Contacts of the strand formed by residues 244 - 247 (chain E) in PDB entry 6DWZ
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 244 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173E ASP* 2.2 48.2 + - - +
174E GLY 5.3 0.2 - - - -
175E ALA 3.4 18.9 + - - +
176E SER* 3.5 3.1 - - - -
177E ALA 3.1 26.0 + - - +
242E SER 3.3 10.1 - - - -
243E ILE* 1.3 69.7 - - - +
245E PHE* 1.3 60.4 + - - +
246E VAL* 4.1 2.2 + - - +
261E ILE* 3.8 11.9 - - + -
263E ILE* 5.0 7.0 - - + -
428E TRP* 3.5 31.8 - - + -
457E LYS* 4.5 1.0 - - - +
560E SER* 3.3 23.7 + - - +
564E ILE* 3.4 39.2 - - + +
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Residues in contact with PHE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ALA* 3.4 28.9 - - + -
179E ILE* 4.3 11.0 - - + -
194E VAL* 5.5 0.2 - - + -
228E LEU* 4.2 24.2 - - + -
232E PHE* 4.0 16.6 - + - -
240E LEU* 4.8 3.4 - - + -
243E ILE* 3.2 46.0 - - + -
244E LYS* 1.3 71.4 - - - +
246E VAL* 1.3 54.5 + - - +
257E LEU* 3.6 29.6 - - + -
260E ASN* 3.7 29.8 - - + -
261E ILE 2.9 19.8 + - - +
262E ARG* 3.0 4.2 - - - -
263E ILE* 2.5 37.0 + - - +
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Residues in contact with VAL 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ALA 3.2 7.1 + - - +
178E THR* 3.3 39.6 + - - +
179E ILE* 3.7 3.1 + - - +
244E LYS 5.0 1.6 - - - +
245E PHE* 1.3 74.3 - - - +
247E THR* 1.3 68.8 + - - +
263E ILE* 3.4 19.3 - - + +
264E ASN 4.3 3.4 - - - +
265E CYS* 4.2 9.0 - - - -
564E ILE* 5.6 1.3 - - + -
565E PRO* 3.6 27.8 - - + -
566E ALA* 4.1 7.4 - - - +
567E SER* 3.7 31.6 - - - +
568E SER* 5.2 0.2 - - - -
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Residues in contact with THR 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ILE* 2.9 29.5 + - - +
246E VAL* 1.3 78.9 - - - +
248E ASP* 1.3 73.5 + - - +
253E VAL* 3.1 24.1 - - + +
257E LEU* 5.1 5.6 - - + -
262E ARG* 3.0 33.4 - - - +
263E ILE 3.0 4.9 + - - -
264E ASN* 3.3 6.2 - - - -
265E CYS* 2.5 35.5 + - - -
568E SER* 4.5 5.2 - - - -
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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