 6.0 1.6 - - - -
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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