Contacts of the strand formed by residues 242 - 248 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 2.7 32.9 - - - +
26C GLU* 3.2 10.7 + - - -
113C PHE* 6.2 3.8 - - - -
144C ASP* 3.1 27.1 + - - +
145C PHE 3.8 14.1 - - - +
146C PRO* 4.8 6.7 - - + -
230C GLY* 3.3 5.5 - - - -
231C ASN* 3.2 34.1 + - - +
232C LEU* 3.6 29.9 - - - +
241C MET* 1.3 79.9 - - - +
243C TYR* 1.3 65.1 + - - +
244C TRP* 3.2 25.6 - - - +
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ASP* 3.1 8.7 - - - +
145C PHE* 2.8 67.1 + + + +
146C PRO 4.2 1.3 - - - -
147C CYS* 3.7 39.7 - - + +
210C TYR 6.1 0.2 - - - -
212C PRO* 3.6 34.3 - - + +
228C ILE* 4.8 4.5 - - + -
229C TYR 3.3 4.9 - - - +
236C LEU* 4.1 23.1 - - + -
237C SER 5.8 0.2 - - - -
240C ASP* 2.9 37.3 + - + -
241C MET* 4.1 5.8 - - - -
242C ARG* 1.3 78.0 - - - +
244C TRP* 1.3 63.3 + - - +
245C ILE 4.3 0.2 - - - -
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Residues in contact with TRP 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLU* 4.1 12.6 - - + -
29C PHE* 3.6 31.7 - + + -
30C VAL* 4.5 10.5 - - + -
112C PHE* 3.8 31.6 - + - -
142C ILE* 3.6 23.3 - - + -
143C THR 3.4 4.5 - - - -
144C ASP* 3.6 27.8 - - + -
227C LYS 3.6 1.2 - - - +
228C ILE* 3.5 4.5 - - - +
229C TYR* 2.8 51.4 + - + +
230C GLY* 4.5 2.0 - - - -
231C ASN 4.9 0.4 - - - +
232C LEU* 3.9 28.3 - - + +
242C ARG* 3.2 46.4 + - - +
243C TYR* 1.3 78.9 - - - +
245C ILE* 1.3 63.5 + - - +
246C VAL* 4.0 3.9 + - + +
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PHE* 3.5 8.7 - - + +
142C ILE* 3.5 5.2 - - - +
143C THR* 2.9 41.1 + - + +
145C PHE* 3.2 29.6 - - + -
212C PRO 4.3 3.8 - - - +
215C VAL* 3.2 31.4 - - + -
216C ARG* 4.4 4.3 - - - +
219C ALA* 4.6 7.9 - - + -
226C VAL* 3.9 18.6 - - + -
227C LYS 3.5 1.6 - - - +
228C ILE* 3.5 35.4 - - + -
244C TRP* 1.3 75.5 - - - +
246C VAL* 1.3 66.4 + - - +
247C GLY 4.2 1.6 - - - +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.9 46.4 - - + -
37C ASP* 4.3 7.0 - - + -
140C VAL* 4.4 5.8 - - + -
141C PHE 3.2 7.2 - - - +
142C ILE* 4.4 6.5 - - + -
225C LYS 3.6 1.0 - - - +
226C VAL* 3.3 4.6 - - - -
227C LYS* 2.9 45.2 + - + +
229C TYR* 4.0 18.4 - - + -
244C TRP 4.7 2.9 - - - +
245C ILE* 1.3 80.8 - - - +
247C GLY* 1.3 63.1 + - - +
248C ILE* 3.9 20.7 + - + +
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Residues in contact with GLY 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLY 3.8 0.2 - - - +
140C VAL* 3.1 6.1 - - - +
141C PHE* 2.8 44.0 + - - +
223C PHE* 3.6 30.6 - - - -
225C LYS 3.5 5.4 - - - -
226C VAL* 4.5 3.4 - - - -
245C ILE* 4.2 2.1 - - - +
246C VAL* 1.3 72.8 - - - +
248C ILE* 1.3 61.1 + - - -
249C ALA 4.0 0.5 + - - -
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP* 3.2 48.9 - - + +
39C LYS* 4.3 17.5 - - + -
138C GLY 4.4 2.7 - - - +
139C GLY 3.6 8.3 - - - +
140C VAL* 4.0 10.1 - - + -
223C PHE* 4.0 3.0 - - - +
224C GLU* 3.5 7.2 + - - +
225C LYS* 2.7 59.9 + - + +
227C LYS* 4.5 8.1 - - + -
246C VAL* 4.1 10.3 - - + +
247C GLY* 1.3 75.7 - - - +
249C ALA* 1.3 73.4 + - - +
250C LYS 3.6 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