Contacts of the strand formed by residues 106 - 111 (chain E) in PDB entry 2F53
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 SER 106 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E GLN* 2.8 26.3 + - - +
5E THR 4.6 1.6 - - - -
6E PRO 2.8 23.4 + - - -
7E LYS 3.5 4.9 - - - -
19E LEU* 4.0 23.0 - - - +
32E TRP* 5.0 0.9 - - - -
85E SER 3.7 1.2 - - - +
86E VAL* 3.3 3.6 - - - +
87E TYR* 2.7 45.7 + - - +
105E GLY* 1.3 73.2 + - - -
107E ARG* 1.3 63.5 + - - +
108E LEU* 3.7 1.4 + - - -
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Residues in contact with ARG 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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40D GLY 3.8 24.3 + - - -
41D LYS* 4.5 13.9 + - - +
42D GLY 5.1 0.4 - - - +
7E LYS* 2.9 19.9 + - - +
8E PHE* 3.2 49.6 - - + -
9E GLN* 2.9 27.3 + - - +
85E SER 3.7 5.4 - - - +
86E VAL* 3.7 34.2 - - + +
88E PHE* 4.6 1.0 - - - -
104E GLU 3.8 22.2 + - - -
105E GLY* 4.5 6.0 + - - -
106E SER* 1.3 71.4 - - - +
108E LEU* 1.3 60.2 + - - +
151E HIS* 3.8 18.5 + - + +
153E GLU* 5.9 0.4 + - - -
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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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9E GLN* 3.3 21.5 - - + +
11E LEU* 3.5 34.8 - - + -
17E MET* 4.6 6.7 - - + -
19E LEU* 5.3 7.9 - - + -
76E LEU* 3.4 34.5 - - + -
83E GLN 4.2 5.8 - - - +
84E THR* 3.3 6.1 - - - +
85E SER 3.1 28.1 + - - +
87E TYR* 4.0 27.4 - - + -
106E SER* 3.7 1.5 + - - -
107E ARG* 1.3 74.1 - - - +
109E THR* 1.3 73.5 + - - +
110E VAL* 4.1 10.1 - - + -
151E HIS* 5.1 0.2 - - - -
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Residues in contact with THR 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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9E GLN 2.9 8.1 + - - -
10E VAL* 3.3 5.6 - - + +
11E LEU* 2.7 32.9 + - - +
84E THR* 3.6 15.6 - - + +
108E LEU* 1.3 76.1 + - - +
110E VAL* 1.3 57.8 + - - +
111E LEU* 3.8 30.3 - - + -
148E TYR* 4.7 5.8 - - + +
149E PRO* 3.6 22.2 - - + +
151E HIS* 3.2 29.4 + - - -
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Residues in contact with VAL 110 (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* 3.1 9.0 - - + +
13E THR* 3.9 13.0 - - + +
79E ALA* 3.9 25.1 - - + -
80E ALA 3.3 45.8 - - - +
81E PRO* 3.6 14.7 - - - +
83E GLN* 4.5 2.5 - - + -
84E THR* 2.7 25.9 + - - +
108E LEU* 4.1 22.9 - - + -
109E THR* 1.3 75.7 - - - +
111E LEU* 1.3 70.8 + - - +
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Residues in contact with LEU 111 (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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10E VAL* 4.2 10.8 - - + -
11E LEU 2.7 13.6 + - - +
12E LYS* 3.1 8.0 - - - +
13E THR* 2.8 26.2 + - - -
81E PRO* 5.3 0.4 - - - -
109E THR* 3.8 15.0 - - + -
110E VAL* 1.3 81.5 - - - +
112E GLU* 1.3 63.3 + - - +
113E ASP 3.5 20.1 + - - +
114E LEU* 4.3 4.0 - - + -
116E ASN* 4.6 5.4 - - + +
117E VAL* 3.5 32.3 - - + -
148E TYR* 3.7 35.0 - - + +
149E PRO* 5.6 0.4 - - + -
182E ASP* 4.8 11.0 - - - +
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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