Contacts of the strand formed by residues 240 - 244 (chain E) in PDB entry 1O04
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 LYS 240 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159E VAL* 3.9 20.0 - - + -
161E VAL 3.3 1.2 + - - -
162E CYS* 3.4 11.2 - - + -
163E GLY 2.8 25.3 + - - -
238E VAL* 3.3 7.7 - - - +
239E ASP* 1.3 80.2 - - - +
241E VAL* 1.3 76.9 + - - +
242E ALA* 4.0 4.9 - - + +
263E LYS* 4.3 1.6 - - - -
264E ARG* 3.2 20.8 - - + +
265E VAL 4.0 2.6 - - - +
266E THR* 2.8 41.5 + - - +
484E ALA* 3.6 28.9 - - - +
485E TYR* 3.8 34.3 - - + -
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Residues in contact with VAL 241 (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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163E GLY* 3.3 11.9 - - - +
165E ILE* 4.1 25.4 - - + -
232E ILE* 4.7 4.7 - - + -
233E ALA* 4.8 6.3 - - - -
238E VAL* 5.1 1.1 - - + -
240E LYS* 1.3 81.2 + - - +
242E ALA* 1.3 68.2 + - - +
243E PHE 4.1 0.7 - - - +
253E ILE* 3.9 25.6 - - + -
257E ALA* 4.8 1.1 - - + -
263E LYS* 3.8 20.6 - - + -
264E ARG 2.8 18.8 + - - +
265E VAL* 3.4 19.5 - - + -
266E THR 3.1 23.2 + - - +
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Residues in contact with ALA 242 (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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163E GLY 2.8 10.2 + - - +
164E GLN* 3.4 3.3 - - + -
165E ILE 3.0 25.1 + - - -
178E LYS* 3.6 19.6 - - + -
240E LYS* 4.0 5.8 - - + +
241E VAL* 1.3 75.8 - - - +
243E PHE* 1.3 59.7 + - - +
266E THR* 3.6 17.9 - - - +
476E GLU* 4.6 4.0 - - - +
485E TYR* 3.4 25.4 - - - +
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Residues in contact with PHE 243 (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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165E ILE* 3.6 20.2 - - + -
178E LYS* 4.7 0.4 - - - -
241E VAL* 4.7 2.7 - - + -
242E ALA* 1.3 73.9 - - - +
244E THR* 1.3 63.5 + - - +
245E GLY* 3.5 30.5 - - - -
246E SER 3.6 6.7 - - - -
249E ILE* 3.4 30.7 - - + -
250E GLY* 3.7 7.2 - - - -
253E ILE* 3.7 26.0 - - + -
266E THR 3.0 6.9 + - - +
267E LEU* 3.4 22.3 - - + -
268E GLU* 2.9 25.1 + - - +
269E LEU* 3.6 23.3 - - + -
476E GLU* 5.7 0.2 - - - +
6505E NAD 3.1 30.7 - - - -
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Residues in contact with THR 244 (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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165E ILE 3.0 11.8 + - - +
166E ILE* 4.7 1.1 - - - -
167E PRO* 3.4 29.2 - - + +
174E MET* 4.2 5.7 - - - -
178E LYS* 2.8 28.7 + - - -
243E PHE* 1.3 75.8 - - - +
245E GLY* 1.3 58.2 + - - +
268E GLU* 3.2 18.1 - - - +
476E GLU* 4.1 1.7 + - - -
6505E NAD 3.2 62.0 - - + +
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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