Contacts of the helix formed by residues 402 - 408 (chain A) in PDB entry 5I74
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 GLY 402 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 3.5 35.6 - - - -
400A ASP* 4.0 4.5 + - - -
401A ALA* 1.3 75.4 - - - +
403A PRO* 1.3 77.1 - - - +
404A SER* 3.1 3.6 - - - -
405A LEU* 3.1 18.9 + - - +
406A LEU 4.0 1.2 + - - -
490A LYS* 6.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 4.9 12.5 - - + +
179A ILE* 5.4 11.2 - - + -
182A TRP* 4.5 14.4 - - + -
232A TYR* 4.1 11.4 - - + +
402A GLY* 1.3 82.5 - - - +
404A SER* 1.3 53.5 + - - +
406A LEU* 2.9 11.1 + - + +
407A PHE* 2.6 62.9 + - + -
489A VAL* 6.6 0.2 - - + -
490A LYS* 6.4 1.6 - - - -
565A LEU* 6.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 4.0 5.0 - - - -
400A ASP* 3.5 30.8 + - - -
402A GLY 3.1 1.0 - - - -
403A PRO* 1.3 80.0 - - - +
405A LEU* 1.3 57.8 + - - +
408A ILE* 3.0 42.1 + - - +
409A THR* 3.1 12.2 + - - -
565A LEU* 5.3 3.3 - - - +
566A PHE* 3.2 31.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 5.2 11.9 - - + +
107A TYR* 4.7 18.6 - - + -
379A ILE* 3.8 28.5 - - + -
383A LEU* 4.1 27.1 - - + -
397A VAL 5.7 0.2 - - - +
398A ALA* 4.6 11.4 - - + +
400A ASP* 3.7 24.4 + - - +
401A ALA* 5.0 2.7 - - - -
402A GLY 3.1 14.3 + - - +
403A PRO 3.1 1.0 - - - -
404A SER* 1.3 78.9 - - - +
406A LEU* 1.3 68.7 - - + +
409A THR* 3.4 11.9 - - - +
410A TYR* 2.8 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 5.3 5.2 - - + -
102A VAL* 4.9 8.5 - - + -
103A TRP* 3.9 40.8 - - + -
379A ILE* 3.7 27.6 - - + -
402A GLY 5.0 2.0 - - - +
403A PRO* 2.9 9.8 + - + +
405A LEU* 1.3 83.1 - - + +
407A PHE* 1.3 68.1 + - + +
408A ILE 3.4 0.2 - - - -
410A TYR* 3.5 7.4 - - + +
411A ALA* 3.3 21.3 + - - +
427A PHE* 3.7 33.3 - - + -
428A PHE* 5.1 0.2 - - - -
431A LEU* 4.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 4.1 14.4 - - + -
182A TRP* 3.9 27.1 - + + -
183A ALA* 3.8 22.9 - - + -
186A TYR* 3.5 53.2 + + + +
197A TRP* 6.1 0.2 - - - -
228A ALA* 4.9 2.9 - - - +
232A TYR* 4.0 27.3 - + + +
403A PRO* 2.6 50.3 + - + +
406A LEU* 1.3 78.7 - - + +
408A ILE* 1.3 59.5 + - - +
411A ALA* 3.3 15.5 - - - +
428A PHE* 4.9 6.3 - + - -
431A LEU* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 4.4 5.2 - - - +
228A ALA* 3.9 7.9 - - + +
229A GLU* 3.6 46.4 - - + +
232A TYR* 3.6 36.3 - - + -
233A THR* 4.9 0.4 - - - +
404A SER* 3.0 25.7 + - - +
406A LEU 3.4 0.2 - - - -
407A PHE* 1.3 81.3 - - - +
409A THR* 1.3 65.0 + - - +
410A TYR 3.5 0.2 - - - -
411A ALA 3.9 0.2 - - - -
412A GLU* 2.7 41.8 + - - +
566A PHE* 4.4 9.2 - - + -
----------------------------------------------------------
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