Contacts of the strand formed by residues 219 - 224 (chain C) in PDB entry 5U07
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 VAL 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C THR* 1.3 77.9 - - + +
220C SER* 1.3 58.2 + - - +
221C TYR* 3.1 49.8 - - + +
313C LEU* 3.3 14.0 - - - +
314C ILE* 4.7 3.7 - - + +
326C ARG* 4.9 11.2 - - + +
328C ALA* 4.4 15.8 - - + +
332C ARG* 6.2 1.8 - - - +
337C ASP* 6.2 0.2 - - + -
376C ALA* 3.7 13.0 - - + -
377C PHE 2.9 23.8 - - - +
378C GLY* 3.6 10.5 - - - +
391C PHE* 4.6 8.7 - - + -
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Residues in contact with SER 220 (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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66C ALA* 3.3 29.5 - - - +
70C ARG* 4.3 12.6 - - - -
191C TYR* 5.1 2.9 - - - -
215C LEU* 5.5 0.7 - - - -
218C THR 3.8 1.6 + - - -
219C VAL* 1.3 71.1 - - - +
221C TYR* 1.3 60.6 + - - +
222C HIS* 3.6 20.0 + - - -
312C TYR* 4.4 2.7 - - - -
313C LEU* 3.6 16.1 - - - +
375C ARG 3.7 0.9 - - - +
376C ALA* 3.3 4.9 - - - -
377C PHE* 2.8 41.0 + - - +
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Residues in contact with TYR 221 (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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219C VAL* 3.1 49.2 - - + +
220C SER* 1.3 69.3 - - - +
222C HIS* 1.3 64.8 + - - +
223C PRO* 3.8 5.6 - - - +
312C TYR* 3.4 36.6 + - - +
314C ILE* 3.2 31.4 - - + +
334C ILE* 4.7 12.0 - - + +
337C ASP* 3.9 21.3 - - + +
338C LEU* 6.0 1.8 - - - -
341C LEU* 4.0 25.1 - - + -
352C PRO* 6.2 0.9 - - + -
354C ILE* 4.6 3.9 - - + +
355C LEU* 6.3 1.1 - - + -
374C LEU* 4.1 17.4 - - + +
375C ARG 3.3 4.5 - - - +
376C ALA* 3.2 23.8 - - + +
391C PHE* 5.9 0.5 - - - -
395C THR* 6.2 0.7 - - + -
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Residues in contact with HIS 222 (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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66C ALA* 3.8 14.3 + - - -
69C TRP* 3.4 47.4 - + + +
70C ARG* 4.4 0.9 - - + -
220C SER* 3.6 19.2 + - - -
221C TYR* 1.3 72.6 - - - +
223C PRO* 1.3 67.1 - - - +
224C LEU* 4.6 1.2 - - + +
235C ASN* 3.3 16.8 + - - +
312C TYR* 3.5 46.0 - + - -
374C LEU* 4.2 1.1 - - - -
375C ARG* 2.9 38.7 + - + +
377C PHE* 3.9 17.5 - + + -
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Residues in contact with PRO 223 (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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221C TYR 3.8 7.4 - - - +
222C HIS* 1.3 87.7 - - - +
224C LEU* 1.3 62.6 + - - +
231C SER* 3.9 14.5 - - - +
234C LEU* 4.1 31.2 - - + +
235C ASN* 3.6 16.8 + - - +
354C ILE* 4.4 15.0 - - + -
355C LEU* 5.0 14.1 - - + -
358C CYS* 5.2 4.3 - - + -
372C LEU* 4.3 20.9 - - + -
373C ARG 4.2 2.0 - - - +
374C LEU* 4.1 15.9 - - + -
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Residues in contact with LEU 224 (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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56C ASP* 4.8 12.3 - - + +
69C TRP* 4.7 16.8 - - + -
222C HIS* 4.6 0.9 - - + +
223C PRO* 1.3 77.0 - - - +
225C GLY* 1.3 65.4 + - - +
227C THR 5.2 2.7 - - - +
228C LEU* 5.8 0.7 - - - -
231C SER* 3.7 25.8 - - - +
234C LEU* 6.0 2.4 - - - +
235C ASN* 6.3 0.2 - - - +
372C LEU* 3.0 14.0 - - - +
373C ARG* 2.9 53.0 + - + +
374C LEU 5.4 0.2 - - - -
375C ARG* 4.1 34.3 - - + +
394C THR* 5.1 9.4 - - + -
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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