Contacts of the helix formed by residues 384 - 394 (chain B) in PDB entry 4XJO
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 ASP 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B PRO 3.6 3.8 + - - +
383B VAL* 1.3 70.2 - - - +
385B LEU* 1.3 55.9 + - - +
386B ALA* 3.5 16.1 + - - +
387B VAL* 3.1 29.6 + - + +
388B ALA* 2.7 35.4 + - - +
433B VAL* 5.3 1.8 - - - +
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Residues in contact with LEU 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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33B VAL* 5.6 1.9 - - - +
383B VAL* 3.1 25.1 + - + +
384B ASP* 1.3 74.5 + - - +
386B ALA* 1.3 61.7 + - - +
388B ALA* 4.4 4.0 - - - +
389B THR* 2.8 36.2 + - - +
390B PRO* 4.0 0.2 - - - +
400B ARG* 4.3 30.1 - - - +
401B PRO* 3.5 39.5 - - + +
402B PHE* 4.6 5.8 - - + -
403B ARG 5.4 1.6 - - - +
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Residues in contact with ALA 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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32B ALA* 5.9 3.8 - - + -
33B VAL* 4.3 25.4 - - + +
384B ASP* 3.3 13.9 + - - +
385B LEU* 1.3 77.4 - - - +
387B VAL* 1.3 60.7 + - + +
390B PRO* 3.2 20.0 - - - +
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Residues in contact with VAL 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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384B ASP* 3.1 32.0 + - + +
386B ALA* 1.3 83.4 - - + +
388B ALA* 1.3 64.5 + - - +
389B THR 3.4 0.4 - - - -
390B PRO* 3.3 5.5 - - - +
391B ALA* 3.2 20.5 + - + +
432B LEU* 5.0 27.6 - - + +
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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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383B VAL* 3.7 24.5 - - + -
384B ASP 2.7 22.1 + - - +
385B LEU* 4.5 2.5 - - - -
387B VAL* 1.3 75.7 - - - +
389B THR* 1.3 62.3 + - - +
391B ALA* 3.3 7.5 + - - +
392B ALA* 3.0 24.6 + - - +
399B LEU* 6.4 0.2 - - - -
401B PRO* 4.0 14.6 - - + -
429B VAL* 3.8 18.8 - - + +
432B LEU* 6.3 0.2 - - - -
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Residues in contact with THR 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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36B VAL* 5.5 3.6 - - + -
385B LEU* 2.8 24.7 + - - +
388B ALA* 1.3 77.4 - - - +
390B PRO* 1.4 69.8 - - + +
392B ALA* 3.4 3.7 + - - +
393B LEU* 3.0 35.2 + - + +
398B TRP* 3.7 33.0 - - + -
399B LEU 4.4 14.6 + - - +
400B ARG* 4.4 13.6 + - - +
401B PRO* 4.8 5.1 - - - +
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Residues in contact with PRO 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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50B ARG* 3.4 21.7 + - - +
385B LEU 4.0 0.2 - - - +
386B ALA 3.2 28.0 - - - +
387B VAL* 3.3 12.3 - - - +
389B THR* 1.4 96.1 - - + +
391B ALA* 1.3 53.5 + - - -
393B LEU* 4.2 4.7 - - + -
394B ASP* 2.8 40.0 + - - +
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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 VAL* 3.2 20.9 + - + +
388B ALA* 3.4 9.2 - - - +
389B THR 3.2 0.2 - - - -
390B PRO* 1.3 78.3 - - - +
392B ALA* 1.3 59.1 + - - +
394B ASP* 3.7 8.7 + - - +
395B ARG* 3.6 26.0 + - - +
425B ALA 5.9 0.2 - - - -
428B GLU* 6.0 0.4 - - + -
429B VAL* 4.5 8.3 - - + -
432B LEU* 3.8 29.4 - - + -
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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 3.0 15.0 + - - +
389B THR* 3.9 4.5 - - - +
391B ALA* 1.3 74.3 - - - +
393B LEU* 1.3 61.8 + - - +
395B ARG* 2.9 17.0 + - - +
396B GLY 3.1 0.5 + - - -
397B VAL* 3.0 33.6 + - + +
399B LEU* 3.8 36.3 - - + +
425B ALA* 4.6 8.3 - - + -
429B VAL* 4.3 5.8 - - + +
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Residues in contact with LEU 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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36B VAL* 4.5 20.4 - - + -
48B LEU* 3.8 27.1 - - + -
50B ARG* 3.7 35.3 + - - +
55B ILE* 4.6 6.6 - - + +
57B VAL* 4.1 19.3 - - + +
389B THR* 3.0 36.1 + - + +
390B PRO* 3.7 5.8 - - + +
392B ALA* 1.3 71.7 - - - +
394B ASP* 1.3 58.3 + - - +
395B ARG 3.0 4.9 - - - -
396B GLY* 2.9 18.9 + - - -
397B VAL 3.3 14.6 + - - +
398B TRP* 3.9 12.6 - - + -
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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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50B ARG* 2.5 41.4 + - - +
390B PRO* 2.8 24.9 + - - +
391B ALA* 3.7 10.2 - - - +
392B ALA 3.3 0.2 - - - -
393B LEU* 1.3 75.4 - - - +
395B ARG* 1.3 62.0 + - + +
396B GLY 3.4 1.0 + - - -
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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