Contacts of the helix formed by residues 325 - 335 (chain C) in PDB entry 1XPU
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 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B GLU* 3.6 21.2 + - - +
336B LYS* 4.8 2.0 - - - -
272C ARG* 4.2 10.3 + - - -
323C THR* 3.5 6.2 - - - -
324C GLY* 1.3 79.0 - - - +
326C LYS* 1.3 66.6 + - - +
327C MET* 3.8 12.6 + - - +
328C ASP* 3.1 37.1 + - - +
329C GLU* 3.3 18.7 + - - +
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Residues in contact with LYS 326 (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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287C GLY* 4.1 19.3 - - - +
324C GLY 4.3 0.6 + - - -
325C SER* 1.3 73.7 + - - +
327C MET* 1.3 60.5 + - - +
329C GLU* 3.6 10.4 + - + +
330C VAL* 3.2 34.5 + - + +
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Residues in contact with MET 327 (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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286B THR* 6.0 6.1 - - - -
334B GLU* 5.8 2.9 - - - +
272C ARG* 3.8 42.0 - - + +
275C ASN* 3.7 23.3 - - + +
276C THR* 6.3 2.7 - - + -
287C GLY 4.0 7.1 + - - +
288C GLY* 4.0 30.5 - - - +
289C VAL* 4.3 8.9 - - + +
325C SER* 3.2 10.2 + - - +
326C LYS* 1.3 75.6 - - - +
328C ASP* 1.3 69.1 + - - +
330C VAL* 3.1 6.8 + - - +
331C ILE* 3.0 41.7 + - + +
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Residues in contact with ASP 328 (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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268C THR* 4.2 12.4 - - - +
269C ARG* 3.8 8.0 + - - -
272C ARG* 3.4 43.1 + - - +
320C LEU* 3.9 22.7 - - - +
321C ILE* 5.5 0.2 - - - +
323C THR* 3.4 30.4 + - - +
325C SER* 3.1 16.3 + - - +
327C MET* 1.3 75.4 - - - +
329C GLU* 1.3 61.7 + - - +
331C ILE* 3.6 9.6 + - - +
332C TYR* 3.3 22.3 + - - +
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Residues in contact with GLU 329 (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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321C ILE* 3.9 14.4 - - - +
322C ASP* 3.0 39.8 + - - +
323C THR* 3.4 8.7 + - - -
324C GLY* 4.1 4.8 + - - -
325C SER 3.3 17.6 - - - +
326C LYS* 3.9 13.7 - - + +
327C MET 3.2 1.0 - - - -
328C ASP* 1.3 78.1 - - - +
330C VAL* 1.3 63.1 + - + +
332C TYR* 3.7 7.8 + - - +
333C GLU* 3.3 25.2 + - - +
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Residues in contact with VAL 330 (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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286C THR* 3.8 24.5 - - + +
287C GLY* 4.8 5.8 - - - +
289C VAL* 3.6 27.4 - - + -
294C LEU* 5.4 1.6 - - + -
326C LYS* 3.2 23.4 + - + +
327C MET* 3.1 5.0 + - - +
329C GLU* 1.3 77.3 - - + +
331C ILE* 1.3 64.7 + - - +
333C GLU* 3.2 18.7 + - + +
334C GLU* 3.3 21.3 + - + +
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Residues in contact with ILE 331 (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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267C ILE* 4.6 1.6 - - + +
268C THR* 3.6 40.4 - - + +
271C ALA* 3.9 27.6 - - + -
272C ARG* 4.4 2.7 - - + +
289C VAL* 5.0 6.5 - - + -
294C LEU* 4.1 16.8 - - + -
327C MET* 3.0 47.8 + - + +
328C ASP* 3.8 9.6 - - - +
329C GLU 3.4 0.2 - - - -
330C VAL* 1.3 75.9 - - - +
332C TYR* 1.3 62.0 + - - +
334C GLU* 3.3 8.4 + - - +
335C PHE* 3.1 38.3 - - + -
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Residues in contact with TYR 332 (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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175C LEU* 4.2 13.7 - - + -
177C VAL* 3.5 26.8 - - + +
268C THR* 4.8 4.2 - - + +
319C ALA* 3.7 21.8 - - + -
320C LEU 5.3 0.2 - - - +
321C ILE* 3.5 36.5 - - + +
328C ASP 3.3 14.1 + - - +
329C GLU* 3.9 8.3 - - - +
330C VAL 3.3 0.2 - - - -
331C ILE* 1.3 78.8 - - - +
333C GLU* 1.3 63.8 + - + +
335C PHE* 3.4 5.5 + - + +
336C LYS* 3.2 56.0 + - + +
342C GLU* 4.4 4.7 + - - -
344C HIS* 3.5 26.0 - - - -
4701D FPD 4.8 5.0 - - - -
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Residues in contact with GLU 333 (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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329C GLU 3.3 16.1 + - - +
330C VAL* 3.2 16.5 + - + +
332C TYR* 1.3 79.7 - - + +
334C GLU* 1.3 63.1 + - + +
336C LYS* 2.8 54.2 + - - +
269D ARG* 5.3 0.5 + - - -
272D ARG* 4.7 11.1 + - - -
324D GLY 3.4 9.4 - - - +
325D SER* 3.2 31.6 + - - -
326D LYS 4.7 0.9 + - - -
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Residues in contact with GLU 334 (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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294C LEU* 3.6 29.8 - - + +
298C LYS* 2.8 49.0 + - - -
330C VAL* 3.3 12.5 + - + +
331C ILE 3.3 8.5 + - - +
333C GLU* 1.3 78.5 - - + +
335C PHE* 1.3 63.3 + - + +
336C LYS 3.3 2.4 - - - +
338C THR* 3.8 8.0 - - - +
269D ARG* 4.8 11.2 + - - +
272D ARG* 3.7 23.6 + - - +
276D THR* 5.9 2.8 - - - +
327D MET* 6.1 0.5 - - - +
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Residues in contact with PHE 335 (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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175C LEU* 4.3 22.1 - - + +
267C ILE* 3.7 28.3 - - + -
271C ALA* 5.0 0.2 - - + -
294C LEU* 4.5 11.0 - - + -
297C PRO* 3.6 37.7 - - + -
298C LYS* 3.9 19.1 - - + -
301C PHE* 3.9 28.7 - + + -
331C ILE* 3.1 42.1 + - + +
332C TYR* 3.4 7.6 + - + +
333C GLU 3.3 0.8 - - - -
334C GLU* 1.3 78.1 - - + +
336C LYS* 1.3 63.8 + - - +
337C GLY 3.2 2.3 + - - -
338C THR* 2.7 36.3 + - + +
339C GLY 4.4 0.5 + - - -
232D PHE* 5.7 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