Contacts of the strand formed by residues 227 - 235 (chain C) in PDB entry 6RQT
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 TYR 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938B PHE* 3.8 15.2 - + + -
939B SER 3.0 18.7 - - - +
940B GLU* 3.1 13.0 - - - +
1014B TYR* 3.8 10.3 - - + -
64C ALA* 3.2 48.0 - - + -
67C PHE* 2.8 33.7 + - - +
68C ARG* 3.5 12.8 - - + -
71C MET* 6.2 0.7 - - + -
225C ALA* 3.4 16.4 - - + -
226C SER* 1.3 84.2 + - - +
228C ARG* 1.3 62.9 + - - +
229C LEU* 6.2 0.2 - - + -
298C PHE* 5.0 6.3 - + + -
299C ILE* 4.1 5.4 - - - +
300C PHE* 3.3 56.7 - + + -
301C ASN* 5.8 0.7 - - - -
302C VAL* 5.8 1.6 - - + -
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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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940B GLU* 3.4 44.6 + - + +
1014B TYR* 3.3 8.7 - - - +
227C TYR* 1.3 80.7 - - - +
229C LEU* 1.3 74.7 + - - +
231C PRO* 4.3 16.4 - - + +
271C ARG* 3.5 25.7 + - - +
273C ASP 3.1 25.9 + - - -
274C THR* 4.7 2.4 - - - +
275C VAL* 5.8 4.7 - - + -
293C ARG* 6.0 0.9 - - - +
298C PHE* 4.0 3.1 - - - +
299C ILE* 3.2 63.5 + - + +
301C ASN* 5.1 0.6 + - - -
172N ALA* 3.8 29.0 + - - +
173N THR 4.7 1.4 - - - +
174N GLY* 4.1 7.3 - - - +
175N TYR* 5.2 0.2 - - - -
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Residues in contact with LEU 229 (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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1014B TYR* 2.5 51.5 + - + +
1019B GLY 5.2 3.4 - - - +
1021B GLU* 4.4 11.4 - - + +
61C THR* 4.9 9.0 - - + -
227C TYR* 6.2 0.7 - - + -
228C ARG* 1.3 88.1 + - - +
230C LEU* 1.3 64.0 - - - +
231C PRO* 3.2 13.5 - - - +
293C ARG* 3.7 27.3 + - + +
294C VAL 3.4 19.1 - - - +
295C ARG* 3.7 23.1 - - + -
297C HIS 3.8 4.5 - - - -
298C PHE* 3.5 28.3 - - + -
299C ILE* 4.7 2.8 - - - +
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Residues in contact with LEU 230 (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 LEU* 1.3 72.9 - - - +
231C PRO* 1.3 78.0 - - + +
270C ALA* 3.8 26.5 - - + -
271C ARG* 3.9 19.5 - - + +
293C ARG* 3.6 4.1 - - - +
294C VAL* 3.0 39.7 + - + +
297C HIS* 3.0 64.3 + - + +
298C PHE* 5.0 0.2 - - - +
299C ILE* 5.4 3.8 - - + +
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Residues in contact with PRO 231 (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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228C ARG* 4.3 12.8 - - + +
229C LEU 3.2 10.5 - - - +
230C LEU* 1.3 105.0 - - + +
232C GLN* 1.3 60.0 + - - +
233C ILE* 3.7 6.7 + - + +
270C ALA* 4.3 20.0 - - - +
271C ARG* 4.8 0.4 - - - -
273C ASP* 4.1 25.6 - - - +
275C VAL* 3.6 31.9 - - + +
292C GLY 3.8 5.4 - - - +
293C ARG* 4.1 5.6 - - - +
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Residues in contact with GLN 232 (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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230C LEU 3.5 0.8 + - - -
231C PRO* 1.3 71.2 - - - +
233C ILE* 1.3 69.8 + - - +
234C ASN* 2.7 38.6 + - - +
291C LEU* 4.9 0.4 - - - -
292C GLY* 2.5 53.7 + - - +
293C ARG 3.7 2.0 - - - +
294C VAL* 3.6 33.9 - - + +
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Residues in contact with ILE 233 (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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231C PRO* 3.7 6.8 + - + +
232C GLN* 1.3 91.4 - - - +
234C ASN* 1.3 63.7 + - - +
235C ILE* 5.6 0.7 - - + -
247C PHE* 5.1 8.7 - - + -
251C PHE* 4.0 32.3 - - + -
255C VAL* 5.9 2.2 - - + -
256C ILE* 5.9 0.2 - - + -
267C VAL* 3.8 40.6 - - + -
270C ALA* 6.0 6.3 - - + -
273C ASP* 6.1 0.4 - - - +
279C VAL* 5.7 1.1 - - + -
289C VAL* 5.6 2.2 - - + -
290C LYS 3.5 16.4 - - - +
291C LEU* 3.7 19.3 - - + +
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Residues in contact with ASN 234 (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 GLN* 2.7 39.2 + - - +
233C ILE* 1.3 74.6 - - - +
235C ILE* 1.3 68.6 + - - +
289C VAL* 3.3 9.4 - - - +
290C LYS* 2.7 63.9 + - + +
291C LEU 4.1 6.1 - - - +
292C GLY* 4.2 4.0 - - - +
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Residues in contact with ILE 235 (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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233C ILE* 5.6 1.1 - - + -
234C ASN* 1.3 82.7 - - - +
236C LEU* 1.3 67.1 + - - +
237C GLN 4.2 9.9 - - - +
239C ILE* 5.7 5.4 - - + -
247C PHE* 4.5 15.3 - - + -
264C GLU* 3.5 29.2 - - + +
265C ALA 4.9 10.8 - - - +
266C TYR* 5.7 4.3 - - - -
267C VAL* 4.9 16.6 - - + -
288C LYS 3.8 0.9 - - - -
289C VAL* 3.7 21.8 - - + -
290C LYS* 5.2 2.0 + - - -
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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