Contacts of the helix formed by residues 39 - 51 (chain G) in PDB entry 1R4N
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 THR 39 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ASN* 3.4 4.6 + - + -
38G ALA* 1.3 74.7 - - - +
40G ALA* 1.3 61.2 + - - +
41G THR 3.3 3.5 + - - -
42G GLY 3.7 5.6 + - - +
43G THR* 2.8 30.1 + - - -
69G ASP* 4.8 7.0 - - - +
73G ASN* 3.3 8.7 - - - +
85G ARG* 3.5 33.2 - - - +
129G THR* 4.0 2.6 + - - -
130G GLN* 3.4 26.2 - - + +
489G GLU* 3.1 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G THR* 1.3 77.0 - - - +
41G THR* 1.3 51.8 + - - +
43G THR* 3.5 2.1 - - - -
44G GLU* 2.7 39.8 + - - +
72G ASN* 3.5 29.3 - - - +
73G ASN* 3.6 12.4 - - - +
489G GLU* 3.3 23.1 + - + +
491G HIS* 4.3 6.3 - - - +
494G ALA* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G THR* 4.1 3.1 - - - -
40G ALA* 1.3 69.3 - - - +
42G GLY* 1.3 66.6 + - - +
44G GLU* 3.2 2.8 + - - +
45G ILE* 2.9 42.1 + - + +
129G THR* 4.6 5.2 - - + -
130G GLN* 4.0 5.4 + - - -
153G CYS* 4.4 8.5 - - + -
154G ARG 4.9 0.4 - - - +
155G THR* 2.7 32.8 + - - +
489G GLU* 2.4 26.0 + - - -
494G ALA* 3.4 17.9 - - - +
497G LEU* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 3.1 26.1 - - - +
37G ASN 3.7 7.2 - - - -
39G THR* 3.5 8.1 + - - -
40G ALA 3.4 0.2 - - - -
41G THR* 1.3 78.2 - - - +
43G THR* 1.3 61.7 + - - +
45G ILE* 3.1 5.3 + - - +
46G LEU 3.0 19.6 + - - -
129G THR* 3.6 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 4.1 5.1 - - - +
38G ALA* 4.5 3.8 + - - +
39G THR 2.8 24.8 + - - +
40G ALA* 3.7 4.9 - - - +
42G GLY* 1.3 73.6 - - - +
44G GLU* 1.3 72.0 + - - +
46G LEU* 3.3 3.6 + - - +
47G LYS* 2.9 22.3 + - - +
73G ASN* 3.2 28.9 + - - +
74G PHE 4.8 0.7 - - - +
75G PHE* 3.2 33.5 - - + +
89G ALA* 4.3 15.1 - - - +
93G LEU* 3.9 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ALA 2.7 24.3 + - - +
41G THR 3.7 3.8 - - - +
43G THR* 1.3 84.4 - - - +
45G ILE* 1.3 63.7 + - - +
47G LYS* 2.8 33.7 + - - +
48G ASN* 2.9 31.1 + - - +
74G PHE* 4.2 1.0 - - - +
75G PHE* 4.1 4.4 - - - -
491G HIS* 3.1 25.1 + - + -
494G ALA 4.0 10.3 - - - +
495G ALA* 3.9 21.5 - - - +
498G GLY* 4.2 4.7 - - - -
62H GLU* 3.7 2.3 - - - +
65H LYS* 3.1 26.7 + - - +
297H ALA* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 5.7 0.4 - - + -
41G THR* 2.9 20.5 + - + +
42G GLY* 3.1 5.8 + - - +
44G GLU* 1.3 75.4 - - - +
46G LEU* 1.3 64.6 + - + +
48G ASN* 2.9 17.0 + - - +
49G LEU* 3.3 20.4 + - + +
127G VAL* 4.0 17.9 - - + -
