Contacts of the strand formed by residues 243 - 250 (chain C) in PDB entry 1ML3
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 LEU 243 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 5.3 3.6 - - + -
175C VAL* 4.4 13.0 - - + -
185C VAL* 3.9 19.3 - - + -
188C GLY* 3.2 29.6 - - - +
229C ALA* 4.0 14.6 - - + +
230C LYS* 3.8 21.5 + - - +
232C VAL* 4.0 24.2 - - + -
233C GLY 5.2 0.2 - - - +
239C THR* 3.6 35.8 + - + +
241C GLY* 3.6 4.5 + - - +
242C LYS* 1.3 90.8 + - - +
244C THR* 1.3 62.7 + - - +
260C LEU* 4.8 10.3 - - + -
320D LEU* 3.7 3.6 - - - +
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Residues in contact with THR 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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188C GLY 3.4 3.1 + - - +
189C LEU* 3.2 33.7 - - + -
190C MET 3.0 18.7 + - - -
226C THR 5.3 2.1 + - - -
229C ALA* 3.3 13.7 - - - +
230C LYS* 4.1 17.4 - - - +
243C LEU* 1.3 75.2 - - - +
245C GLY* 1.3 64.3 + - - +
318D ASN* 3.8 10.7 - - - +
319D ASN 3.7 27.0 + - - -
320D LEU* 3.8 10.5 - - + +
321D PRO* 5.6 2.7 - - - +
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Residues in contact with GLY 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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189C LEU* 5.0 1.1 - - - -
190C MET* 2.9 21.5 - - - -
226C THR* 3.5 24.4 + - - +
229C ALA* 3.6 4.8 - - - +
244C THR* 1.3 85.8 + - - +
246C MET* 1.3 62.2 + - - +
318D ASN* 3.9 15.7 - - - +
328D LYS* 5.1 2.2 - - - -
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Residues in contact with MET 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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190C MET* 2.9 13.9 + - - +
191C THR* 3.3 17.3 - - - +
192C THR 3.0 21.1 + - - -
223C PRO* 4.2 13.5 - - + -
224C SER 3.5 7.0 - - - +
226C THR* 3.6 9.0 - - - -
245C GLY* 1.3 75.0 - - - -
247C SER* 1.3 71.4 + - - +
248C PHE* 3.7 29.8 - - + -
314D ALA* 4.3 10.1 - - + +
318D ASN* 3.5 34.5 - - + +
328D LYS* 3.7 28.0 - - - -
330D VAL* 3.7 13.9 - - - -
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Residues in contact with SER 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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192C THR* 3.5 23.7 + - - +
194C HIS* 3.7 2.3 - - - +
223C PRO* 3.5 2.3 - - - +
224C SER* 2.8 40.6 + - - +
226C THR* 4.5 7.2 - - - -
246C MET* 1.3 78.9 - - - +
248C PHE* 1.3 79.3 + - - +
249C ARG* 3.6 15.0 - - - -
2166C CYX 3.2 22.6 + - - -
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Residues in contact with PHE 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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191C THR* 3.4 32.5 - - + -
192C THR 2.9 7.7 + - - +
193C ILE* 3.6 6.6 - - - -
194C HIS 2.8 23.7 + - - +
221C ILE* 4.1 23.6 - - + -
222C ILE 3.4 4.0 - - - -
223C PRO* 4.0 26.7 - - + -
246C MET* 3.7 29.2 - - + -
247C SER* 1.3 80.1 + - - +
249C ARG* 1.3 64.1 + - - +
250C VAL* 3.3 6.8 + - + +
193D ILE* 4.2 18.6 - - + -
257D VAL* 4.1 24.9 - - + -
259D ASP* 4.2 9.2 - - + -
330D VAL* 4.1 17.3 - - + -
332D TRP* 4.8 1.1 - + - -
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Residues in contact with ARG 249 (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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194C HIS* 3.0 18.6 - - - +
195C SER 3.9 3.5 + - - +
196C TYR* 4.8 0.9 - - + -
197C THR* 3.2 31.9 + - - +
199C THR* 4.3 8.1 + - - -
200C GLN* 2.6 59.8 - - - +
213C GLY* 6.6 0.4 - - - -
217C ALA 5.3 1.1 - - - +
220C ASN 3.7 2.8 - - - +
221C ILE* 3.5 3.8 - - - -
222C ILE* 2.7 51.2 + - + +
224C SER* 4.7 16.1 + - - -
247C SER* 3.6 13.6 + - - +
248C PHE* 1.3 70.5 - - - +
250C VAL* 1.3 59.6 + - - +
2166C CYX 3.2 37.1 + - - +
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Residues in contact with VAL 250 (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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193C ILE* 3.6 28.7 - - + -
194C HIS 2.5 21.1 + - - +
195C SER* 3.8 0.2 - - - -
196C TYR* 3.4 21.1 + - - -
217C ALA 4.5 1.6 - - - -
220C ASN 4.4 0.9 - - - -
221C ILE* 4.2 15.0 - - + -
248C PHE* 3.7 8.5 - - + +
249C ARG* 1.3 79.4 - - - +
251C PRO* 1.3 62.1 - - + +
252C THR* 2.8 22.6 + - + +
193D ILE* 4.1 13.5 - - + -
221D ILE* 3.9 20.0 - - + -
250D VAL* 4.1 17.0 - - + -
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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