Contacts of the helix formed by residues 79 - 94 (chain S) 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 ASP 79 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S LEU* 3.9 3.1 - - - -
77S CYS* 3.5 8.0 - - - -
78S THR* 1.3 82.2 + - - +
80S PRO* 1.3 65.2 - - - +
81S ALA* 3.2 29.1 + - - +
82S GLN* 2.9 42.1 + - + +
83S VAL 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S ALA* 5.2 2.5 - - + +
30S VAL* 3.9 16.1 - - + +
31S ASP* 3.7 28.3 - - - +
34S LEU* 3.4 21.9 - - + -
78S THR 3.7 8.1 - - - +
79S ASP* 1.3 90.1 - - - +
81S ALA* 1.3 62.8 + - + +
83S VAL* 3.1 14.1 + - + +
84S LEU* 3.1 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S ASP* 3.2 20.1 + - - +
80S PRO* 1.3 79.8 - - + +
82S GLN* 1.3 56.9 + - - +
84S LEU* 3.9 10.7 - - - +
85S ASN* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S MET* 3.2 28.3 - - + +
77S CYS* 4.0 12.3 - - + -
79S ASP* 2.9 28.9 + - + +
81S ALA* 1.3 81.0 - - - +
83S VAL* 1.3 58.2 + - - +
85S ASN* 3.5 10.8 - - - +
86S GLU* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S VAL* 4.1 24.2 - - + -
33S LEU* 6.4 0.2 - - + -
34S LEU* 4.8 2.0 - - + -
40S PRO* 3.8 35.2 - - + -
42S LEU* 4.2 18.6 - - + +
74S MET* 4.1 11.0 - - - -
77S CYS* 4.1 14.8 - - - -
79S ASP 4.4 1.8 - - - +
80S PRO* 3.1 8.4 + - + +
82S GLN* 1.3 72.8 - - - +
84S LEU* 1.3 65.2 + - - +
85S ASN 3.1 1.1 - - - -
86S GLU* 3.2 4.9 + - - +
87S LEU* 3.1 19.8 + - - +
101S ILE* 4.4 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S THR 5.7 1.3 - - - +
26S LEU* 4.1 35.0 - - + -
27S ALA* 4.6 22.2 - - + -
30S VAL* 4.4 14.1 - - + -
80S PRO* 3.1 22.9 + - + +
81S ALA* 4.0 8.5 - - - +
83S VAL* 1.3 77.2 - - - +
85S ASN* 1.3 62.3 + - - +
87S LEU* 3.3 15.3 + - + +
88S GLU* 3.2 26.9 + - + +
101S ILE* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81S ALA* 2.9 18.8 + - - +
82S GLN* 3.5 13.5 - - - +
84S LEU* 1.3 77.6 - - - +
86S GLU* 1.3 64.4 + - + +
88S GLU* 3.2 10.4 + - - +
89S GLU* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S LEU* 3.8 13.9 - - + -
70S TRP* 2.9 33.5 + - + +
71S LYS* 3.0 30.3 + - - +
74S MET* 3.6 30.8 - - + +
82S GLN* 3.3 13.0 + - - +
83S VAL 3.2 9.0 + - - +
85S ASN* 1.3 79.0 + - - +
87S LEU* 1.3 60.6 + - - +
89S GLU* 3.6 9.6 - - - +
90S CYS* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S LEU* 4.0 27.6 - - + -
42S LEU* 3.6 11.8 - - + +
83S VAL 3.1 12.3 + - - +
84S LEU* 3.3 20.4 - - + +
85S ASN 3.2 0.2 - - - -
86S GLU* 1.3 78.3 - - - +
88S GLU* 1.3 64.2 + - - +
90S CYS* 3.3 1.0 + - - +
91S LYS* 3.0 52.3 + - + +
99S ILE* 3.9 27.4 - - + -
101S ILE* 4.5 9.6 - - + -
117S ALA* 4.1 24.5 - - + +
118S TYR* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S LEU 3.2 12.3 + - - +
85S ASN* 3.2 10.1 + - - +
87S LEU* 1.3 85.3 - - - +
89S GLU* 1.3 56.7 + - - +
91S LYS* 3.3 33.5 + - - +
92S LYS* 3.0 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S TRP* 3.8 15.8 - - + -
71S LYS* 3.4 26.2 + - - -
85S ASN* 3.1 22.6 + - - +
86S GLU* 3.2 14.7 + - - +
88S GLU* 1.3 78.2 - - - +
90S CYS* 1.3 62.0 + - - +
92S LYS* 3.2 24.1 + - - +
93S GLU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S LEU* 4.3 6.5 - - + -
43S GLU 5.6 0.2 - - - -
44S PHE* 4.1 18.4 - - - -
70S TRP* 3.7 45.0 - - + -
86S GLU 2.8 17.8 + - - +
87S LEU 3.7 4.0 - - - +
89S GLU* 1.3 76.9 - - - +
91S LYS* 1.3 52.6 + - - +
93S GLU* 3.2 1.9 + - - +
94S TYR* 2.8 36.6 + - - +
99S ILE* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S LEU* 3.0 34.5 + - + +
88S GLU* 3.3 36.2 + - - +
89S GLU 3.3 0.2 - - - -
90S CYS* 1.3 75.0 - - - +
92S LYS* 1.3 63.6 + - - +
94S TYR 4.2 2.9 - - - -
95S PRO* 3.1 28.7 - - - +
99S ILE* 3.6 22.0 - - + -
117S ALA 5.6 1.0 + - - +
118S TYR* 3.6 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88S GLU* 3.0 14.4 + - + +
89S GLU* 3.4 25.1 - - - +
90S CYS 3.2 0.2 - - - -
91S LYS* 1.3 78.9 - - - +
93S GLU* 1.3 59.6 + - - +
95S PRO* 3.8 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S TRP* 3.5 21.7 - - + -
89S GLU 3.1 13.9 + - - +
90S CYS 3.9 0.9 - - - +
92S LYS* 1.3 78.1 - - - +
94S TYR* 1.3 95.5 + - + +
95S PRO* 3.6 5.7 - - - +
96S ASN* 5.0 0.3 - - - +
3T VAL* 4.4 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S PHE* 3.6 40.6 - + + -
46S THR* 4.0 13.2 - - + -
70S TRP* 4.2 10.8 - + - -
90S CYS* 2.8 22.0 + - - +
91S LYS* 3.4 6.5 - - - +
93S GLU* 1.3 106.8 + - + +
95S PRO* 1.3 60.6 - - - +
96S ASN* 3.1 9.0 + - - -
97S ALA* 3.3 22.0 + - + +
99S ILE* 4.3 2.6 - - - +
118S TYR* 4.1 7.4 - - - -
3T VAL* 5.0 2.7 + - + +
4T TRP 4.2 1.6 + - - -
5T PRO* 3.4 30.8 - - - +
6T THR* 3.6 12.8 + - - -
7T GLN* 3.7 25.6 - - + -
----------------------------------------------------------
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