Contacts of the strand formed by residues 242 - 248 (chain A) in PDB entry 1WZN
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 ARG 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 4.2 14.2 - - - +
26A GLU* 2.8 38.1 + - - +
113A PHE* 6.1 3.1 - - - -
114A SER* 6.0 1.3 - - - -
144A ASP* 3.2 20.9 + - - +
145A PHE 3.7 15.5 - - - +
146A PRO* 4.4 6.3 - - + -
230A GLY* 3.4 5.9 - - - -
231A ASN* 3.3 34.0 + - - +
232A LEU* 3.9 19.6 - - - +
241A MET* 1.3 78.7 - - - +
243A TYR* 1.3 70.2 + - - +
244A TRP* 3.2 31.5 - - - +
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Residues in contact with TYR 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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144A ASP* 3.1 8.3 - - - +
145A PHE* 2.8 68.0 + + + +
146A PRO 4.2 2.0 - - - -
147A CYS* 3.5 39.6 - - - +
212A PRO* 3.6 33.4 - - + -
228A ILE* 4.7 5.8 - - + -
229A TYR 3.4 4.7 - - - +
236A LEU* 4.0 22.4 - - + -
240A ASP* 2.9 37.7 + - + -
241A MET* 4.1 4.3 - - - -
242A ARG* 1.3 76.4 - - - +
244A TRP* 1.3 65.4 + - - +
245A ILE 4.3 0.2 - - - -
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Residues in contact with TRP 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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26A GLU* 4.5 12.1 - - + -
29A PHE* 3.6 32.1 - + + -
30A VAL* 4.4 10.8 - - + -
112A PHE* 3.8 30.7 - + - -
142A ILE* 3.5 24.2 - - + -
143A THR 3.4 4.5 - - - -
144A ASP* 3.6 33.4 - - + +
227A LYS 3.6 1.0 - - - +
228A ILE* 3.3 5.9 - - - +
229A TYR* 2.8 46.5 + - + +
230A GLY* 4.6 0.2 - - - -
231A ASN* 4.8 1.0 - - - +
232A LEU* 3.9 31.0 - - + +
242A ARG* 3.2 34.5 - - - +
243A TYR* 1.3 81.2 - - - +
245A ILE* 1.3 64.7 + - - +
246A VAL* 4.0 6.7 + - + -
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Residues in contact with ILE 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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128A PHE* 5.7 0.2 - - + -
141A PHE* 3.6 8.9 - - + +
142A ILE* 3.5 5.0 - - - +
143A THR* 2.9 40.7 + - + +
145A PHE* 3.3 27.4 - - + -
212A PRO 4.1 5.6 - - - +
215A VAL* 3.3 31.4 - - + -
216A ARG* 4.4 3.8 - - - +
219A ALA* 4.5 9.4 - - + -
226A VAL* 3.8 19.7 - - + -
227A LYS 3.4 0.7 - - - -
228A ILE* 3.5 34.8 - - + -
244A TRP* 1.3 75.1 - - - +
246A VAL* 1.3 64.5 + - - +
247A GLY* 4.8 1.6 - - - +
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Residues in contact with VAL 246 (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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33A ILE* 3.8 45.8 - - + -
37A ASP* 4.3 15.7 - - + -
140A VAL* 4.5 5.2 - - + -
141A PHE 3.2 7.4 - - - +
142A ILE* 4.4 6.3 - - + -
225A LYS 3.8 0.7 - - - +
226A VAL* 3.2 5.3 - - - +
227A LYS* 2.8 46.3 + - + +
229A TYR* 3.9 19.3 - - + -
244A TRP* 4.8 1.8 - - + +
245A ILE* 1.3 81.9 - - - +
247A GLY* 1.3 63.0 + - - +
248A ILE* 4.0 13.3 + - + +
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Residues in contact with GLY 247 (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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139A GLY 3.9 0.3 - - - +
140A VAL* 3.2 6.8 - - - +
141A PHE* 2.8 43.3 + - - +
223A PHE* 3.7 29.7 - - - -
225A LYS 3.6 4.9 - - - -
226A VAL* 4.5 3.6 - - - -
245A ILE* 4.1 2.1 - - - +
246A VAL* 1.3 73.6 - - - +
248A ILE* 1.3 62.1 + - - -
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Residues in contact with ILE 248 (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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37A ASP* 3.6 37.2 - - + +
39A LYS* 4.3 14.8 - - + -
138A GLY 4.3 8.1 - - - +
139A GLY 3.6 8.5 - - - +
140A VAL* 4.1 8.7 - - + -
223A PHE* 3.9 3.5 - - - +
224A GLU* 3.1 24.1 + - - +
225A LYS* 2.8 40.8 + - + +
227A LYS* 4.4 21.5 - - + -
246A VAL* 4.3 8.3 - - + +
247A GLY* 1.3 75.7 - - - +
249A ALA* 1.3 73.3 + - - +
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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