Contacts of the helix formed by residues 81 - 90 (chain H) in PDB entry 4PIW
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 PHE 81 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G LYS* 4.1 14.8 - - - -
56H THR* 5.2 0.7 - - - -
80H THR* 1.3 87.2 + - - +
82H VAL* 1.3 89.1 + - + +
83H SER* 3.1 33.1 + - - +
84H THR* 3.2 17.4 + - - +
181H LLP 3.7 47.3 - + + +
320H HIS* 5.6 0.4 - - - -
321H TYR* 3.4 25.7 - + + -
324H LEU* 3.8 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G LYS* 3.6 29.8 - - + -
80H THR 3.9 0.4 + - - -
81H PHE* 1.3 93.6 - - + +
83H SER* 1.3 59.3 + - - +
84H THR 3.2 0.4 - - - -
85H ALA* 3.3 3.5 + - - +
86H ASN* 2.6 45.0 + - - +
324H LEU* 3.8 25.8 - - + -
327H CYS* 6.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G LYS* 4.2 8.8 - - - -
56H THR* 2.7 45.4 + - - +
59H LEU* 4.0 8.8 - - - +
81H PHE* 3.1 27.4 - - - -
82H VAL* 1.3 76.2 - - - +
84H THR* 1.3 63.7 + - - +
86H ASN* 4.5 4.7 - - - +
87H ALA* 3.1 27.4 + - - +
181H LLP 4.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 4.0 8.9 - - + +
76H MSE 3.2 18.4 - - + +
80H THR* 3.0 27.3 + - + +
81H PHE 3.2 9.8 + - - -
83H SER* 1.3 79.3 - - - +
85H ALA* 1.3 57.5 + - - +
87H ALA* 4.9 0.2 - - - -
88H PHE* 3.2 29.2 - - + -
124H VAL* 4.0 21.8 - - + -
126H VAL* 4.3 5.6 - - + -
152H ASP* 2.7 27.1 + - - +
181H LLP 3.9 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H MSE 3.6 14.3 - - - -
81H PHE 4.1 0.8 + - - -
82H VAL* 3.3 9.1 + - - +
83H SER 3.2 0.2 - - - -
84H THR* 1.3 77.2 - - - +
86H ASN* 1.3 69.1 + - - +
87H ALA 3.1 2.0 - - - -
88H PHE* 3.1 7.3 + - - +
89H VAL* 3.1 31.6 + - + +
95H ILE* 4.1 8.4 - - + +
97H PHE* 5.0 4.7 - - + -
324H LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G LYS* 4.2 9.7 - - + +
228G ASP 3.4 8.2 + - - +
229G ILE* 3.3 14.7 - - - +
230G GLY 3.0 42.0 + - - +
56H THR* 6.0 1.1 - - + -
60H GLU* 5.0 1.6 - - - +
82H VAL* 2.6 42.5 + - - +
83H SER* 4.3 5.2 - - - +
85H ALA* 1.3 80.3 - - - +
87H ALA* 1.3 61.1 + - - +
88H PHE 3.2 0.5 + - - -
89H VAL* 3.8 8.3 - - - -
90H LEU* 3.2 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H THR* 4.6 0.9 - - + +
59H LEU* 3.6 38.6 - - + +
60H GLU* 3.6 23.5 + - + +
63H ALA* 3.2 16.6 - - - +
83H SER 3.1 19.8 + - - +
85H ALA 3.1 0.6 + - - -
86H ASN* 1.3 77.5 - - - +
88H PHE* 1.3 68.2 + - + +
90H LEU* 4.7 3.3 + - - +
91H ARG* 4.3 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 4.5 14.1 - - + -
62H ALA 5.1 0.4 - - - -
63H ALA* 3.7 18.8 - - + -
66H LEU* 5.3 0.4 - - + -
68H ILE* 3.5 25.8 - - + -
74H VAL* 3.8 27.8 - - + -
76H MSE 3.8 6.3 - - + -
84H THR* 3.2 25.6 - - + -
85H ALA 3.1 4.7 + - - +
87H ALA* 1.3 86.0 - - + +
89H VAL* 1.3 66.4 + - - +
90H LEU 3.3 2.0 - - - -
91H ARG* 3.1 14.1 + - - +
93H ALA* 3.1 21.2 + - + +
95H ILE* 4.4 5.8 - - + -
122H VAL* 4.3 12.1 - - + -
124H VAL* 4.2 24.5 - - + -
150H VAL* 4.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G ILE* 3.6 19.3 - - + -
85H ALA* 3.1 22.6 + - + +
86H ASN* 4.1 8.7 - - - +
88H PHE* 1.3 76.7 - - - +
90H LEU* 1.3 54.9 + - - +
92H GLY* 2.7 24.4 + - - -
93H ALA 3.7 9.9 - - - +
95H ILE* 3.8 20.4 - - + -
333H PHE* 3.5 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU* 3.9 32.3 - - + -
91G ARG* 2.5 33.4 + - - +
229G ILE* 3.8 32.3 - - + -
230G GLY 3.8 14.6 - - - +
231G SER* 4.8 2.5 - - - -
233G TYR* 5.9 0.7 - - - +
60H GLU* 3.5 30.5 - - + +
86H ASN* 3.2 16.3 + - - +
87H ALA 4.8 3.6 - - - +
88H PHE 3.3 0.6 - - - -
89H VAL* 1.3 77.2 - - - +
91H ARG* 1.3 66.1 + - + +
92H GLY* 3.2 1.4 + - - -
----------------------------------------------------------
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