Contacts of the helix formed by residues 49 - 61 (chain B) 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 PRO 49 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 5.6 8.1 - - - -
47B GLY 3.4 10.1 - - - +
48B VAL* 1.3 88.6 - - + +
50B PRO* 1.3 73.5 - - + +
51B GLU* 3.5 16.8 - - + +
52B GLU* 3.1 18.7 + - + +
53B ALA* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PRO* 4.7 4.3 - - + -
48B VAL 3.6 3.8 - - - +
49B PRO* 1.3 83.3 - - + +
51B GLU* 1.3 75.5 + - - +
53B ALA* 3.8 7.5 - - + +
54B GLY* 2.8 28.2 + - - -
87B ILE* 3.7 16.5 - - + +
95B ASN* 5.8 0.9 - - - +
97B TYR* 3.9 53.4 - - + +
99B CYS* 4.4 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.9 17.5 - - + +
25B TYR* 3.8 43.8 + - + +
49B PRO* 3.5 18.0 - - - +
50B PRO* 1.3 88.9 - - - +
52B GLU* 1.3 57.5 + - - +
54B GLY* 4.0 0.3 - - - -
55B ALA* 3.1 28.1 + - - +
87B ILE* 3.6 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 3.5 16.8 - - - +
20B TYR* 2.8 34.7 + - + -
21B LYS* 2.9 42.3 + - + +
48B VAL* 4.5 9.2 - - + -
49B PRO* 3.1 25.2 + - + +
51B GLU* 1.3 76.9 - - - +
53B ALA* 1.3 60.2 + - - +
55B ALA* 3.7 0.8 - - - +
56B ALA* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.1 6.5 - - + -
44B PRO* 4.0 21.1 - - + -
48B VAL* 4.0 11.4 - - + +
49B PRO 3.0 15.0 + - - +
50B PRO* 3.8 4.0 - - + +
52B GLU* 1.3 74.9 - - - +
54B GLY* 1.3 64.3 + - - +
56B ALA* 3.4 7.0 + - - +
57B VAL* 3.2 28.3 + - - +
129B ALA* 6.3 0.9 - - - -
130B LEU* 3.9 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 5.3 0.7 - - - -
50B PRO 2.8 16.7 + - - -
51B GLU 4.2 0.2 - - - -
53B ALA* 1.3 77.1 - - - +
55B ALA* 1.3 61.5 + - - +
57B VAL* 3.4 8.9 + - - +
58B ALA* 3.1 22.2 + - - +
84B CYS* 3.8 16.4 - - - +
99B CYS* 4.0 23.7 - - - -
101B VAL* 4.7 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.6 6.3 - - - +
21B LYS* 3.4 34.5 - - + +
24B TYR* 3.5 23.4 - - + +
25B TYR* 4.2 1.6 - - + +
51B GLU 3.1 20.0 + - - +
52B GLU 3.7 2.9 - - - +
54B GLY* 1.3 75.6 - - - +
56B ALA* 1.3 60.1 + - - +
58B ALA* 3.3 1.2 + - - -
59B ALA* 2.9 31.4 + - - +
84B CYS* 4.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.5 33.6 - - + +
52B GLU* 2.9 17.7 + - + +
53B ALA* 3.6 8.7 - - - +
54B GLY 3.3 0.2 - - - -
55B ALA* 1.3 76.0 - - - +
57B VAL* 1.3 64.2 + - + +
59B ALA* 3.7 0.3 - - - +
60B GLU* 3.0 30.8 + - - +
124B VAL* 5.0 0.2 - - - -
127B PHE* 4.8 15.0 - - + -
129B ALA* 6.0 4.5 - - + -
130B LEU* 6.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.7 44.2 - - + -
42B VAL* 4.9 5.6 - - + -
53B ALA 3.2 14.5 + - - +
54B GLY* 3.6 10.5 - - - +
55B ALA 3.3 0.2 - - - -
56B ALA* 1.3 80.0 - - + +
58B ALA* 1.3 54.3 + - - +
61B SER* 2.6 34.5 + - - +
99B CYS* 6.4 1.1 - - + -
101B VAL* 4.6 2.2 - - + -
124B VAL* 3.5 18.5 - - + +
130B LEU* 4.1 24.9 - - + -
133B LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 4.2 6.5 - - + +
54B GLY 3.1 13.5 + - - +
55B ALA 3.7 4.5 - - - +
56B ALA 3.3 0.2 - - - -
57B VAL* 1.3 79.0 - - - +
59B ALA* 1.3 55.2 + - - +
61B SER* 3.3 12.9 + - - -
62B SER* 2.7 28.4 + - - -
82B GLY* 4.0 12.0 - - - +
84B CYS 3.9 18.2 - - - +
101B VAL* 3.8 27.6 - - + +
103B TYR* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.5 30.5 - - + -
24B TYR* 3.5 31.6 - - + -
55B ALA 2.9 17.7 + - - +
56B ALA 3.7 0.9 - - - +
58B ALA* 1.3 77.0 - - - +
60B GLU* 1.3 58.2 + - - +
61B SER 3.1 5.0 + - - -
62B SER 3.1 9.4 + - - -
63B THR 3.2 1.2 + - - -
64B GLY* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 2.7 26.6 + - + +
56B ALA 3.0 16.6 + - - +
59B ALA* 1.3 75.5 - - - +
61B SER* 1.3 57.7 + - - +
62B SER 3.4 0.9 - - - -
64B GLY 3.6 16.5 - - - +
65B THR* 3.3 21.2 + - - -
66B TRP* 3.3 4.0 + - - +
119B SER 4.9 0.2 - - - +
123B ASN* 4.9 19.5 + - + +
124B VAL* 3.9 17.4 + - + +
127B PHE* 3.2 34.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 2.6 23.0 + - - -
58B ALA 3.3 3.3 + - - -
59B ALA 3.1 0.4 - - - -
60B GLU* 1.3 78.7 - - - +
62B SER* 1.3 58.2 + - - +
103B TYR* 2.7 37.8 + - - -
107B LEU* 5.3 0.2 - - - +
119B SER* 3.2 43.3 - - - +
120B ILE 4.3 6.1 - - - -
124B VAL* 4.1 10.1 - - - -
----------------------------------------------------------
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