Contacts of the strand formed by residues 97 - 103 (chain C) in PDB entry 1IR1
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 TYR 97 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE 3.4 0.3 - - - +
41C ARG* 3.4 2.8 - - - -
42C VAL* 2.6 47.1 + - + +
44C PRO* 4.1 10.3 - - + -
50C PRO* 3.8 42.2 - - + +
87C ILE* 4.1 19.7 - - + -
88C GLU 3.4 7.0 - - - +
89C PRO* 3.9 26.2 - - + -
90C VAL* 3.8 3.8 - - - +
95C ASN* 3.2 40.1 + - - -
96C GLN* 1.3 82.1 - - - +
98C ILE* 1.3 63.3 + - - +
99C CYS* 3.8 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA* 4.4 9.4 - - + -
40C PHE 3.2 5.8 - - - +
41C ARG* 3.9 32.5 - - + +
86C HIS 3.9 0.7 - - - +
87C ILE* 3.5 4.0 - - - -
88C GLU* 2.9 45.0 + - + -
90C VAL* 3.7 21.8 - - + -
97C TYR* 1.3 72.3 - - - +
99C CYS* 1.3 60.4 + - - +
100C TYR* 3.5 32.6 - - + +
136C GLU* 4.9 1.8 - - + -
358C ARG* 4.5 7.4 - - - +
363C TYR* 4.0 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA 3.6 1.4 - - - +
39C ALA* 3.7 0.3 - - - -
40C PHE* 2.8 36.6 + - + +
42C VAL* 3.7 31.6 - - + -
50C PRO* 4.4 4.7 - - - -
54C GLY* 4.0 18.8 - - - -
57C VAL* 6.4 0.9 - - + -
84C CYS* 4.0 13.2 - - - -
86C HIS 3.5 4.0 - - - -
87C ILE* 4.0 25.4 - - - -
97C TYR* 4.4 5.4 - - - -
98C ILE* 1.3 76.8 - - - +
100C TYR* 1.3 63.3 + - - +
101C VAL* 3.9 4.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA 3.3 4.9 - - - +
39C ALA* 4.2 10.1 - - + -
84C CYS* 3.2 6.8 - - - -
85C TYR* 3.0 51.8 + + + +
86C HIS* 2.9 38.9 + + + +
88C GLU* 3.0 26.8 + - - -
98C ILE* 3.5 25.0 - - + +
99C CYS* 1.3 74.4 - - - +
101C VAL* 1.3 60.0 + - - +
356C LYS* 4.5 6.2 + - - -
358C ARG* 3.4 15.9 + - - -
363C TYR* 3.8 16.5 - + + -
364C PHE* 3.7 34.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE 3.8 0.7 - - - +
37C LEU* 3.4 4.0 - - - -
38C ALA* 2.8 38.5 + - - +
40C PHE* 4.2 20.9 - - + -
54C GLY 4.5 4.3 - - - +
57C VAL* 4.8 1.8 - - + -
58C ALA* 3.9 25.8 - - + +
83C ARG 3.2 19.3 - - - +
84C CYS* 4.2 10.5 - - + -
85C TYR* 3.7 3.9 - - - -
99C CYS* 4.6 5.2 - - + +
100C TYR* 1.3 79.2 - - - +
102C ALA* 1.3 65.5 + - - +
103C TYR* 3.5 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TYR* 3.7 30.1 - - + +
35C ASP* 4.1 4.9 - - - +
36C ILE 3.6 4.0 - - - -
37C LEU* 3.7 20.4 - - + -
82C GLY* 3.1 6.8 - - - -
83C ARG* 2.9 35.5 + - + +
85C TYR* 3.8 9.6 - - + -
101C VAL* 1.3 73.6 - - - +
103C TYR* 1.3 62.2 + - - +
104C PRO* 4.1 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASP* 3.3 5.3 - - - -
36C ILE* 2.8 52.2 + - + +
38C ALA* 3.8 20.2 - - + -
40C PHE* 3.5 22.3 - - - -
57C VAL 4.6 0.5 + - - -
58C ALA 4.6 0.7 - - - -
61C SER* 2.8 47.3 + - - -
62C SER* 4.3 7.2 - - - -
82C GLY* 4.4 0.9 - - - -
101C VAL* 3.5 24.2 - - + +
102C ALA* 1.3 77.9 - - - +
104C PRO* 1.3 68.6 - - + +
107C LEU* 4.3 13.5 - - + -
108C PHE* 3.6 25.6 - + + -
119C SER* 5.8 0.4 - - - -
120C ILE* 4.1 25.2 - - + +
----------------------------------------------------------
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