Contacts of the strand formed by residues 250 - 255 (chain C) in PDB entry 5MLE
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 250 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 4.8 5.4 - - + -
194C ILE* 4.9 0.7 - - - -
195C ALA* 3.5 21.1 - - + +
197C VAL* 4.0 26.2 - - + -
239C ALA* 3.6 32.8 - - + +
240C ILE* 3.6 22.9 - - + +
243C ALA* 3.7 18.6 - - + -
248C CYS 3.3 0.4 + - - -
249C PRO* 1.3 74.8 - - - +
251C TYR* 1.3 63.9 + - - +
252C ILE* 3.8 17.0 - - + -
272C THR* 6.4 0.2 - - + -
273C VAL* 3.1 12.7 + - - +
274C VAL* 3.3 9.8 - - + -
275C TYR* 3.0 28.1 + - - -
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Residues in contact with TYR 251 (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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72C VAL* 3.3 23.7 - - - +
194C ILE* 3.8 12.3 - - + -
195C ALA 3.0 12.9 + - - +
196C GLN* 3.2 30.5 - - + -
197C VAL* 3.1 24.9 + - - +
250C LEU* 1.3 77.0 - - - +
252C ILE* 1.3 63.1 + - - +
253C THR* 3.8 9.4 - - + -
275C TYR* 3.7 22.7 - + + -
277C GLU* 2.7 42.3 + - + +
328C VAL* 3.6 15.9 - - + +
391C VAL* 4.5 9.0 - - + -
392C PHE* 3.3 31.9 - + - -
608C NI 4.2 0.5 - - - +
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Residues in contact with ILE 252 (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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197C VAL* 4.3 13.7 - - + +
199C ALA* 4.4 8.3 - - + -
232C GLU* 5.5 2.7 - - + +
236C VAL* 3.9 36.8 - - + -
239C ALA* 4.9 2.9 - - + -
250C LEU* 3.8 29.8 - - + -
251C TYR* 1.3 77.9 - - - +
253C THR* 1.3 70.5 + - - +
255C VAL* 3.6 7.7 - - + +
260C SER* 6.0 0.2 - - - -
264C ILE* 3.8 25.8 - - + -
274C VAL* 4.0 9.4 - - + -
275C TYR 3.0 17.5 + - - +
277C GLU* 3.0 28.1 + - - +
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Residues in contact with THR 253 (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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73C HIS* 4.1 10.7 - - + +
165C LEU* 3.8 25.4 - - + +
196C GLN* 3.9 11.2 - - + +
197C VAL 2.8 25.4 + - - +
198C HIS* 3.8 9.5 - - - +
199C ALA* 5.1 4.0 + - - +
232C GLU* 5.2 0.5 - - - +
251C TYR* 3.6 20.8 + - + -
252C ILE* 1.3 84.1 - - - +
254C LYS* 1.3 76.3 + - - +
255C VAL 3.5 0.3 + - - -
277C GLU* 3.3 14.6 - - - +
305C PRO* 5.4 1.6 - - - +
608C NI 4.2 5.6 - - + -
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Residues in contact with LYS 254 (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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73C HIS* 3.3 32.1 - - + +
75C ARG* 4.9 10.5 - - - +
198C HIS* 4.4 12.8 + - + -
232C GLU* 3.4 6.4 - - - +
253C THR* 1.3 79.3 - - - +
255C VAL* 1.3 65.2 + - - +
256C MET* 3.2 18.1 + - + +
277C GLU* 2.9 18.1 + - - +
279C ILE* 4.2 16.6 - - + -
303C THR* 4.1 12.5 + - - -
304C SER 2.8 32.6 + - - +
305C PRO* 3.8 15.5 - - + +
332C ALA* 3.9 20.7 + - + +
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Residues in contact with VAL 255 (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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232C GLU* 3.6 4.9 - - - -
252C ILE* 3.6 15.9 - - + +
253C THR 4.4 0.2 - - - -
254C LYS* 1.3 68.8 - - - +
256C MET* 1.3 60.4 + - - +
257C SER 4.3 2.5 - - - +
260C SER* 3.7 16.2 - - - +
261C ALA* 4.1 26.5 - - + +
264C ILE* 3.9 20.2 - - + -
276C GLY* 4.0 1.8 - - - -
277C GLU 2.8 38.9 + - - +
278C PRO* 3.4 14.6 - - + +
282C SER* 2.9 22.7 + - - -
317C LEU* 4.0 7.3 - - + +
326C LEU* 4.5 6.3 - - + -
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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