Contacts of the helix formed by residues 391 - 404 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B ASN* 5.2 0.9 - - - -
389B PRO 3.9 1.0 + - - -
390B MET* 1.3 77.0 - - - +
392B GLU* 1.3 57.3 + - - -
393B ILE* 3.4 2.9 - - - -
394B ASP* 3.8 20.1 + - - +
395B ALA* 2.8 32.8 + - - +
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B SER* 3.7 15.8 + - - +
348B LYS* 3.3 37.9 + - - +
349B ILE* 3.3 21.8 - - + +
358B ILE 5.5 1.0 - - - +
359B ASP* 3.7 23.8 - - - +
361B ASN* 5.4 4.0 - - - +
362B ARG* 3.9 21.0 + - - +
391B GLY* 1.3 73.1 - - - +
393B ILE* 1.3 64.9 + - + +
395B ALA* 3.3 16.9 + - - +
396B MET* 3.7 5.7 + - - +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LYS* 4.1 20.2 - - + +
349B ILE* 3.7 34.1 - - + +
352B LYS* 4.2 36.3 - - + +
354B VAL* 5.8 1.2 - - + +
391B GLY* 5.3 0.7 - - - -
392B GLU* 1.3 75.6 - - + +
394B ASP* 1.3 96.4 + - - +
395B ALA 3.1 2.1 + - - -
396B MET* 3.7 1.7 + - - +
397B GLU* 3.6 30.7 + - - +
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Residues in contact with ASP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B MET* 3.4 19.6 - - + +
391B GLY* 3.3 24.9 + - - +
392B GLU 3.3 0.2 - - - -
393B ILE* 1.3 96.8 - - - +
395B ALA* 1.3 61.7 + - - +
397B GLU* 4.4 7.2 - - - +
398B PHE* 3.3 22.2 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ILE 5.7 0.2 - - - +
359B ASP* 6.2 0.4 - - - -
360B TYR* 5.0 15.3 - - + +
361B ASN* 4.9 9.6 - - - +
387B ILE* 3.7 30.3 - - + +
390B MET* 4.5 1.8 - - + -
391B GLY 2.8 18.1 + - - +
392B GLU* 3.3 9.6 - - - +
393B ILE 3.1 0.4 - - - -
394B ASP* 1.3 76.2 - - - +
396B MET* 1.3 67.1 + - + +
398B PHE* 3.3 7.8 + - - +
399B LEU* 3.3 19.6 + - - +
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Residues in contact with MET 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 3.7 32.8 - - + -
349B ILE* 4.0 16.2 - - + -
354B VAL* 4.6 4.7 - - + -
356B PRO* 3.5 50.9 - - + +
357B ALA 4.1 5.4 - - - +
358B ILE* 3.2 30.3 - - - +
360B TYR* 5.3 5.8 - - - -
392B GLU 3.7 5.7 + - - +
393B ILE 3.7 1.5 + - - +
395B ALA* 1.3 77.0 - - + +
397B GLU* 1.3 54.9 + - - +
399B LEU* 2.9 9.4 + - + +
400B ILE* 2.5 50.1 + - + +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LYS* 3.6 23.8 + - - +
354B VAL* 4.4 26.1 - - + +
393B ILE* 3.6 20.5 + - - +
394B ASP* 4.4 7.1 - - - +
395B ALA 3.4 0.6 - - - -
396B MET* 1.3 77.0 - - - +
398B PHE* 1.3 60.6 + - - +
400B ILE* 4.2 6.3 - - + -
401B ASN* 2.8 39.8 + - - +
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Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B LEU* 5.3 4.0 - - + -
386B ILE* 4.1 30.5 - - + -
387B ILE* 4.2 18.6 - - + -
390B MET* 3.8 26.0 - - + -
394B ASP 3.3 14.7 + - - +
395B ALA 3.3 10.5 + - - +
396B MET 3.2 0.2 - - - -
397B GLU* 1.3 78.6 - - - +
399B LEU* 1.3 62.0 + - + +
401B ASN* 4.5 1.2 - - - +
402B LYS* 3.4 57.6 - - + +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B VAL* 3.6 27.4 - - + -
164B LEU* 4.2 10.5 - - + -
360B TYR* 5.1 4.5 - - + -
383B LEU* 4.0 22.9 - - + -
387B ILE* 3.9 26.2 - - + -
395B ALA 3.3 10.8 + - - +
396B MET* 2.9 17.3 + - + +
398B PHE* 1.3 81.9 - - + +
400B ILE* 1.3 62.7 + - - +
401B ASN 3.5 0.4 - - - -
402B LYS* 4.1 4.9 - - + -
403B LEU* 3.2 69.8 + - + +
411B ASP* 5.6 1.1 - - - +
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 4.0 29.6 - - + +
161B VAL* 4.9 2.2 - - + -
354B VAL* 4.8 9.0 - - + -
355B PHE 3.1 28.9 - - - +
356B PRO* 3.7 15.5 - - + -
396B MET* 2.5 35.9 + - + +
397B GLU* 3.4 7.4 + - + +
399B LEU* 1.3 72.9 - - - +
401B ASN* 1.3 74.3 + - - +
404B ALA* 3.2 31.7 + - + +
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Residues in contact with ASN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B GLU* 2.8 30.8 + - - +
398B PHE 5.1 0.4 - - - +
400B ILE* 1.3 88.0 - - - +
402B LYS* 1.3 65.1 + - + +
404B ALA* 4.1 5.5 + - - +
405B MET* 3.8 21.1 - - - +
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B LEU* 6.6 0.4 - - + -
398B PHE* 3.4 57.9 + - + +
399B LEU* 3.9 6.1 + - + +
400B ILE 3.2 0.6 - - - -
401B ASN* 1.3 81.4 - - + +
403B LEU* 1.3 66.0 + - + +
404B ALA 3.3 1.3 + - - -
405B MET* 3.8 18.1 + - - +
406B THR* 3.8 12.0 + - - +
411B ASP* 4.9 6.1 - - - +
415B MET* 3.6 42.4 - - + +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 4.0 12.6 - - + +
160B ARG* 2.7 75.7 + - + +
161B VAL* 3.8 13.5 - - + +
164B LEU* 4.2 9.6 - - + -
399B LEU* 3.2 46.0 + - + +
402B LYS* 1.3 74.6 - - + +
404B ALA* 1.3 52.8 + - - +
405B MET 2.7 17.7 + - - -
406B THR* 3.1 7.3 + - - +
408B THR* 6.1 0.4 - - + -
411B ASP* 3.2 29.4 - - - +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B THR* 5.2 8.5 - - + -
157B LEU* 4.0 22.4 - - + +
400B ILE* 3.2 22.6 + - + +
401B ASN* 4.4 4.8 - - - +
402B LYS 3.3 0.6 - - - -
403B LEU* 1.3 73.0 - - - +
405B MET* 1.3 66.7 + - - +
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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