Contacts of the strand formed by residues 68 - 77 (chain C) in PDB entry 4OBZ
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 VAL 68 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR 3.8 9.9 - - - +
67C TYR* 1.3 85.6 - - - +
69C LYS* 1.3 71.9 + - + +
70C ASN* 3.7 0.4 + - + -
89C GLN* 2.8 66.9 + - + +
112D ARG* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 3.4 35.9 + - + +
68C VAL* 1.3 83.1 - - + +
70C ASN* 1.3 62.1 - - - +
71C GLY* 5.1 1.1 - - - +
89C GLN* 5.9 0.2 - - - -
1E NAG 4.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 4.7 0.2 + - - -
68C VAL 3.7 2.9 + - - +
69C LYS* 1.3 74.7 - - - +
71C GLY* 1.3 75.1 + - - +
72C THR* 2.8 26.1 + - - -
87C LEU* 3.1 30.3 + - - +
88C SER* 4.5 4.5 - - - +
89C GLN* 5.5 3.8 - - + +
114D VAL* 5.3 2.0 - - + -
1E NAG 1.4 87.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 5.7 0.6 + - - -
69C LYS* 5.1 1.2 - - - +
70C ASN* 1.3 78.8 + - - +
72C THR* 1.4 63.6 + - - +
73C SER* 3.5 5.0 + - - -
86C TYR* 3.5 23.5 - - - +
87C LEU 3.1 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ASN* 2.8 33.2 + - - +
71C GLY* 1.4 68.1 - - - +
73C SER* 1.3 71.3 + - - +
86C TYR* 3.3 0.3 - - - -
87C LEU* 2.7 44.0 + - + +
145D ASN* 4.0 17.9 - - - +
1E NAG 3.5 16.7 + - - +
2E NAG 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLY 3.5 4.2 + - - -
72C THR* 1.3 85.3 - - - +
74C PHE* 1.3 60.3 + - - +
75C ASP* 5.2 3.4 - - - -
85C GLY 3.5 13.5 + - - -
86C TYR* 4.2 1.7 - - - +
145D ASN* 3.6 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 6.1 2.0 - - + -
40C TRP* 4.3 4.5 - - + -
73C SER* 1.3 75.3 - - - +
75C ASP* 1.4 73.8 + - - +
76C ILE* 3.4 37.2 - - + -
83C LEU* 3.8 17.9 - - + -
84C SER* 3.3 5.2 - - - -
85C GLY* 3.2 39.8 + - - +
86C TYR* 3.3 39.9 - - - -
87C LEU* 4.2 14.6 - - + -
116D GLY* 3.6 29.2 - - - -
117D GLU 3.8 3.4 - - - -
118D ALA* 4.1 8.7 - - - -
144D VAL* 4.3 6.7 - - + +
145D ASN* 3.8 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER* 5.2 3.1 - - - -
74C PHE* 1.4 88.0 + - - +
76C ILE* 1.3 61.6 + - - +
77C HIS* 4.3 22.2 + - + +
83C LEU 3.3 7.5 - - - +
84C SER* 3.7 19.4 + - - -
144D VAL* 3.5 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 5.8 1.3 - - - -
38C ASN* 4.8 14.8 - - + +
40C TRP* 3.3 36.1 - - + +
74C PHE* 3.4 30.1 - - + -
75C ASP* 1.3 73.1 - - - +
77C HIS* 1.4 67.6 + - - +
78C TYR* 3.6 29.3 - - + +
82C SER* 3.2 27.2 - - - -
83C LEU* 3.0 22.0 + - + +
144D VAL* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASP* 4.3 26.1 + - + +
76C ILE* 1.4 77.2 + - - +
78C TYR* 1.3 64.7 + - - +
81C GLY 3.9 1.8 - - - -
82C SER* 3.5 25.9 + - - -
83C LEU 5.9 0.2 + - - -
144D VAL* 5.5 1.0 - - - +
----------------------------------------------------------
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