Contacts of the helix formed by residues 383 - 395 (chain B) in PDB entry 2X1L
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 383 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381B GLU* 4.5 4.3 - - + +
382B PHE* 1.3 73.2 - - - +
384B ASP* 1.3 57.5 + - - +
385B GLU* 3.5 13.0 + - - +
386B ASP* 2.9 20.4 + - - -
387B THR* 2.7 35.1 + - - -
446B ARG* 3.0 45.1 + - - +
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Residues in contact with ASP 384 (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 THR* 1.3 75.7 - - - +
385B GLU* 1.3 65.8 + - - +
387B THR* 3.5 7.7 + - - -
388B ALA* 3.1 29.5 + - - +
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Residues in contact with GLU 385 (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 THR* 3.2 11.4 + - - +
384B ASP* 1.3 87.8 + - - +
386B ASP* 1.3 64.5 + - - +
388B ALA* 4.2 4.6 - - - +
389B LEU* 3.4 22.5 + - - +
426B TYR* 4.0 11.1 - - + -
430B GLN* 4.2 22.0 + - - +
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Residues in contact with ASP 386 (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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382B PHE* 3.6 22.0 - - + -
383B THR* 2.9 31.8 + - - +
385B GLU* 1.3 76.8 - - - +
387B THR* 1.3 62.2 + - - +
389B LEU* 3.5 2.8 + - - +
390B LEU* 3.2 29.4 + - - +
426B TYR* 2.5 34.3 + - - -
446B ARG* 2.7 33.6 + - - -
449B THR* 3.6 3.7 - - - +
453B THR* 4.0 10.4 - - - +
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Residues in contact with THR 387 (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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382B PHE* 4.2 13.2 + - - +
383B THR 2.7 23.4 + - - -
384B ASP* 3.7 9.4 + - - -
386B ASP* 1.3 76.1 - - - +
388B ALA* 1.3 57.4 + - - +
390B LEU* 3.4 10.1 + - - +
391B ALA* 2.9 30.3 + - + +
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Residues in contact with ALA 388 (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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384B ASP 3.1 17.9 + - - +
385B GLU* 3.7 6.0 + - - +
387B THR* 1.3 76.7 - - - +
389B LEU* 1.3 63.0 + - - +
391B ALA* 3.5 7.4 + - - +
392B ALA* 3.2 21.8 + - - +
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Residues in contact with LEU 389 (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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385B GLU 3.4 15.8 + - - +
386B ASP 3.8 2.9 - - - +
387B THR 3.3 0.6 - - - -
388B ALA* 1.3 76.9 - - - +
390B LEU* 1.3 64.3 + - - +
392B ALA* 3.3 7.2 + - + +
393B ALA* 3.1 21.7 + - - +
419B VAL* 4.2 6.9 - - + +
422B ALA* 3.7 18.8 - - + +
423B ALA* 3.6 34.5 - - + +
426B TYR* 3.6 37.0 - - + -
453B THR* 4.0 13.7 - - + +
454B THR* 5.4 1.1 - - - +
457B VAL* 3.8 21.5 - - + -
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Residues in contact with LEU 390 (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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382B PHE* 4.1 31.9 - - + -
386B ASP 3.2 19.8 + - - +
387B THR* 3.7 8.1 - - - +
389B LEU* 1.3 75.3 - - - +
391B ALA* 1.3 53.5 + - - +
393B ALA* 3.2 5.9 + - + +
394B ASP* 2.7 41.3 + - - +
452B TYR* 5.7 1.1 - - + -
453B THR* 3.9 22.2 - - + +
456B GLU* 3.7 33.4 - - + -
457B VAL* 4.7 4.5 - - + -
495B ARG* 3.7 27.8 - - - +
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Residues in contact with ALA 391 (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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387B THR* 2.9 20.4 + - + +
388B ALA* 3.7 9.4 - - - +
390B LEU* 1.3 77.6 - - - +
392B ALA* 1.3 61.0 + - - +
394B ASP* 3.6 7.5 + - - +
395B ALA* 3.2 24.8 + - - +
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Residues in contact with ALA 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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388B ALA 3.2 14.5 + - - +
389B LEU* 3.6 12.8 - - + +
390B LEU 3.3 0.4 - - - -
391B ALA* 1.3 74.8 - - - +
393B ALA* 1.3 62.3 + - - +
395B ALA* 3.6 12.5 + - - +
396B LEU* 3.6 8.0 + - - +
399B ARG* 5.4 1.6 + - - -
419B VAL* 3.6 28.8 - - + +
422B ALA* 5.8 3.6 - - + -
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Residues in contact with ALA 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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389B LEU 3.1 13.4 + - - +
390B LEU* 3.6 8.3 - - + +
392B ALA* 1.3 77.5 - - - +
394B ASP* 1.3 62.1 + - - +
396B LEU* 3.2 24.3 + - + +
397B LEU 4.6 0.5 + - - -
419B VAL* 4.0 19.6 - - + +
457B VAL* 4.1 17.9 - - + +
460B ILE* 3.6 33.7 - - + +
492B ILE* 5.6 0.5 - - - +
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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 LEU 2.7 27.0 + - - +
391B ALA* 4.0 6.7 + - - +
392B ALA 3.4 0.2 - - - -
393B ALA* 1.3 73.0 - - - +
395B ALA* 1.3 59.2 + - - +
396B LEU 3.2 0.6 + - - -
397B LEU* 4.3 9.2 + - - +
398B GLU* 5.3 2.1 + - - +
460B ILE* 3.5 14.1 - - - +
492B ILE* 5.1 9.5 - - - +
495B ARG* 2.8 44.4 + - - -
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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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391B ALA 3.2 17.6 + - - +
392B ALA* 3.9 8.3 - - - +
393B ALA 3.2 0.6 - - - -
394B ASP* 1.3 75.8 - - - +
396B LEU* 1.3 64.6 + - - +
397B LEU 3.5 0.6 + - - -
398B GLU* 3.7 8.5 + - - +
399B ARG* 3.4 29.5 + - - +
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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