Contacts of the strand formed by residues 92 - 100 (chain X) 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 ALA 92 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X LYS* 3.7 18.4 - - + -
39X GLN 2.9 19.1 - - - +
40X ALA* 3.2 13.7 - - + -
41X PRO* 3.9 9.9 - - - -
90X ASP 3.5 1.8 + - - -
91X THR* 1.3 80.9 - - - +
93X VAL* 1.3 66.7 + - - +
94X TYR* 3.8 5.7 - - + -
112X THR 3.4 0.5 - - - +
113X LEU* 3.3 7.1 - - - +
114X VAL 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X VAL 3.6 1.9 - - - +
38X LYS* 3.4 2.1 - - - -
39X GLN* 2.7 47.5 + - + +
41X PRO* 6.3 0.4 - - + -
92X ALA* 1.3 71.8 - - - +
94X TYR* 1.3 63.2 + - - +
95X TYR* 3.9 23.1 + - + +
110X GLN 5.1 0.2 - - - +
111X GLY* 3.6 13.2 - - - -
112X THR 3.1 24.7 - - - +
113X LEU* 3.3 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X GLN* 2.4 25.2 + - - +
20X LEU* 3.5 23.3 - - + -
37X VAL 3.5 2.5 - - - -
38X LYS* 2.4 53.7 + - + +
48X ILE* 3.7 15.7 - - + -
64X PHE* 5.4 0.2 - + - -
81X MET* 3.1 26.5 - - + -
83X LEU* 3.7 20.4 - - + +
86X LEU* 5.5 0.2 - - - +
90X ASP* 2.6 25.3 + - - +
92X ALA 3.8 11.9 - - - -
93X VAL* 1.3 73.6 - - - +
95X TYR* 1.3 55.0 + - - +
112X THR* 2.7 34.6 + - - +
114X VAL* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X GLN* 3.0 6.3 - - - +
36X TRP* 3.2 8.2 - - - -
37X VAL* 2.7 40.7 + - + +
39X GLN* 4.2 19.8 + - + -
45X LEU* 5.2 2.0 - - + -
93X VAL* 4.0 20.9 - - + +
94X TYR* 1.3 71.7 - - - +
96X CYS* 1.3 59.4 + - - +
97X THR* 4.1 0.4 + - - -
108X TRP* 3.5 32.5 - + + -
109X GLY 3.4 11.4 - - - -
110X GLN 3.0 24.1 + - - -
111X GLY* 3.1 17.5 - - - -
42Y GLN* 3.7 14.9 + - - -
45Y GLY 4.3 5.5 + - - -
46Y GLN 3.4 19.8 + - - -
47Y PRO* 3.3 20.0 - - + +
48Y PRO* 4.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X LEU* 3.6 15.5 - - - -
6X GLN* 2.8 18.3 + - - +
22X CYS* 2.0 55.0 - - + -
34X MET* 4.5 3.1 - - - -
35X TYR 3.6 7.2 - - - +
36X TRP* 3.9 21.5 - - + -
95X TYR* 1.3 73.4 - - - +
97X THR* 1.3 59.3 + - - +
108X TRP* 3.5 1.0 - - - +
109X GLY* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X LEU* 3.6 1.6 - - - -
34X MET* 2.9 8.3 - - - +
35X TYR* 2.7 45.8 + - + +
37X VAL* 3.8 14.8 - - + -
95X TYR 4.8 0.4 - - - +
96X CYS* 1.3 76.9 - - - +
98X ARG* 1.3 57.6 + - - +
105X MET* 3.4 40.4 - - + +
107X SER 2.6 22.2 + - - -
108X TRP* 3.4 26.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X VAL* 3.4 32.9 - - - +
4X LEU* 3.6 5.3 - - + +
27X TYR* 3.4 50.0 - - + +
32X TYR* 3.4 49.3 + - + -
33X TYR 3.9 0.9 - - - +
34X MET* 3.5 7.9 - - - -
97X THR* 1.3 69.4 - - - +
99X SER* 1.3 61.4 + - - +
100X ASP* 4.8 0.8 + - - +
105X MET* 3.5 2.2 - - - -
106X ASP* 2.5 76.1 + - - +
107X SER* 3.0 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32X TYR* 3.4 21.5 - - - +
33X TYR* 2.8 27.6 + - - +
35X TYR* 3.3 39.3 - - - -
97X THR 3.8 1.6 + - - -
98X ARG* 1.3 74.1 - - - +
100X ASP* 1.3 59.3 + - - +
101X GLY 3.4 1.9 + - - -
102X ARG* 2.8 25.0 + - - -
104X ASP 3.6 6.3 - - - -
105X MET* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C SER* 4.3 5.7 + - - -
32X TYR* 4.2 15.9 - - - -
98X ARG* 3.8 0.9 + - - +
99X SER* 1.3 70.4 - - - +
101X GLY* 1.3 63.6 + - - +
102X ARG 3.1 0.6 + - - +
103X ASN* 3.5 7.4 + - - +
104X ASP* 2.8 52.0 + - - +
106X ASP* 3.4 15.5 - - - +
500X ZN 2.9 18.1 - - - -
53Y LYS* 3.5 9.9 + - - -
54Y TYR* 4.0 4.9 + - - -
----------------------------------------------------------
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