Contacts of the strand formed by residues 110 - 119 (chain E) in PDB entry 1PF7
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 THR 110 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E GLN 3.2 4.3 + - - -
27E VAL* 3.6 6.2 - - + -
28E ALA 3.0 11.9 + - - -
108E VAL* 3.0 21.3 - - - +
109E ASP* 1.3 93.3 + - - +
111E LEU* 1.3 64.7 + - - +
112E VAL 4.3 0.2 - - - -
233E LEU* 4.4 1.1 - - - -
234E ARG* 2.9 48.6 + - + +
236E PHE* 4.0 22.7 - - + -
282E ILE* 3.4 22.1 - - + +
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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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28E ALA* 3.3 24.7 - - + +
30E ILE* 3.5 32.8 - - + -
100E VAL* 4.7 6.1 - - + -
103E PHE* 4.4 7.0 - - + -
110E THR* 1.3 76.0 - - - +
112E VAL* 1.3 61.0 + - - +
113E VAL* 3.4 26.7 - - + -
224E GLU* 4.3 9.6 - - + +
228E ALA* 3.6 24.2 - - + -
233E LEU* 3.9 16.6 - - + -
234E ARG 2.7 11.6 + - - +
235E VAL* 3.4 14.6 - - + +
236E PHE* 3.3 24.1 + - - +
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Residues in contact with VAL 112 (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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27E VAL* 3.8 14.8 - - + -
28E ALA 2.9 4.7 + - - +
29E ILE* 3.4 31.1 - - + +
30E ILE 3.1 23.6 + - - -
111E LEU* 1.3 72.7 - - - +
113E VAL* 1.3 63.3 + - - +
114E THR* 4.2 15.9 - - + -
236E PHE* 3.2 36.6 - - + +
238E PHE* 4.6 2.9 - - + -
275E VAL* 4.1 22.7 - - + -
279E MET* 4.1 11.7 - - + -
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Residues in contact with VAL 113 (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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30E ILE* 3.8 11.2 - - + -
84E ARG* 4.1 13.2 - - - +
111E LEU* 3.4 33.2 - - + -
112E VAL* 1.3 73.0 - - - +
114E THR* 1.3 62.2 + - - +
132E ILE* 4.6 3.4 - - + -
166E TYR* 4.8 1.8 - - + -
221E THR* 3.4 28.9 - - + -
224E GLU* 4.6 3.6 - - + -
225E VAL* 4.1 16.6 - - + -
235E VAL* 4.7 2.5 - - + -
236E PHE 3.2 6.0 + - - +
237E GLY* 2.9 14.9 - - - +
238E PHE 2.9 25.0 + - - +
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Residues in contact with THR 114 (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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29E ILE* 5.0 5.4 - - + -
30E ILE 2.9 15.2 + - - +
31E CYS* 3.1 6.2 - - - -
32E GLY 2.9 22.8 + - - -
35E LEU* 3.7 17.2 - - + +
38E LEU* 5.3 3.7 - - + +
84E ARG* 2.6 30.7 + - - -
112E VAL* 4.2 9.9 - - + -
113E VAL* 1.3 80.4 - - - +
115E ASN* 1.3 56.0 + - - +
221E THR* 4.5 0.4 - - - -
238E PHE* 3.2 12.3 - - + +
271E LEU* 4.5 7.9 - - + -
275E VAL* 4.1 26.2 - - + -
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Residues in contact with ASN 115 (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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32E GLY* 3.9 3.6 - - - -
35E LEU* 3.8 7.7 - - - +
84E ARG* 3.8 3.4 - - - +
114E THR* 1.3 74.5 - - - +
116E ALA* 1.3 58.5 + - - +
117E ALA* 3.7 2.8 - - - +
132E ILE* 3.6 13.0 - - - +
192E TYR* 3.4 26.7 - - - +
220E SER* 3.9 6.1 - - - +
221E THR* 2.7 27.8 + - - +
238E PHE 3.2 5.2 + - - +
239E SER* 2.6 33.5 + - - -
240E LEU* 2.7 33.4 + - - +
293E SO4 3.3 12.3 - - - +
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Residues in contact with ALA 116 (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 SER* 4.1 21.3 - - - +
115E ASN* 1.3 75.1 + - - +
117E ALA* 1.3 62.1 + - - +
218E GLY* 4.4 2.9 - - - -
240E LEU* 3.2 8.7 - - + -
242E THR* 3.4 23.6 - - + +
290E IMH 3.0 40.6 - - - +
293E SO4 2.7 11.1 + - - +
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Residues in contact with ALA 117 (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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115E ASN* 3.7 5.2 - - - +
116E ALA* 1.3 76.3 - - - +
118E GLY* 1.3 60.7 + - - +
192E TYR* 3.9 9.9 - - + -
216E ALA* 3.9 12.1 - - + -
217E VAL 3.3 13.9 - - - +
239E SER* 3.0 25.4 - - - +
240E LEU 2.9 7.1 + - - -
241E ILE* 3.4 7.5 - - + -
242E THR* 2.9 26.6 + - - -
290E IMH 3.8 7.4 - - - -
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Residues in contact with GLY 118 (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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117E ALA* 1.3 74.7 - - - +
119E GLY* 1.3 63.5 + - - -
216E ALA* 3.2 9.0 - - - +
217E VAL* 2.9 37.4 + - - +
241E ILE* 4.4 1.1 - - - -
243E ASN* 3.3 21.5 - - - -
245E VAL* 4.3 3.1 - - - -
290E IMH 3.8 11.8 + - - -
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Residues in contact with GLY 119 (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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118E GLY* 1.3 70.3 - - - -
120E LEU* 1.3 57.3 + - - -
121E ASN 4.4 0.4 - - - -
124E PHE* 4.5 5.4 - - - -
215E ASP 3.9 4.0 - - - -
241E ILE* 3.7 12.6 - - - +
243E ASN 2.8 17.9 + - - -
244E LYS* 3.3 28.5 + - - +
245E VAL* 3.1 28.0 + - - +
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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