Contacts of the helix formed by residues 391 - 404 (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 GLY 391 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389F PRO 3.9 1.6 + - - -
390F MET* 1.3 75.0 - - - +
392F GLU* 1.3 58.1 + - - -
393F ILE* 3.4 3.4 - - - -
394F ASP* 3.0 17.5 + - - +
395F ALA* 2.6 34.5 + - - +
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Residues in contact with GLU 392 (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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346F SER* 2.8 28.1 + - - -
348F LYS* 3.1 32.6 + - + +
349F ILE* 3.4 21.2 - - + +
358F ILE 5.5 1.4 - - - +
359F ASP* 3.1 28.5 - - - +
362F ARG* 5.0 10.9 + - - +
390F MET 3.9 0.8 + - - -
391F GLY* 1.3 71.2 - - - +
393F ILE* 1.3 70.9 - - + +
395F ALA* 3.8 5.7 - - - +
396F MET* 3.4 16.8 + - - +
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Residues in contact with ILE 393 (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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348F LYS* 4.1 38.8 - - + +
349F ILE* 4.0 17.5 - - + -
352F LYS* 3.8 47.6 - - + +
354F VAL* 4.4 7.0 - - + -
391F GLY 5.3 0.4 - - - -
392F GLU* 1.3 81.9 - - + +
394F ASP* 1.3 63.9 + - - +
396F MET* 3.6 2.8 + - - +
397F GLU* 3.1 39.0 + - - +
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Residues in contact with ASP 394 (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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390F MET* 4.3 8.2 - - + +
391F GLY* 3.0 20.7 + - - +
393F ILE* 1.3 79.2 - - - +
395F ALA* 1.3 59.9 + - - +
397F GLU* 3.5 14.0 + - - +
398F PHE* 3.0 30.9 + - - +
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Residues in contact with ALA 395 (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* 5.2 8.2 - - + +
361F ASN* 5.0 3.6 - - - +
387F ILE* 3.9 19.8 - - + +
390F MET* 3.7 28.2 - - + +
391F GLY 2.6 22.3 + - - +
392F GLU* 3.8 6.5 - - - +
394F ASP* 1.3 72.5 - - - +
396F MET* 1.3 60.4 + - - +
398F PHE* 3.8 4.2 - - - +
399F LEU* 3.4 27.0 + - - +
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Residues in contact with MET 396 (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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161F VAL* 3.7 39.9 - - + -
349F ILE* 3.6 27.6 - - + -
354F VAL* 4.2 1.3 - - + +
355F PHE 3.2 21.5 - - - +
356F PRO* 3.0 20.6 - - + +
358F ILE 3.3 20.6 - - - +
360F TYR* 5.5 3.4 - - - -
392F GLU 3.4 7.6 + - - +
393F ILE 4.0 0.4 - - - +
394F ASP 3.2 0.6 - - - -
395F ALA* 1.3 77.0 - - - +
397F GLU* 1.3 64.4 + - - +
398F PHE 3.1 1.8 - - - -
399F LEU* 3.2 16.9 + - + -
400F ILE* 3.0 40.8 + - + +
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Residues in contact with GLU 397 (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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354F VAL* 3.4 39.8 - - + +
393F ILE* 3.1 27.4 + - - +
394F ASP* 3.9 14.9 - - - +
396F MET* 1.3 78.3 - - - +
398F PHE* 1.3 57.1 + - - +
400F ILE* 4.3 2.4 - - - +
401F ASN* 2.9 35.0 + - - +
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Residues in contact with PHE 398 (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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383F LEU* 6.0 0.7 - - + -
386F ILE* 3.9 31.0 - - + -
387F ILE* 4.0 19.5 - - + -
390F MET* 3.6 36.6 - - + -
394F ASP 3.0 18.1 + - - +
395F ALA 3.8 4.5 - - - +
396F MET 3.1 0.2 - - - -
397F GLU* 1.3 77.6 - - - +
399F LEU* 1.3 67.6 + - + +
401F ASN* 3.9 4.4 - - - +
402F LYS* 3.2 65.5 + - + +
415F MET* 4.4 9.2 - - + -
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Residues in contact with LEU 399 (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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161F VAL* 4.4 9.6 - - + -
164F LEU* 4.2 5.6 - - + -
360F TYR* 3.6 38.1 - - + -
383F LEU* 4.1 20.6 - - + -
387F ILE* 3.8 17.5 - - + -
395F ALA 3.4 7.2 + - - +
396F MET* 3.2 27.6 + - + +
398F PHE* 1.3 81.0 - - + +
400F ILE* 1.3 56.2 + - - +
402F LYS* 3.4 0.8 + - - -
403F LEU* 2.7 65.2 + - + +
411F ASP* 4.8 5.8 - - - +
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Residues in contact with ILE 400 (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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157F LEU* 4.1 29.2 - - + -
161F VAL* 4.8 7.9 - - + -
354F VAL* 3.7 17.7 - - + -
355F PHE 3.4 31.9 - - - +
356F PRO* 4.5 7.9 - - + -
396F MET* 3.0 29.9 + - + +
397F GLU* 4.3 3.1 - - - +
399F LEU* 1.3 74.8 - - - +
401F ASN* 1.3 61.4 + - - +
403F LEU* 4.6 3.1 - - - -
404F ALA* 3.1 31.6 + - + +
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Residues in contact with ASN 401 (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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397F GLU 2.9 21.3 + - - +
398F PHE* 3.9 6.1 + - - +
400F ILE* 1.3 79.2 - - - +
402F LYS* 1.3 77.6 - - - +
404F ALA* 4.2 4.2 + - - +
405F MET* 3.7 25.5 - - - +
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Residues in contact with LYS 402 (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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398F PHE* 3.2 44.9 + - + +
399F LEU* 4.4 1.1 - - - +
401F ASN* 1.3 91.6 - - - +
403F LEU* 1.3 63.2 + - - +
404F ALA 3.4 0.2 - - - -
405F MET* 3.9 21.6 - - + +
406F THR* 4.8 2.1 + - - -
411F ASP* 3.5 12.4 - - - +
414F GLU* 3.8 17.2 - - - +
415F MET* 3.5 40.4 - - + +
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Residues in contact with LEU 403 (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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157F LEU* 4.6 11.4 - - + +
160F ARG* 3.6 22.9 - - + -
161F VAL* 4.2 19.3 - - + +
164F LEU* 3.8 28.3 - - + -
399F LEU* 2.7 37.3 + - + +
400F ILE* 4.5 2.5 - - - +
402F LYS* 1.3 68.6 - - - +
404F ALA* 1.3 52.4 + - - +
405F MET 2.8 18.2 + - - -
406F THR* 3.4 16.1 + - - +
407F LYS 3.2 28.2 - - - +
408F THR* 4.7 3.4 - - - -
411F ASP* 3.6 19.2 + - + +
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Residues in contact with ALA 404 (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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157F LEU* 3.6 29.5 - - + +
400F ILE* 3.1 22.4 + - + +
401F ASN* 4.5 4.4 - - - +
402F LYS 3.4 0.4 - - - -
403F LEU* 1.3 73.3 - - - +
405F MET* 1.3 64.4 + - - +
406F THR 5.5 0.7 - - - -
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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