Contacts of the strand formed by residues 103 - 108 (chain E) in PDB entry 1ACB
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 ILE 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E VAL* 3.6 18.4 - - + -
54E THR 3.5 2.9 - - - -
56E ALA* 3.5 6.6 - - - +
91E ASN* 3.2 47.5 + - + +
101E ASN 3.1 6.1 + - - +
102E ASP* 1.3 74.6 - - - +
104E THR* 1.3 68.2 + - - +
105E LEU* 4.2 4.9 - - + -
212E ILE* 3.3 29.6 - - + -
231E VAL* 5.0 8.5 - - + -
234E LEU* 4.1 32.5 - - + -
237E TRP* 3.7 11.1 - - + -
238E VAL* 4.2 15.3 - - + -
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Residues in contact with THR 104 (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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53E VAL* 3.4 3.6 - - - +
54E THR* 2.9 36.0 + - + +
55E ALA 4.0 7.2 - - - -
56E ALA* 3.2 25.7 + - - +
60E VAL* 5.3 3.6 - - + +
88E VAL* 3.5 20.9 - - + -
89E PHE 3.4 8.5 - - - +
90E LYS* 3.4 16.6 - - - +
103E ILE* 1.3 74.1 + - - +
105E LEU* 1.3 67.4 + - - +
106E LEU* 3.1 24.9 - - + -
237E TRP* 4.6 0.2 - - - -
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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 22.4 - - + -
51E TRP* 3.9 18.8 - - + -
52E VAL 3.4 9.0 - - - +
53E VAL* 4.2 11.9 - - + -
88E VAL* 3.6 0.2 - - - -
89E PHE* 2.6 49.3 + - + +
103E ILE* 4.2 1.1 - - + -
104E THR* 1.3 79.3 - - - +
106E LEU* 1.3 64.8 + - - +
237E TRP* 3.0 37.9 - - + -
238E VAL* 4.0 15.0 - - + -
241E THR* 4.7 2.5 - - + -
242E LEU* 3.7 28.9 - - + -
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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
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33E LEU* 4.6 6.5 - - + -
51E TRP* 3.3 13.4 - - - -
52E VAL* 2.8 58.9 + - + +
54E THR* 3.9 18.8 - - + -
60E VAL* 4.3 13.0 - - + -
66E VAL* 4.4 5.8 - - + -
85E ILE* 4.0 36.6 - - + -
87E LYS 3.6 2.7 - - - -
88E VAL* 3.9 8.7 - - + -
104E THR* 3.1 25.6 - - + -
105E LEU* 1.3 83.6 - - - +
107E LYS* 1.3 62.0 + - - +
108E LEU* 3.8 4.1 + - + +
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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 ASN* 3.8 10.1 - - + +
51E TRP* 3.8 27.3 - - + +
85E ILE* 3.4 5.2 - - - +
86E ALA* 2.4 45.7 + - + -
87E LYS* 2.8 25.9 + - + +
89E PHE* 4.1 14.6 - - + -
106E LEU* 1.3 71.6 - - - +
108E LEU* 1.3 63.0 + - - +
245E ASN* 2.7 35.1 + - - -
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Residues in contact with LEU 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* 4.6 4.3 - - + -
49E GLU 3.8 19.5 - - - +
50E ASN* 3.3 27.1 + - - +
51E TRP 4.5 0.4 - - - +
52E VAL* 4.1 21.1 - - + -
66E VAL* 3.5 34.3 - - + -
83E LEU* 3.8 26.2 - - + -
84E LYS 3.3 13.0 - - - +
85E ILE* 4.6 2.9 - - + -
86E ALA* 3.8 3.7 - - - +
106E LEU* 4.4 3.8 - - + +
107E LYS* 1.3 82.9 - - - +
109E SER* 1.3 66.3 + - - +
110E THR* 3.1 17.5 + - - +
111E ALA 4.7 0.3 + - - -
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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