Contacts of the strand formed by residues 241 - 245 (chain A) in PDB entry 4WPN
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ILE* 4.1 11.4 - - + -
162A VAL 3.4 1.6 + - - -
163A CYS* 3.3 15.3 - - + -
164A GLY 2.7 31.9 + - - -
239A ILE* 3.3 7.5 - - - +
240A ASP* 1.3 81.0 - - - +
242A VAL* 1.3 62.0 + - - +
243A ALA* 4.4 1.8 - - + +
264A LYS* 4.3 1.6 - - - -
265A ARG* 3.2 27.5 - - + +
267A THR* 3.5 31.9 + - - +
485A GLU* 2.6 45.5 + - - +
486A TYR* 3.7 36.1 - - + -
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY 3.1 9.4 - - - +
166A ILE* 4.2 10.5 - - + -
233A ILE* 4.1 20.2 - - + -
234A SER* 4.8 4.9 - - - -
239A ILE* 5.2 0.2 - - + -
241A LYS* 1.3 78.8 - - - +
243A ALA* 1.3 71.7 + - - +
244A PHE* 5.0 0.7 - - + -
254A ILE* 3.9 26.5 - - + -
258A ALA* 4.8 0.7 - - + -
264A LYS* 3.6 24.7 - - + -
265A ARG 2.9 9.1 + - - -
266A VAL* 3.4 23.2 - - + -
267A THR* 3.0 25.8 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY 2.8 9.4 + - - +
165A GLN* 3.4 2.8 - - + -
166A ILE* 2.8 27.7 + - - +
179A LYS* 4.2 21.3 - - + -
241A LYS* 4.4 2.4 - - - +
242A VAL* 1.3 77.1 - - - +
244A PHE* 1.3 62.3 + - - +
267A THR* 3.4 17.3 - - - +
477A GLU* 5.7 0.2 - - - +
486A TYR* 3.3 26.5 - - - +
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.6 37.0 - - + -
179A LYS* 4.5 2.6 + - - +
243A ALA* 1.3 76.6 - - - +
245A THR* 1.3 69.8 + - - +
246A GLY* 3.6 28.5 - - - -
247A SER 3.7 15.9 - - - -
250A VAL* 3.4 31.4 - - + -
251A GLY* 3.7 14.6 - - - -
254A ILE* 4.1 19.3 - - + -
267A THR 3.1 5.9 + - - -
268A LEU* 3.4 17.8 - - + -
269A GLU* 2.9 24.6 + - - +
270A LEU* 3.8 13.5 - - + -
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE 3.4 7.6 + - - +
167A ILE 4.6 0.3 - - - -
168A PRO* 3.5 46.4 - - + +
170A ASN* 5.6 2.5 - - - +
175A MET* 4.5 10.1 - - - -
179A LYS* 2.5 33.1 + - - -
244A PHE* 1.3 86.1 + - - +
246A GLY* 1.3 59.4 + - - +
269A GLU* 3.0 38.4 - - + +
303A CYS* 5.8 1.6 - - + -
477A GLU* 4.4 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