Contacts of the strand formed by residues 238 - 244 (chain C) in PDB entry 5IWM
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 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C ARG* 3.2 15.8 - - - +
233C ALA* 3.8 4.9 + - - -
236C THR* 2.9 21.0 + - - +
237C GLY* 1.3 85.5 - - - +
239C GLY* 1.3 58.8 + - - +
333C VAL 3.3 8.8 + - - +
334C ASN* 3.6 37.5 + - - +
345C LEU* 4.2 17.7 - - + -
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Residues in contact with GLY 239 (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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229C GLY 4.2 15.0 - - - -
232C ARG* 4.5 9.4 - - - -
233C ALA* 4.2 2.9 - - - -
238C ARG* 1.3 77.9 - - - +
240C SER* 1.3 61.8 + - - -
331C PHE 3.7 0.5 - - - +
332C GLY* 3.7 1.8 - - - -
333C VAL* 2.8 35.8 + - - +
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Residues in contact with SER 240 (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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229C GLY* 3.3 20.8 + - - -
232C ARG* 5.1 6.3 + - - +
239C GLY* 1.3 72.7 - - - -
241C ILE* 1.3 60.4 + - - +
242C GLN* 3.2 27.4 + - - +
330C SER* 3.9 8.8 + - - -
331C PHE 3.9 3.3 - - - -
332C GLY* 4.6 3.9 - - - -
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Residues in contact with ILE 241 (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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184C PRO* 5.1 0.4 - - + -
216C PRO* 3.7 26.7 - - + -
218C PHE* 5.3 2.0 - - + -
224C ILE* 3.6 38.8 - - + -
229C GLY* 3.8 19.3 - - - +
230C ILE* 3.9 20.4 - - + +
233C ALA* 4.7 1.8 - - + -
234C TYR* 6.2 0.7 - - + -
240C SER* 1.3 76.5 + - - +
242C GLN* 1.3 65.7 + - - +
243C MET* 3.5 5.5 + - + -
330C SER* 3.3 1.3 - - - -
331C PHE* 2.7 50.5 + - + +
333C VAL* 3.8 24.5 - - + -
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Residues in contact with GLN 242 (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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224C ILE* 3.5 5.4 - - - +
225C LEU* 3.1 56.2 + - + +
240C SER* 3.2 28.9 + - - +
241C ILE* 1.3 72.4 - - - +
243C MET* 1.3 61.9 + - - +
328C GLN* 3.9 19.5 + - - +
329C THR 4.2 2.0 - - - -
330C SER* 3.3 23.5 + - - -
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Residues in contact with MET 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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218C PHE* 3.8 37.5 - - + -
223C LEU 3.4 7.6 - - - +
224C ILE* 4.8 0.7 - - + +
241C ILE* 4.2 9.9 - - + +
242C GLN* 1.3 75.0 - - - +
244C ARG* 1.3 62.3 + - - +
265C PRO* 4.1 13.2 - - + -
266C PHE* 3.8 37.9 - - - +
328C GLN* 3.3 12.6 - - - +
329C THR* 2.8 61.8 + - + +
330C SER 4.0 2.9 - - - +
331C PHE* 3.9 24.0 - - + +
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Residues in contact with ARG 244 (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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222C GLY* 3.8 3.5 - - - -
223C LEU* 2.9 47.5 + - + +
225C LEU* 3.8 37.4 - - + +
243C MET* 1.3 78.5 - - - +
245C SER* 1.3 62.0 + - - +
265C PRO* 4.5 6.9 - - - +
319C ASN* 4.9 6.9 + - - +
322C TYR* 3.4 56.5 - - + +
327C LEU 3.8 3.8 - - - -
328C GLN* 2.9 28.0 + - + +
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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