Contacts of the strand formed by residues 74 - 79 (chain Y) in PDB entry 1I9R
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 ASP 74 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y CYS 3.6 3.4 - - - +
24Y ARG* 2.6 59.6 + - - +
70Y GLY* 3.1 4.3 - - - -
71Y SER 3.0 28.2 + - - +
72Y GLY 3.7 0.4 - - - -
73Y THR* 1.3 89.3 + - - +
75Y PHE* 1.3 63.2 + - - +
76Y THR* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Y SER* 3.1 5.7 - - - -
23Y CYS* 2.7 37.2 + - + +
29Y VAL* 3.7 9.9 - - + -
30Y SER* 4.2 0.4 - - - -
35Y SER* 3.6 22.2 - - - -
37Y MET* 3.3 38.6 - - + -
39Y TRP* 3.7 17.7 - - + +
55Y ALA* 3.9 11.9 - - + -
69Y SER 3.3 9.0 - - - +
70Y GLY* 3.2 17.7 - - - -
71Y SER* 2.9 36.8 - - - -
72Y GLY 3.5 20.9 - - - -
73Y THR* 3.9 3.6 - - - -
74Y ASP* 1.3 80.9 - - - +
76Y THR* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Y THR* 4.8 7.6 - - - +
21Y ILE 3.1 14.8 - - - +
22Y SER* 4.1 10.3 - - - -
39Y TRP* 3.3 14.0 + - - -
68Y GLY* 3.3 3.3 - - - -
69Y SER* 2.8 45.8 + - - +
74Y ASP 5.8 0.2 - - - -
75Y PHE* 1.3 80.5 - - - +
77Y LEU* 1.3 59.4 + - - +
78Y THR* 4.5 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y ALA 3.9 0.6 - - - +
20Y THR* 3.3 1.7 - - - -
21Y ILE* 3.0 47.8 + - + +
39Y TRP* 3.4 43.7 - - + +
51Y LEU* 5.6 1.6 - - + -
52Y ILE* 3.3 19.7 - - + -
66Y PHE* 4.3 11.2 - - + -
67Y SER 2.9 25.4 - - - +
68Y GLY* 4.1 0.2 - - - -
76Y THR* 1.3 72.7 - - - +
78Y THR* 1.3 67.2 + - - +
79Y ILE* 4.8 8.3 - - + -
90Y TYR* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Y ARG* 4.2 15.3 + - - +
19Y ALA 3.2 12.5 + - - -
20Y THR* 3.3 26.2 - - + +
65Y ARG 2.9 15.6 - - - +
67Y SER* 2.6 38.5 + - - +
68Y GLY* 5.4 1.1 - - - -
76Y THR* 4.5 10.1 - - - +
77Y LEU* 1.3 83.3 - - - +
79Y ILE* 1.3 67.1 + - - +
80Y SER* 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Y ARG* 3.7 4.5 - - - +
19Y ALA* 3.0 28.4 + - + +
21Y ILE* 6.5 0.4 - - + -
65Y ARG* 3.6 27.4 - - + +
66Y PHE* 3.5 31.2 - - + +
77Y LEU* 4.8 6.5 - - + -
78Y THR* 1.3 73.9 - - - +
80Y SER* 1.3 66.2 + - - +
81Y SER 3.4 10.9 + - - +
82Y VAL* 4.1 8.5 - - + +
86Y ASP* 3.2 31.9 - - + +
90Y TYR* 3.7 18.8 - - + +
108Y LEU* 4.1 16.4 - - + -
----------------------------------------------------------
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