Contacts of the strand formed by residues 299 - 306 (chain C) in PDB entry 1XPM
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 THR 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C ASN* 4.3 2.6 + - - +
222C LYS* 5.6 5.6 - - - +
226C ASP 4.5 10.4 + - - -
227C PHE* 3.7 15.9 - - + -
228C ALA* 2.9 32.7 + - - +
297C GLY 4.2 4.5 + - - -
298C GLU* 1.3 76.8 - - - +
300C ILE* 1.3 73.6 + - - +
315C SER* 3.6 21.3 - - - +
316C ALA 3.4 13.5 - - - +
317C THR* 3.6 11.1 + - - -
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Residues in contact with ILE 300 (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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169C LEU* 4.1 21.3 - - + -
227C PHE* 3.7 2.7 - - - -
228C ALA* 5.5 0.2 - - + -
229C SER* 3.3 13.5 - - - +
231C CYS* 4.1 9.0 - - + -
285C LEU* 4.4 11.9 - - + -
288C LEU* 3.9 22.7 - - + -
289C LEU* 4.5 8.7 - - + -
294C LEU* 3.8 30.7 - - + -
299C THR* 1.3 77.5 - - - +
301C GLY* 1.3 67.5 + - - +
302C LEU* 3.5 19.8 - - + +
315C SER* 3.2 6.6 - - - -
316C ALA* 2.8 35.4 + - + +
318C LEU* 4.5 6.7 - - + -
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Residues in contact with GLY 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE* 3.4 22.3 - - - -
229C SER 3.0 10.6 + - - -
230C LEU* 3.0 9.7 - - - +
231C CYS 2.8 24.9 + - - +
300C ILE* 1.3 72.5 - - - +
302C LEU* 1.3 60.7 + - - -
313C PHE* 3.8 15.7 - - - -
314C TYR 3.7 4.7 - - - -
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Residues in contact with LEU 302 (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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169C LEU* 5.9 0.2 - - + -
231C CYS* 3.1 13.0 - - + +
281C LEU* 4.4 14.4 - - + -
282C TYR* 4.8 0.7 - - + -
285C LEU* 4.2 32.1 - - + -
300C ILE* 3.5 31.6 - - + +
301C GLY* 1.3 75.6 - - - +
303C PHE* 1.3 60.1 + - - +
304C SER 4.2 0.2 - - - -
312C GLU 3.6 1.1 - - - +
313C PHE* 3.2 10.7 - - - -
314C TYR* 2.7 83.3 + - + +
316C ALA* 4.1 15.5 - - + +
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TYR* 4.3 16.2 - + - -
208C SER* 3.6 13.7 - - - -
209C PHE* 3.4 68.6 - + + -
212C SER* 3.7 15.9 - - - -
231C CYS 3.0 7.5 + - - -
232C PHE* 3.4 17.4 - + + -
233C HIS 3.3 24.1 + - - -
281C LEU* 3.8 5.3 - - - +
301C GLY 4.3 0.2 + - - -
302C LEU* 1.3 74.7 - - - +
304C SER* 1.3 73.7 + - - +
305C TYR* 3.7 20.6 - + + -
311C GLY* 3.8 1.1 - - - -
312C GLU 3.3 24.2 - - - -
313C PHE* 4.1 6.1 - - + -
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Residues in contact with SER 304 (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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111C SCY 4.3 3.5 + - - -
112C TYR* 3.5 23.0 + - - -
115C THR* 2.6 37.5 + - - -
233C HIS* 4.8 1.1 - - - -
281C LEU* 3.6 15.9 - - - +
282C TYR* 5.1 0.7 - - - -
302C LEU 4.2 0.6 - - - -
303C PHE* 1.3 78.8 - - - +
305C TYR* 1.3 60.8 + - - +
311C GLY* 3.2 4.9 - - - -
312C GLU 2.9 34.7 + - - -
314C TYR* 5.0 1.8 - - - -
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Residues in contact with TYR 305 (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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111C SCY 3.1 29.1 + - - +
112C TYR* 3.8 4.0 - - - -
184C ASP* 2.9 21.1 + - - -
204C ALA* 3.4 17.3 - - - +
205C TYR* 3.5 37.2 - + + -
208C SER* 3.5 37.9 - - - -
233C HIS* 4.1 12.7 - + + +
303C PHE* 3.7 14.6 - + + -
304C SER* 1.3 76.2 + - - +
306C GLY* 1.3 72.4 + - - +
307C SER* 3.7 20.6 - - - -
309C SER* 3.3 24.4 - - - -
310C VAL 3.6 4.7 - - - -
3402C CAA 3.7 20.4 - - + -
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Residues in contact with GLY 306 (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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109C GLU* 3.5 4.7 - - - -
111C SCY 3.3 9.6 - - - -
112C TYR* 3.6 20.8 - - - +
305C TYR* 1.3 79.4 - - - +
307C SER* 1.3 69.3 + - - -
309C SER* 3.1 4.7 - - - -
310C VAL 2.9 30.8 + - - +
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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