Contacts of the strand formed by residues 84 - 90 (chain C) in PDB entry 1CT8
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 84 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLN* 5.2 1.3 - - - -
38C GLN 3.6 12.3 - - - -
39C LYS* 4.6 2.0 - - - -
82C ASP 3.6 1.2 + - - -
83C PHE* 1.3 83.7 - - - +
85C ILE* 1.3 64.3 + - - -
86C TYR* 3.8 8.1 - - - -
102C THR 3.6 1.0 - - - +
103C LYS* 3.6 9.6 - - - +
104C LEU* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR 3.7 0.5 - - - +
37C GLN* 3.5 4.2 - - - -
38C GLN* 2.8 41.7 + - + +
84C GLY* 1.3 75.8 - - - -
86C TYR* 1.3 64.7 + - - +
87C PHE* 3.5 41.1 + - + -
100C ALA 4.8 1.1 - - - +
101C GLY* 4.0 9.6 - - - -
102C THR 3.3 5.6 - - - +
103C LYS* 3.6 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 2.9 19.4 + - - -
21C LEU* 3.4 26.9 - - + -
35C TRP* 4.8 3.4 - - + -
36C TYR 3.3 7.0 - - - +
37C GLN* 2.8 32.3 + - + -
47C LEU* 3.5 27.4 - - + -
62C PHE* 3.9 13.0 - + - -
73C LEU* 3.6 22.2 - - + -
75C ILE* 4.2 7.4 - - + -
82C ASP* 2.8 30.4 + - - +
84C GLY* 3.8 10.8 - - - -
85C ILE* 1.3 77.1 - - - +
87C PHE* 1.3 61.1 + - - +
101C GLY* 3.2 1.6 - - - -
102C THR 2.8 30.6 + - - +
104C LEU* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.5 2.2 - - - -
34C HIS 3.7 0.2 - - - +
35C TRP* 3.3 8.3 - - - -
36C TYR* 2.9 45.3 + - + +
38C GLN* 3.6 30.7 - - + -
44C PRO* 5.6 0.2 - - + -
85C ILE* 3.5 25.1 - - + -
86C TYR* 1.3 73.5 - - - +
88C CYS* 1.3 64.3 + - - +
98C PHE* 4.5 11.2 - - + -
99C GLY 3.2 18.6 - - - -
100C ALA 3.4 21.5 - - - -
101C GLY* 3.5 9.6 - - - -
39D GLN* 4.2 3.6 - - - -
43D GLN 3.9 19.3 - - - -
44D SER* 3.4 21.1 - - - -
45D LEU* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C MET* 4.1 10.9 - - - +
6C GLN* 3.3 24.1 + - - -
23C CYS* 2.0 51.8 - - + -
33C LEU* 4.0 8.1 - - + -
34C HIS 3.0 9.4 - - - +
35C TRP* 3.9 10.1 - - + -
87C PHE* 1.3 76.0 - - - +
89C HIS* 1.3 62.7 + - - +
98C PHE* 3.3 5.2 - - - +
99C GLY 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C MET* 4.3 2.7 - - - -
33C LEU* 3.2 4.0 - - - +
34C HIS* 2.8 37.8 + + + +
36C TYR* 2.9 43.2 + - + -
88C CYS* 1.3 77.4 - - - +
90C GLN* 1.3 69.0 + - - +
91C THR* 3.5 21.4 - - + +
96C LEU* 3.7 19.0 - - - +
97C THR 3.0 27.1 - - - -
98C PHE* 3.6 32.7 - + + -
37D LEU* 5.5 0.2 - - - +
100D PHE* 3.7 23.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 3.5 26.2 - - + +
4C MET* 3.8 16.0 - - + -
29C VAL* 3.7 20.9 - - + -
32C LYS 3.1 10.1 - - - +
33C LEU* 4.5 1.3 - - + -
89C HIS* 1.3 77.6 - - - +
91C THR* 1.3 59.0 + - - +
92C HIS* 2.7 31.5 + - - +
93C GLY 2.9 26.1 + - - -
95C PRO 3.2 11.9 + - - -
96C LEU* 3.6 5.4 - - - -
97C THR* 3.0 47.7 + - - +
----------------------------------------------------------
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