Contacts of the strand formed by residues 263 - 269 (chain C) in PDB entry 4G5S
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 SER 263 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C THR* 3.1 18.1 + - - +
220C ALA* 3.3 11.7 - - - +
221C ILE 2.9 28.9 + - - +
261C GLU 4.0 1.9 + - - -
262C THR* 1.3 70.8 - - - +
264C ILE* 1.3 62.5 + - - +
265C ILE* 4.7 3.1 - - - -
318C GLU 6.0 0.2 - - - -
320C TYR* 4.4 15.9 - - - -
342C VAL* 5.8 1.0 - - - +
343C ILE* 5.6 7.6 - - - +
346C ASN* 3.3 27.7 + - - +
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Residues in contact with ILE 264 (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 ILE* 4.0 28.0 - - + +
223C PHE* 5.8 1.8 - - + -
250C PHE* 3.8 32.1 - - + -
253C ILE* 4.5 13.2 - - + -
254C CYS* 4.0 24.2 - - - +
259C PHE* 4.7 10.1 - - + +
262C THR 3.4 15.5 + - - +
263C SER* 1.3 75.8 - - - +
265C ILE* 1.3 64.9 + - - +
318C GLU 4.4 8.3 + - - +
319C ILE* 3.8 12.3 - - + -
320C TYR* 2.9 30.3 + - - +
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Residues in contact with ILE 265 (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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36C LEU* 5.2 0.4 - - + -
220C ALA* 4.0 23.1 - - + -
221C ILE 2.9 13.5 + - - +
222C ILE* 3.4 14.8 - - + -
223C PHE* 2.7 34.1 + - - +
263C SER* 4.4 4.9 - - - +
264C ILE* 1.3 79.6 - - - +
266C LEU* 1.3 59.1 + - - +
267C PHE* 3.4 31.1 + - + -
320C TYR* 3.4 26.9 - - + +
322C HIS* 4.4 2.2 - - + -
339C VAL* 3.5 38.1 - - + -
342C VAL* 6.3 0.7 - - + -
343C ILE* 5.1 3.4 - - + -
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Residues in contact with LEU 266 (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 PHE* 3.5 34.1 - - + +
225C VAL* 3.9 6.7 - - + -
250C PHE* 4.1 14.8 - - + -
264C ILE 4.2 0.4 - - - -
265C ILE* 1.3 72.6 - - - +
267C PHE* 1.3 64.6 + - - +
268C LEU* 3.7 28.7 - - + -
304C GLN 5.1 2.9 - - - +
307C PHE* 3.7 31.4 - - + -
308C GLU* 5.2 0.9 - - + +
319C ILE* 4.4 12.3 - - + -
320C TYR 2.9 12.3 + - - +
321C THR* 3.6 21.0 - - + +
322C HIS* 2.9 28.8 + - - +
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Residues in contact with PHE 267 (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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49C ILE* 4.0 33.2 - - + -
222C ILE* 3.7 30.1 - - + -
223C PHE 2.7 14.3 + - - +
224C CYS* 4.2 11.7 - - + -
225C VAL* 2.8 26.7 + - - -
265C ILE* 3.4 23.6 - - + -
266C LEU* 1.3 78.8 - - - +
268C LEU* 1.3 64.5 + - - +
269C ASN* 2.9 6.3 + - + +
322C HIS* 3.7 6.7 - - + -
324C THR* 3.7 28.3 - - + +
332C VAL* 5.9 3.1 - - + -
335C VAL* 3.8 26.5 - - + -
336C PHE* 5.5 8.5 - + + -
339C VAL* 4.4 8.5 - - + -
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Residues in contact with LEU 268 (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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225C VAL* 3.6 22.2 - - + -
227C LEU* 3.3 29.4 - - + +
266C LEU* 3.7 31.9 - - + -
267C PHE* 1.3 68.4 - - - +
269C ASN* 1.3 61.4 + - - +
271C LYS* 4.4 0.5 - - - +
303C ILE* 4.4 11.2 - - + -
304C GLN* 3.8 32.8 - - + +
307C PHE* 4.8 4.3 - - + -
321C THR* 4.1 7.9 - - + -
322C HIS 2.9 14.5 + - - +
323C PHE* 3.8 29.3 - - + -
324C THR* 3.3 18.3 + - - +
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Residues in contact with ASN 269 (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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44C SER 3.4 23.5 + - - +
45C GLY* 4.0 1.8 - - - -
49C ILE* 5.6 2.4 - - - +
224C CYS* 5.2 1.3 - - + -
225C VAL 2.8 14.2 + - - +
226C ALA* 5.2 0.4 - - - +
227C LEU* 3.3 18.5 + - - +
267C PHE* 2.9 11.3 + - + +
268C LEU* 1.3 73.7 - - - +
270C LYS* 1.3 77.3 + - + +
271C LYS 3.2 2.4 + - - -
324C THR* 2.9 25.0 + - - +
326C ALA* 2.8 33.4 + - - +
401C GDP 3.0 34.7 + - - +
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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