129G THR* 3.8 20.4 - - + -
153G CYS* 3.8 31.6 - - + -
497G LEU 5.0 0.2 - - - +
498G GLY* 3.3 24.9 - - - -
501G ALA* 3.9 5.6 - - + -
502G ALA* 3.9 20.3 - - - +
505G VAL* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G VAL* 4.2 20.0 - - + -
35G LEU* 3.7 16.3 - - + +
42G GLY 3.0 15.2 + - - +
43G THR 3.7 4.3 - - - +
45G ILE* 1.3 76.1 - - + +
47G LYS* 1.3 53.0 + - - +
49G LEU* 2.9 13.5 + - + +
50G VAL* 2.7 46.3 + - + +
54G ILE* 5.5 0.4 - - + -
57G PHE* 3.4 50.7 - - + -
59G ILE* 3.6 26.9 - - + -
93G LEU* 3.7 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G THR 2.9 14.7 + - - +
44G GLU* 2.8 34.3 + - - +
45G ILE 3.1 0.2 + - - -
46G LEU* 1.3 76.6 - - - +
48G ASN* 1.3 83.2 + - - +
49G LEU 2.9 5.4 + - - -
50G VAL* 4.0 1.2 - - - +
51G LEU* 2.9 60.7 + - + +
75G PHE* 3.3 32.3 - - + -
93G LEU* 4.2 2.8 - - + +
96G LEU* 3.6 17.0 - - + -
62H GLU* 2.9 22.9 + - - -
65H LYS* 3.7 10.1 - - - +
92H PHE* 4.2 11.6 - - + -
293H ALA* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 2.9 17.9 + - - +
45G ILE 2.9 2.5 + - - +
47G LYS* 1.3 95.0 - - - +
49G LEU* 1.3 62.6 + - - +
52G PRO* 3.0 21.6 - - - +
495G ALA 4.8 0.4 + - - -
498G GLY 2.9 29.5 + - - -
499G GLY* 3.5 6.8 - - - +
502G ALA* 3.3 20.7 - - + +
506G ILE* 4.8 1.0 - - - +
62H GLU* 4.6 0.9 - - - +
293H ALA* 3.7 21.8 - - + +
294H SER* 4.4 7.6 + - - +
297H ALA* 3.7 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU* 5.8 1.1 - - + -
33G VAL* 4.1 23.8 - - + -
45G ILE* 3.5 22.4 - - + +
46G LEU* 2.9 15.3 + - + +
48G ASN* 1.3 82.9 - - - +
50G VAL* 1.3 63.3 + - - +
52G PRO* 2.9 20.6 - - - +
54G ILE* 3.2 35.2 + - + +
502G ALA* 3.3 29.2 - - + +
505G VAL* 4.0 26.2 - - + -
506G ILE* 3.9 17.9 - - + -
509G ILE* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU* 2.7 32.2 + - + +
47G LYS* 4.0 4.7 - - - +
49G LEU* 1.3 73.0 - - - +
51G LEU* 1.3 64.1 + - - +
53G GLY* 2.9 10.7 + - - -
54G ILE* 3.6 9.6 - - + -
57G PHE* 3.7 33.4 - - + -
93G LEU* 4.0 12.1 - - + +
94G GLN* 5.4 0.9 - - - +
96G LEU* 3.9 18.8 - - + -
97G ASN* 3.5 17.0 - - + +
100G VAL* 3.4 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 3.6 6.2 - - - -
47G LYS* 2.9 47.0 + - + +
48G ASN* 4.3 3.8 - - - -
50G VAL* 1.3 73.8 - - - +
52G PRO* 1.3 60.7 - - + +
53G GLY 2.7 15.6 + - - -
96G LEU* 4.2 22.0 - - + +
97G ASN* 3.5 17.7 + - - +
88H LEU 4.3 15.0 - - - +
89H ASN* 3.8 20.3 - - - +
90H ARG* 4.4 8.3 - - - +
92H PHE* 3.8 34.8 - - + +
293H ALA* 4.3 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