Contacts of the helix formed by residues 392 - 401 (chain A) in PDB entry 5BUK
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 TYR 392 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.6 28.2 - + - -
386A PHE* 3.5 50.9 - + + +
389A ASP* 2.9 18.9 + - + +
391A ARG* 1.3 125.9 + - + +
393A ARG* 1.3 67.1 + - - +
394A ILE 3.3 2.9 - - - -
395A ASP* 3.2 12.7 + - + +
396A VAL* 3.0 22.5 + - - +
412A ALA* 5.9 0.2 - - + -
415A ALA* 5.5 4.5 - - + -
419A ILE* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 2.8 39.3 + - - -
102A ILE* 3.6 15.4 - - + +
106A GLU* 2.8 43.4 + - - +
386A PHE 3.6 9.4 - - - -
387A VAL* 3.0 31.7 + - - +
388A GLN* 3.2 27.1 + - - +
389A ASP 2.9 11.7 + - - +
390A PRO* 4.1 13.6 - - + +
391A ARG 3.8 0.6 - - - -
392A TYR* 1.3 76.6 - - - +
394A ILE* 1.3 60.4 + - + +
396A VAL* 3.3 3.2 + - - +
397A LEU* 2.8 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.8 33.0 - - + +
107A ARG* 3.5 33.5 + - + +
390A PRO 5.1 7.4 + - - +
391A ARG 5.5 0.4 + - - -
392A TYR 3.3 0.6 - - - -
393A ARG* 1.3 84.5 - - + +
395A ASP* 1.3 66.3 + - - +
397A LEU* 3.3 5.2 + - + +
398A LYS* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ARG 4.6 9.6 - - - +
392A TYR* 3.2 10.4 + - - +
394A ILE* 1.3 80.8 - - - +
396A VAL* 1.3 63.7 + - - +
398A LYS* 3.6 20.1 + - - +
399A MET* 3.8 8.5 + - - +
411A LYS* 3.7 40.6 + - + +
412A ALA* 3.8 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 3.9 21.3 - - + -
383A PHE* 5.5 0.4 - - + -
386A PHE* 3.6 42.4 - - + +
387A VAL* 3.8 28.0 - - + -
392A TYR 3.0 14.3 + - - +
393A ARG* 3.6 7.0 - - - +
395A ASP* 1.3 75.4 - - - +
397A LEU* 1.3 66.0 + - - +
399A MET* 3.0 17.0 + - - +
400A LEU* 3.1 16.3 + - + +
412A ALA* 3.7 11.9 - - + -
416A MET* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 3.9 41.3 - - + +
103A MET 3.6 17.9 - - - +
104A PHE* 4.0 8.5 - - + +
106A GLU* 3.6 11.9 - - + -
107A ARG* 3.5 35.2 - - + +
393A ARG* 2.8 23.4 + - + +
394A ILE* 3.3 10.1 + - + +
396A VAL* 1.3 74.2 - - - +
398A LYS* 1.3 55.9 + - - +
400A LEU* 3.1 9.8 + - + -
401A GLN* 2.8 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 3.4 45.0 - - - +
394A ILE 3.1 8.6 + - - +
395A ASP* 3.6 15.9 - - - +
396A VAL 3.2 0.4 - - - -
397A LEU* 1.3 78.6 - - - +
399A MET* 1.3 72.5 + - + +
401A GLN* 3.6 6.5 + - - +
403A ASP* 2.6 61.4 + - + +
404A VAL* 4.8 0.4 - - - +
406A ASP* 3.2 36.8 + - - +
407A ASP* 4.8 5.4 - - - +
108B THR* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASN* 4.8 2.5 - - - +
369A TRP* 3.2 17.3 - - - -
372A PHE* 3.5 21.8 - - + -
395A ASP 4.0 9.9 - - - +
396A VAL* 3.0 14.5 + - - +
398A LYS* 1.3 92.2 - - + +
400A LEU* 1.3 60.5 + - - +
401A GLN 3.1 0.2 - - - -
402A GLY* 2.9 18.0 + - - -
403A ASP 3.7 19.7 - - - +
404A VAL* 4.0 19.8 - - + +
407A ASP* 5.8 0.7 - - + -
410A PRO* 3.7 40.4 - - + -
412A ALA* 5.0 3.4 - - + -
413A LEU* 4.2 24.7 - - + -
416A MET* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.5 21.3 - - - +
77A TRP* 3.7 34.2 - - + -
102A ILE* 4.1 14.8 - - + -
104A PHE* 3.8 7.4 - - - -
323A PHE* 3.6 30.8 - - + +
369A TRP* 4.7 4.0 - - - -
372A PHE* 3.4 25.1 - - + -
383A PHE* 4.6 0.4 - - + -
387A VAL* 4.2 11.9 - - + -
396A VAL* 3.1 29.7 + - + +
397A LEU* 3.1 15.2 + - + +
399A MET* 1.3 78.8 - - - +
401A GLN* 1.3 57.9 + - - +
402A GLY* 3.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.6 4.0 - - - +
49A PRO* 3.5 10.9 - - + +
50A ALA* 2.9 28.9 + - - +
104A PHE* 2.9 45.4 + - + +
107A ARG* 2.7 56.0 + - - +
109A GLN* 3.3 30.7 + - - +
397A LEU* 2.8 28.4 + - + +
398A LYS* 3.7 5.5 - - - +
400A LEU* 1.3 77.5 - - - +
402A GLY* 1.3 57.5 + - - +
403A ASP 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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