Contacts of the strand formed by residues 218 - 228 (chain C) in PDB entry 6GR2
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 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C LEU* 3.6 29.2 - - + -
215C ASP* 2.7 32.6 + - + +
216C PRO 4.3 2.4 - - - +
217C LYS* 1.3 78.3 - - - +
219C ALA* 1.3 61.5 + - - +
220C VAL* 5.3 1.1 - - + -
295C LEU* 4.8 0.2 - - + -
300C TYR* 3.4 39.5 - - + +
339C TYR* 3.8 17.0 - - + -
355C LEU* 3.3 37.0 - - + -
356C LEU 3.5 15.3 - - - +
358C ALA* 4.2 2.4 - - - +
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Residues in contact with ALA 219 (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 LEU* 1.3 75.3 - - - +
220C VAL* 1.3 64.3 + - - +
221C LEU* 4.0 1.6 - - + +
354C THR 3.7 0.7 - - - +
355C LEU* 3.6 7.6 - - - +
356C LEU* 2.9 36.3 + - + +
357C GLU 4.6 1.8 - - - +
358C ALA* 3.7 22.6 - - + +
361C ALA* 4.8 6.7 - - + -
380C LEU* 4.6 18.4 - - + -
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 4.8 0.4 - - + -
40C LEU* 4.4 7.4 - - + -
55C MET* 3.9 24.5 - - + -
213C LEU* 4.7 19.5 - - + -
218C LEU* 5.3 1.3 - - + -
219C ALA* 1.3 72.9 - - - +
221C LEU* 1.3 59.2 + - - +
222C ILE* 3.8 8.5 + - + +
353C VAL* 3.8 27.1 - - + -
354C THR 3.5 3.1 - - - +
355C LEU* 3.6 24.9 - - + -
379C TYR 3.6 12.0 - - - +
380C LEU* 3.8 5.0 - - - +
381C SER 3.6 27.4 + - - +
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Residues in contact with LEU 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 ALA* 4.0 1.9 - - + -
220C VAL* 1.3 71.8 - - - +
222C ILE* 1.3 74.3 + - - +
223C THR* 3.9 13.9 - - - +
332C ALA* 6.4 0.9 - - + -
352C THR 3.4 3.3 - - - +
353C VAL* 3.4 0.7 - - - -
354C THR* 2.7 59.3 + - + +
356C LEU* 5.8 4.0 - - + -
361C ALA* 5.1 3.4 - - + +
364C ALA* 4.3 20.2 - - + -
365C MET* 4.0 21.1 - - + +
368C ILE* 5.8 2.2 - - + -
378C PHE* 3.8 24.9 - - + -
379C TYR 3.9 3.6 - - - +
380C LEU* 3.8 24.0 - - + -
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Residues in contact with ILE 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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38C VAL* 3.7 25.8 - - + -
57C LEU* 3.4 39.5 - - + -
139C LEU* 3.9 9.2 - - + -
220C VAL* 4.5 11.9 - - + +
221C LEU* 1.3 76.0 - - - +
223C THR* 1.3 62.8 + - - +
224C ASN 4.1 0.4 + - - -
351C CYS* 3.8 31.2 - - + -
352C THR 3.3 4.7 - - - +
353C VAL* 4.7 1.1 - - + -
377C THR 3.6 0.5 - - - +
378C PHE* 3.2 6.4 - - - -
379C TYR* 3.0 56.5 + - + +
381C SER* 4.6 7.2 - - - -
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Residues in contact with THR 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 LEU* 3.9 11.4 + - - +
222C ILE* 1.3 71.7 - - - +
224C ASN* 1.3 61.7 + - - +
225C SER 3.6 0.9 + - - -
328C LEU* 4.1 25.8 - - + +
351C CYS* 3.0 4.7 - - - -
352C THR* 2.6 53.4 + - - +
354C THR* 5.1 1.6 + - - -
368C ILE* 5.3 3.1 - - + +
376C ALA* 4.1 14.8 - - + -
377C THR 3.3 4.7 - - - +
378C PHE* 3.3 35.0 - - + -
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Residues in contact with ASN 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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134C PRO* 4.3 18.0 - - - +
137C GLY* 3.8 25.6 + - - +
222C ILE 4.1 1.0 + - - -
223C THR* 1.3 71.6 - - - +
225C SER* 1.3 63.6 + - - +
226C ASN* 2.6 45.2 + - - +
227C VAL 4.6 0.3 + - - +
350C GLY* 3.3 8.5 - - - +
351C CYS* 3.6 20.2 - - - -
376C ALA* 3.5 6.1 - - - +
377C THR* 2.8 42.8 + - - +
379C TYR* 4.7 8.6 + - + -
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Residues in contact with SER 225 (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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223C THR 3.6 2.6 + - - -
224C ASN* 1.3 71.7 - - - +
226C ASN* 1.3 68.6 + - - +
227C VAL* 3.1 19.6 + - - +
324C GLU* 4.7 4.7 - - - +
325C LEU* 4.4 8.1 - - - -
328C LEU* 3.7 21.0 - - - +
349C GLY* 4.0 3.5 - - - -
350C GLY 2.8 34.7 + - - -
372C TYR* 3.0 32.6 + - - -
375C THR 3.6 6.2 - - - +
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Residues in contact with ASN 226 (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 ASN* 2.6 45.8 + - - +
225C SER* 1.3 70.7 + - - +
227C VAL* 1.3 59.2 + - - +
375C THR* 3.1 29.6 + - - +
376C ALA* 3.8 0.2 - - - +
377C THR* 3.1 28.6 + - - +
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Residues in contact with VAL 227 (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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136C GLY 5.2 3.3 - - - +
224C ASN* 5.4 0.2 - - - +
225C SER* 3.0 23.2 + - - +
226C ASN* 1.3 80.8 - - - +
228C ARG* 1.3 66.5 + - - +
229C HIS* 4.0 18.8 - - + +
322C CYS* 5.4 1.3 - - - -
324C GLU* 3.8 30.7 - - + +
349C GLY* 3.5 6.6 - - - -
350C GLY* 3.3 23.6 + - - -
372C TYR* 3.5 14.4 - - - +
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Residues in contact with ARG 228 (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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136C GLY 4.9 10.8 - - - +
227C VAL* 1.3 78.3 - - - +
229C HIS* 1.3 63.5 + - - +
348C PHE 4.2 3.8 - - - -
349C GLY* 4.9 0.2 - - - -
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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