Contacts of the helix formed by residues 388 - 402 (chain B) in PDB entry 4XHS
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 GLU 388 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B GLU 3.5 8.3 + - - +
387B LEU* 1.3 75.4 - - - +
389B ALA* 1.3 67.7 + - - +
390B VAL* 3.2 11.2 - - + +
391B GLU* 2.9 42.4 + - + +
392B LEU* 2.9 11.8 + - - +
449B ARG* 5.0 2.6 + - - +
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Residues in contact with ALA 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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387B LEU 3.8 0.4 + - - -
388B GLU* 1.3 74.6 + - - +
390B VAL* 1.3 62.2 + - - +
392B LEU* 3.3 8.5 + - - +
393B LYS* 3.1 22.2 + - - +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLU* 4.4 9.6 - - + -
389B ALA* 1.3 79.3 - - - +
391B GLU* 1.3 70.8 + - + +
393B LYS* 3.5 13.6 + - + +
394B LYS* 3.1 40.3 + - + +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.6 13.0 - - + -
388B GLU* 2.9 38.1 + - + +
390B VAL* 1.3 83.1 - - + +
392B LEU* 1.3 59.3 + - - +
394B LYS* 3.2 11.7 + - + +
395B PHE* 2.8 29.6 + - - +
447B ILE* 3.6 16.4 - - + +
449B ARG* 2.9 48.8 + - + +
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Residues in contact with LEU 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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384B LEU* 4.8 15.7 - - + +
387B LEU* 3.9 26.6 - - + +
388B GLU 2.9 10.8 + - - +
389B ALA* 3.7 11.7 - - - +
391B GLU* 1.3 76.2 - - - +
393B LYS* 1.3 58.7 + - - +
395B PHE* 3.3 12.6 + - + +
396B LYS* 3.0 47.8 + - - +
418B ALA 4.1 18.8 - - - +
419B GLY* 5.0 0.4 - - - -
420B PRO* 4.6 20.6 - - + -
423B MET* 4.7 9.4 - - + -
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Residues in contact with LYS 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 ALA 3.1 13.5 + - - +
390B VAL* 3.6 16.2 - - + +
391B GLU 3.2 0.2 - - - -
392B LEU* 1.3 76.5 - - - +
394B LYS* 1.3 58.1 + - + +
396B LYS* 3.2 12.0 + - - +
397B LEU* 3.0 53.3 + - + +
412B TRP* 4.6 6.9 - - + -
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Residues in contact with LYS 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B VAL* 3.1 31.8 + - + +
391B GLU* 3.2 13.2 + - + +
393B LYS* 1.3 73.1 - - + +
395B PHE* 1.3 65.8 + - - +
397B LEU* 3.3 14.4 + - + +
398B TYR* 2.9 48.9 + - + -
447B ILE* 4.1 30.7 - - + +
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Residues in contact with PHE 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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384B LEU* 3.6 21.8 - - + -
387B LEU* 3.9 11.4 - - + -
391B GLU 2.8 17.5 + - - +
392B LEU* 3.3 13.9 + - + +
394B LYS* 1.3 74.0 - - - +
396B LYS* 1.3 63.7 + - - +
398B TYR* 3.5 2.9 + - - +
399B LEU* 3.2 53.0 + - + +
423B MET* 4.0 13.5 - - + -
427B LEU* 3.9 17.5 - - + -
440B ALA* 3.8 15.5 - - + -
443B THR* 3.5 34.7 - - + +
444B PHE* 3.7 33.2 - + - -
447B ILE* 4.0 6.2 - - + +
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Residues in contact with LYS 396 (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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392B LEU* 3.0 34.9 + - + +
393B LYS* 3.5 10.8 - - - +
395B PHE* 1.3 79.2 - - - +
397B LEU* 1.3 62.1 + - - +
399B LEU* 3.2 1.9 + - - +
400B GLY 3.0 18.7 + - - -
412B TRP* 3.6 23.9 - - + -
415B MET* 2.8 42.1 + - - +
416B GLU* 3.2 18.8 + - - +
417B LYS 4.2 0.6 - - - -
418B ALA 2.7 29.2 + - - +
423B MET* 3.7 31.6 - - + -
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Residues in contact with LEU 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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393B LYS* 3.0 45.3 + - + +
394B LYS* 3.3 14.1 + - + +
396B LYS* 1.3 75.4 - - - +
398B TYR* 1.3 67.2 + - + +
400B GLY* 3.3 1.4 + - - +
401B THR* 3.0 34.8 + - + +
412B TRP* 3.5 30.3 - - + -
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Residues in contact with TYR 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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394B LYS* 2.9 49.5 + - + +
395B PHE 3.9 3.8 - - - +
397B LEU* 1.3 81.5 - - + +
399B LEU* 1.3 60.5 + - + +
401B THR* 3.6 5.3 + - - -
402B ALA* 3.1 35.6 + - + +
443B THR* 4.2 11.9 - - + +
446B ARG* 3.3 59.8 + - + -
447B ILE* 4.2 11.4 - - + -
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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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395B PHE* 3.2 43.7 + - + +
396B LYS 3.2 8.1 + - - +
398B TYR* 1.3 78.9 - - + +
400B GLY* 1.3 60.4 + - - +
402B ALA* 4.5 6.6 + - - +
410B ILE* 5.2 11.0 + - + +
415B MET* 4.2 12.0 - - - +
423B MET* 4.4 7.0 - - + -
427B LEU* 3.5 27.8 - - + -
431B PHE* 5.6 2.9 - - + -
439B LEU* 4.1 25.4 - - + -
443B THR* 3.6 24.0 - - + +
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Residues in contact with GLY 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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396B LYS 3.0 14.5 + - - -
397B LEU 3.3 1.5 + - - -
398B TYR 3.2 0.6 - - - -
399B LEU* 1.3 76.1 - - - +
401B THR* 1.3 65.0 + - - +
410B ILE 4.8 6.8 - - - +
412B TRP* 5.0 6.7 - - - -
415B MET* 3.8 15.0 - - - -
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Residues in contact with THR 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 LEU* 3.0 24.0 + - + +
398B TYR* 3.6 6.8 + - - -
400B GLY* 1.3 84.7 - - - +
402B ALA* 1.3 70.6 + - - +
403B THR* 3.4 6.4 + - - +
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Residues in contact with ALA 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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398B TYR 3.1 18.6 + - - +
399B LEU* 4.5 8.4 + - + +
400B GLY 3.8 0.8 - - - -
401B THR* 1.3 80.4 + - - +
403B THR* 1.3 69.5 + - - +
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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