Contacts of the helix formed by residues 399 - 408 (chain B) in PDB entry 3U44
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 ARG 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLU* 5.5 5.3 + - - -
760A ARG* 5.1 11.3 - - - +
763A ARG* 5.8 0.6 - - - +
392B ASP 5.6 0.9 + - - +
393B VAL* 4.5 0.6 + - - +
396B GLY* 3.4 26.4 - - - +
397B ASN 3.4 0.9 + - - -
398B TRP* 1.3 75.0 - - - +
400B TYR* 1.3 61.6 + - - +
401B GLU* 3.0 25.9 + - + +
402B ALA* 2.8 32.7 + - + +
403B VAL 3.3 7.1 + - - -
439B LYS* 4.7 32.3 - - - +
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Residues in contact with TYR 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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759A PHE* 4.5 3.4 - + - -
763A ARG* 2.5 26.1 + - - -
398B TRP 3.2 6.4 + - - -
399B ARG* 1.3 70.9 - - - +
401B GLU* 1.3 89.3 + - + +
403B VAL* 4.2 9.4 - - - -
404B PHE* 3.1 36.7 + + + -
430B GLU* 5.2 1.8 - - + -
433B CYS* 3.9 23.3 - - + -
434B ILE* 3.4 42.6 + - + +
437B GLY* 4.8 7.9 - - - -
438B ILE 3.3 27.7 + - - +
439B LYS* 4.8 4.2 - - + +
443B TRP* 3.9 14.1 - - + -
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A PHE* 4.0 16.7 - - + -
760A ARG* 4.0 24.2 - - + +
763A ARG* 2.7 36.4 + - - +
399B ARG* 3.7 25.4 + - + +
400B TYR* 1.3 115.5 + - + +
402B ALA* 1.3 57.1 + - - +
404B PHE* 4.0 2.8 - - - +
405B ARG* 3.1 35.9 + - - +
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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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389B SER* 4.1 4.0 - - - +
392B ASP* 4.3 7.6 - - + +
393B VAL* 3.7 29.2 - - + +
399B ARG* 2.8 22.7 + - + +
401B GLU* 1.3 73.5 - - - +
403B VAL* 1.3 65.6 + - - +
405B ARG* 3.0 34.7 + - - +
406B CYS* 3.0 17.7 + - - -
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Residues in contact with VAL 403 (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 VAL* 3.8 17.0 - - + -
398B TRP* 4.0 30.1 - - + +
399B ARG 3.3 11.4 + - - +
400B TYR* 3.3 7.8 + - - +
402B ALA* 1.3 76.1 - - - +
404B PHE* 1.3 60.1 + - + +
406B CYS* 3.2 6.9 + - - +
407B VAL* 3.0 30.7 + - + +
443B TRP* 3.8 38.8 - - + +
481B ILE* 4.0 23.1 - - + -
485B LEU* 4.7 6.2 - - + +
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Residues in contact with PHE 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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400B TYR* 3.1 29.9 + + + +
401B GLU* 4.3 2.7 - - - +
403B VAL* 1.3 78.0 - - + +
405B ARG* 1.3 60.3 + - - +
406B CYS 3.2 0.9 - - - -
407B VAL* 3.7 8.3 - - + -
408B LYS* 2.9 41.3 + - - +
426B VAL* 3.3 41.1 - - + -
429B LEU* 3.5 29.2 - - + -
430B GLU* 3.3 54.1 - - + +
433B CYS* 3.5 23.6 - - + -
443B TRP* 3.7 12.1 - + - -
481B ILE* 5.3 2.5 - - + -
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Residues in contact with ARG 405 (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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756A ARG* 3.5 25.4 + - - +
757A GLY* 6.0 4.3 - - - -
760A ARG* 4.3 22.2 - - - +
385B GLU* 3.4 17.2 - - + +
389B SER* 3.0 25.1 + - - +
392B ASP* 3.1 32.5 + - - +
401B GLU* 3.1 24.8 + - - +
402B ALA* 3.0 36.2 + - - +
404B PHE* 1.3 79.1 - - - +
406B CYS* 1.3 56.7 + - - +
408B LYS* 4.4 4.3 - - - +
409B THR* 3.3 21.8 + - - +
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Residues in contact with CYS 406 (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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386B PHE* 3.7 14.5 - - + +
389B SER* 3.2 17.5 - - - -
390B SER* 3.2 44.0 - - - +
393B VAL* 3.6 8.5 - - - -
402B ALA 3.0 11.3 + - - -
403B VAL 3.2 6.9 + - - +
405B ARG* 1.3 75.3 - - - +
407B VAL* 1.3 64.1 + - - +
408B LYS 3.1 2.0 - - - -
409B THR* 2.6 29.8 + - - -
410B GLU 3.8 0.9 + - - -
411B LEU 4.5 0.9 + - - -
412B LEU* 4.3 16.1 - - + +
485B LEU* 4.4 4.7 - - + -
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Residues in contact with VAL 407 (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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403B VAL* 3.0 21.2 + - + +
404B PHE* 3.6 10.3 + - + -
406B CYS* 1.3 75.0 - - - +
408B LYS* 1.3 56.6 + - - +
410B GLU* 2.9 14.7 + - - -
412B LEU* 4.1 14.8 - - + -
413B PHE* 3.1 13.4 - - + -
426B VAL* 3.7 37.2 - - + -
480B TRP* 3.8 18.8 - - + -
481B ILE* 3.6 37.5 - - + -
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Residues in contact with LYS 408 (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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634A ASP* 2.9 38.4 + - - +
702A ARG* 5.7 0.9 - - - +
706A LYS* 4.6 11.1 - - - +
759A PHE* 4.7 2.2 - - + +
404B PHE* 2.9 28.4 + - - +
405B ARG* 4.4 5.2 - - - +
406B CYS 3.1 0.4 - - - -
407B VAL* 1.3 76.2 - - - +
409B THR* 1.3 58.8 + - - +
410B GLU* 2.9 15.3 + - - +
413B PHE* 5.2 1.8 - - - -
426B VAL* 4.5 13.7 - - + -
427B ASP* 4.5 11.7 - - - +
430B GLU* 2.8 42.7 + - - -
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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