Contacts of the helix formed by residues 373 - 388 (chain F) 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 THR 373 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F ARG* 6.0 1.5 - - - +
372F THR* 1.3 76.1 - - - +
374F GLN* 1.3 54.0 + - - +
375F GLU* 4.2 7.8 + - - +
376F GLU* 2.9 25.1 + - - +
377F LEU* 2.6 36.4 + - - +
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Residues in contact with GLN 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F THR 4.1 0.6 + - - -
373F THR* 1.3 72.6 - - - +
375F GLU* 1.3 60.5 + - - +
377F LEU* 4.2 15.0 - - + -
378F GLN* 3.2 39.9 + - + +
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Residues in contact with GLU 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F THR* 3.2 8.8 + - - +
374F GLN* 1.3 78.8 - - - +
376F GLU* 1.3 57.9 + - - +
378F GLN* 4.5 2.6 - - - +
379F LYS* 3.3 45.5 + - - +
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Residues in contact with GLU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ARG* 4.1 5.2 + - - -
146F ARG* 3.0 39.8 + - - -
164F LEU* 5.3 2.8 - - - +
372F THR* 3.5 21.8 - - - +
373F THR* 2.9 21.6 + - - +
375F GLU* 1.3 80.1 - - - +
377F LEU* 1.3 58.6 + - - +
378F GLN 3.3 0.7 - - - -
379F LYS* 3.3 7.7 + - + +
380F MET* 2.9 37.7 + - + +
409F ASN* 4.7 14.9 + - - +
412F PHE* 4.1 25.4 - - + -
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Residues in contact with LEU 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F GLU* 3.8 12.3 - - + +
369F GLU* 3.7 35.4 - - + +
372F THR* 3.6 23.1 - - - +
373F THR 2.6 21.9 + - - +
374F GLN* 4.1 15.3 - - + +
376F GLU* 1.3 70.7 - - - +
378F GLN* 1.3 66.4 + - + +
380F MET* 3.2 10.2 + - + +
381F TRP* 3.0 44.1 + - + +
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Residues in contact with GLN 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F GLN* 3.2 27.2 + - + +
375F GLU* 4.7 3.4 - - - +
377F LEU* 1.3 81.0 - - + +
379F LYS* 1.3 61.7 - - + +
381F TRP* 3.4 4.7 + - - +
382F ILE* 3.0 40.8 + - + +
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Residues in contact with LYS 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375F GLU* 3.3 34.6 + - - +
376F GLU* 3.3 11.5 + - + +
378F GLN* 1.3 78.3 - - + +
380F MET* 1.3 61.3 + - - +
382F ILE* 3.6 7.9 + - - +
383F LEU* 3.3 15.9 + - - +
409F ASN* 3.9 15.3 + - - +
412F PHE* 3.2 59.5 + - + +
413F PHE* 3.5 31.5 - - - -
416F MET* 4.9 18.2 - - + +
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Residues in contact with MET 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ARG* 5.0 0.7 - - - -
163F ASP 4.2 13.5 - - - +
164F LEU* 4.0 25.8 - - + +
167F PRO* 4.0 6.3 - - + -
360F TYR* 4.5 5.3 + - - -
368F GLU* 3.9 33.2 - - + +
372F THR* 3.7 33.9 - - + +
376F GLU* 2.9 23.0 + - + +
377F LEU* 3.2 12.7 + - + +
379F LYS* 1.3 76.4 - - - +
381F TRP* 1.3 60.3 + - + +
383F LEU* 3.2 6.9 + - - +
384F ARG* 3.1 27.4 + - - +
412F PHE* 3.6 22.9 - - + -
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Residues in contact with TRP 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F THR 6.1 0.9 - - - -
368F GLU* 2.8 36.0 + - + +
377F LEU* 3.0 33.4 + - + +
378F GLN* 4.3 3.6 - - - +
380F MET* 1.3 74.7 - - + +
382F ILE* 1.3 63.3 + - + +
384F ARG* 3.8 30.8 - - + +
385F LYS* 2.8 59.3 + - + +
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Residues in contact with ILE 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378F GLN* 3.0 37.6 + - + +
379F LYS* 3.7 9.2 - - - +
381F TRP* 1.3 76.3 - - + +
383F LEU* 1.3 58.4 + - - +
384F ARG 3.1 3.8 - - - -
385F LYS* 3.0 31.4 + - + +
386F ILE* 3.1 26.4 + - + +
416F MET* 4.1 28.7 - - + -
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Residues in contact with LEU 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU* 4.4 7.9 - - + -
360F TYR* 3.7 15.5 - - + +
379F LYS 3.3 8.5 + - - +
380F MET* 3.2 9.7 + - - +
382F ILE* 1.3 78.9 - - - +
384F ARG* 1.3 57.9 + - - +
386F ILE* 3.3 34.3 - - + +
387F ILE* 3.4 35.3 - - + +
398F PHE* 6.0 0.9 - - + -
399F LEU* 4.1 16.4 - - + -
411F ASP* 3.6 25.1 - - - +
412F PHE* 3.8 23.1 - - + -
415F MET* 5.0 14.1 - - + -
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Residues in contact with ARG 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU 3.6 6.1 + - - -
165F ALA* 3.2 26.4 + - - +
360F TYR* 3.5 51.8 + - + -
361F ASN* 4.4 6.7 + - - +
363F SER 2.7 32.3 + - - -
364F GLY* 3.5 3.9 - - - -
368F GLU* 4.5 11.2 + - - -
380F MET* 3.1 17.2 + - - +
381F TRP* 3.9 42.9 - - + +
382F ILE 3.1 0.6 - - - -
383F LEU* 1.3 77.1 - - - +
385F LYS* 1.3 60.1 + - + +
386F ILE 3.3 0.4 - - - -
387F ILE* 3.4 1.0 + - - +
388F HIS* 3.1 29.3 + - - +
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Residues in contact with LYS 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F TRP* 2.8 54.9 + - + +
382F ILE* 3.0 20.2 + - + +
384F ARG* 1.3 78.0 - - + +
386F ILE* 1.3 62.2 + - + +
388F HIS* 4.3 5.7 - - - +
389F PRO* 3.9 13.7 - - - +
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Residues in contact with ILE 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F ILE* 3.1 26.2 + - + +
383F LEU* 3.3 29.8 - - + +
384F ARG 3.3 0.4 - - - -
385F LYS* 1.3 79.0 - - + +
387F ILE* 1.3 64.1 + - + +
388F HIS 3.6 0.2 - - - -
389F PRO* 3.9 7.6 - - - +
390F MET* 4.5 13.3 - - - +
398F PHE* 3.9 29.2 - - + -
415F MET* 4.5 18.4 - - + -
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Residues in contact with ILE 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F TYR* 3.8 20.2 - - + -
361F ASN* 3.3 17.0 + - - +
383F LEU* 3.4 39.0 + - + +
384F ARG 3.4 3.9 + - - +
385F LYS 3.4 0.2 - - - -
386F ILE* 1.3 85.0 - - + +
388F HIS* 1.3 65.6 + - - +
389F PRO* 3.3 4.3 - - - -
390F MET* 2.8 21.7 + - - +
395F ALA* 3.9 23.6 - - + +
398F PHE* 4.0 19.3 - - + -
399F LEU* 3.8 28.9 - - + -
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Residues in contact with HIS 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F ASN* 3.1 37.2 + - + +
384F ARG 3.1 16.1 + - - +
385F LYS* 4.4 7.2 - - - +
387F ILE* 1.3 76.6 - - - +
389F PRO* 1.3 72.0 - - + +
390F MET 3.2 2.1 + - - +
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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