Contacts of the helix formed by residues 75 - 86 (chain A) in PDB entry 3UON
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 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 2.8 25.3 + - + +
74A VAL* 1.3 111.4 - - + +
76A SER* 1.3 66.8 + - - +
77A MET 3.4 1.8 - - - -
78A ASN 3.4 1.4 + - - -
79A LEU* 3.0 42.7 + - + +
99A TRP* 4.0 10.5 - + + -
102A LEU* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.7 3.3 + - - +
72A ILE* 3.2 38.8 + - - +
75A PHE* 1.3 78.4 - - - +
77A MET* 1.3 64.4 + - - +
80A TYR* 3.0 28.2 + - - +
99A TRP* 3.3 14.0 + - - +
102A LEU* 5.7 1.4 - - - +
103A ASP* 3.5 21.0 + - - +
106A VAL* 5.4 0.2 - - - +
430A TYR* 3.7 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 5.6 0.4 - - - +
33A LEU* 4.0 15.9 - - + -
34A SER* 3.9 26.2 - - - +
37A THR* 3.7 14.4 - - + +
72A ILE* 2.9 21.0 + - + +
73A GLY* 4.0 14.4 - - - +
76A SER* 1.3 73.5 - - - +
78A ASN* 1.3 58.8 + - - +
80A TYR* 3.7 1.6 - - - +
81A THR* 2.9 34.3 + - - -
427A TRP* 3.8 18.0 - - + -
430A TYR* 3.6 46.0 - - + +
431A ILE* 3.7 4.3 - - - +
434A THR* 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 4.8 2.3 - - - +
31A GLY* 5.2 3.8 - - - -
34A SER* 3.1 30.4 + - - -
38A ILE* 6.1 1.2 - - - +
73A GLY 3.6 0.8 + - - -
74A VAL* 2.7 34.1 + - - +
75A PHE 3.4 1.8 + - - +
77A MET* 1.3 78.8 - - - +
79A LEU* 1.3 69.0 + - + +
81A THR* 3.2 9.0 + - - +
82A LEU* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL 5.1 1.1 - - - +
75A PHE* 3.0 37.0 + - + +
78A ASN* 1.3 81.7 - - + +
80A TYR* 1.3 57.5 + - - +
82A LEU* 3.3 11.3 + - + +
83A TYR* 2.9 28.1 + - - +
89A TRP* 3.8 24.1 - - + -
91A LEU* 4.5 16.2 - - + -
95A VAL* 4.7 9.6 - - + -
99A TRP* 3.5 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER 3.0 21.7 + - - +
77A MET 3.7 1.8 - - - +
79A LEU* 1.3 72.9 - - - +
81A THR* 1.3 67.5 + - - +
83A TYR* 3.1 12.5 + + - +
84A THR* 2.9 48.1 + - + +
99A TRP* 3.5 26.4 - + + -
419A ASN* 5.5 0.2 + - - -
422A TRP* 4.5 0.3 - - - +
423A THR* 3.3 32.2 + - + -
426A TYR* 3.7 39.5 - + + +
427A TRP* 3.4 39.5 - + - -
430A TYR* 3.8 13.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.7 13.7 - - + +
27A VAL* 5.4 8.3 - - + -
30A ALA* 3.4 21.8 - - + +
77A MET 2.9 10.4 + - - -
78A ASN* 3.4 11.2 - - - +
80A TYR* 1.3 76.7 - - - +
82A LEU* 1.3 66.1 + - - +
84A THR* 2.9 9.8 + - - +
85A VAL* 2.8 34.1 + - + +
427A TRP* 3.0 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN 3.0 12.9 + - - +
79A LEU* 3.3 15.0 - - + +
81A THR* 1.3 76.1 - - - +
83A TYR* 1.3 63.1 + - - +
85A VAL* 3.3 10.4 - - + +
86A ILE* 3.2 51.6 + - + +
89A TRP* 5.6 2.5 - - + -
90A PRO* 4.2 15.3 - - + -
91A LEU* 3.9 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 2.9 14.1 + - - +
80A TYR* 3.1 21.3 + + - +
82A LEU* 1.3 77.3 - - - +
84A THR* 1.3 70.2 + - + +
87A GLY* 3.5 13.0 + - - -
88A TYR* 3.2 36.1 + - - +
89A TRP* 3.4 49.8 - + + -
90A PRO* 5.4 0.2 - - - -
99A TRP* 5.0 6.7 - + + -
174A GLY 3.7 3.7 + - - -
175A GLU* 3.5 10.9 - - - +
176A CYS* 3.3 31.6 + - + -
177A TYR* 5.6 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 6.1 0.9 - - - +
80A TYR* 2.9 54.2 + - + +
81A THR* 2.9 20.3 + - - +
83A TYR* 1.3 83.4 - - + +
85A VAL* 1.3 64.0 + - - +
86A ILE 3.4 0.4 + - - -
87A GLY* 3.7 8.2 + - - -
423A THR* 4.8 11.4 - - + +
427A TRP* 5.1 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.1 35.1 - - + +
26A ILE* 5.0 23.8 - - + -
27A VAL* 5.3 5.6 - - + -
81A THR* 2.8 33.6 + - + +
82A LEU* 3.3 17.5 - - + +
84A THR* 1.3 75.7 + - - +
86A ILE* 1.3 67.4 + - + +
87A GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.2 29.9 + - + +
85A VAL* 1.3 81.8 - - + +
87A GLY* 1.3 56.8 + - - +
88A TYR* 2.9 67.4 - - + +
90A PRO* 4.2 17.0 - - + -
----------------------------------------------------------
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