Contacts of the helix formed by residues 13 - 29 (chain G) in PDB entry 1S72
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 13 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11480 C 3.3 28.0 - - - +
11490 U 5.1 3.6 - - - +
11500 A 4.7 6.2 - - + +
12G ILE* 1.3 93.5 - - - +
14G GLU* 1.3 63.8 + - - +
15G TRP* 3.7 26.0 - - + +
16G LYS* 3.4 30.7 + - + +
17G GLN* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ILE 3.2 2.2 + - - +
13G PRO* 1.3 68.0 - - - +
15G TRP* 1.3 61.1 + - - +
16G LYS 2.9 1.6 - - - -
17G GLN* 2.7 40.0 + - + +
18G GLU* 2.8 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12100 G 4.8 4.9 - - - -
13G PRO* 3.7 19.8 - - + +
14G GLU* 1.3 79.3 - - - +
16G LYS* 1.3 89.0 + - + +
18G GLU* 3.6 13.8 + - - +
19G GLU* 3.1 27.7 + - + +
63G ARG* 3.6 36.3 - - - -
66G LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11480 C 5.1 5.6 + - - -
11490 U 3.9 3.8 + - - -
11500 A 2.8 47.0 + - + +
11510 G 2.6 38.1 + - - -
13G PRO* 3.4 30.2 + - + +
14G GLU 2.9 0.4 - - - -
15G TRP* 1.3 120.5 - - + +
17G GLN* 1.3 63.3 + - - +
19G GLU* 3.4 4.6 + - - +
20G VAL* 3.1 29.1 + - - +
63G ARG* 3.9 5.3 - - - +
66G LEU* 4.4 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11500 A 3.9 27.4 - - + +
12G ILE* 2.9 47.2 + - - +
13G PRO 3.3 7.7 + - - +
14G GLU* 2.7 23.6 + - - +
16G LYS* 1.3 75.0 - - - +
18G GLU* 1.3 59.9 + - + +
20G VAL* 3.5 5.1 + - - +
21G ASP* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G GLU* 2.8 34.2 + - + +
15G TRP* 3.9 10.1 + - - +
17G GLN* 1.3 76.5 - - + +
19G GLU* 1.3 60.1 + - - +
21G ASP* 3.1 12.3 + - - +
22G ALA* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11880 A 4.4 20.7 - - - +
15G TRP* 3.1 23.3 + - + +
16G LYS 3.7 5.4 - - - +
17G GLN 3.3 0.2 - - - -
18G GLU* 1.3 73.5 - - - +
20G VAL* 1.3 54.0 + - - +
21G ASP 2.9 4.5 - - - -
22G ALA* 3.1 13.5 + - - +
23G ILE* 2.7 62.4 + - + +
26G MET* 5.9 1.0 - - - +
63G ARG 5.3 4.7 + - - -
66G LEU* 3.6 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11500 A 3.4 24.9 - - + +
16G LYS 3.1 18.4 + - - +
17G GLN* 3.8 6.3 - - - +
18G GLU 3.4 0.2 - - - -
19G GLU* 1.3 75.6 - - - +
21G ASP* 1.3 58.2 + - - +
23G ILE* 4.0 9.0 - - - +
24G VAL* 2.9 26.8 + - + +
66G LEU* 4.0 13.0 - - + +
69G ARG* 3.5 33.0 - - + +
70G ALA 4.2 3.4 - - - +
73G ASP* 3.8 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLN* 3.0 18.6 + - - +
18G GLU* 3.1 12.2 + - - +
19G GLU 2.9 0.4 - - - -
20G VAL* 1.3 76.5 - - - +
22G ALA* 1.3 55.5 + - - +
23G ILE 3.0 0.9 - - - -
24G VAL* 2.9 8.5 + - - +
25G GLU* 2.7 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G GLU 2.9 15.2 + - - +
19G GLU* 3.7 16.4 - - - +
21G ASP* 1.3 75.5 - - - +
23G ILE* 1.3 62.3 + - - +
25G GLU* 3.2 13.5 + - - +
26G MET* 3.1 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLU* 2.7 56.9 + - + +
20G VAL 4.0 1.1 - - - +
22G ALA* 1.3 70.5 - - + +
24G VAL* 1.3 60.7 + - - +
26G MET* 3.3 11.1 + - + +
27G ILE* 2.9 42.0 + - + +
63G ARG 5.8 0.7 - - - +
66G LEU* 3.4 26.7 - - + +
67G LEU* 3.5 33.9 - - + -
70G ALA* 3.1 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G VAL* 2.9 23.5 + - + +
21G ASP* 2.9 8.1 + - - +
23G ILE* 1.3 76.9 - - - +
25G GLU* 1.3 57.5 + - - +
27G ILE* 3.6 10.6 - - + +
28G GLU* 2.9 45.0 + - + +
70G ALA* 3.3 33.2 - - + +
73G ASP* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP* 2.7 15.0 + - - +
22G ALA* 3.3 16.2 - - - +
23G ILE 3.1 0.2 - - - -
24G VAL* 1.3 78.4 - - - +
26G MET* 1.3 60.1 + - + +
28G GLU* 3.0 27.2 + - + +
29G SER* 3.1 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11880 A 4.9 16.4 - - - +
19G GLU* 5.9 1.3 - - - +
22G ALA* 3.1 32.6 + - + +
23G ILE* 3.3 9.6 + - + +
25G GLU* 1.3 78.1 - - + +
27G ILE* 1.3 61.1 + - + +
28G GLU 3.5 0.2 + - - -
29G SER* 3.6 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ILE* 2.9 29.0 + - + +
24G VAL* 3.6 8.5 - - + +
26G MET* 1.3 78.9 - - + +
28G GLU* 1.3 63.0 + - - +
29G SER 4.7 1.9 - - - +
67G LEU* 4.7 0.7 - - + +
70G ALA* 3.4 36.6 - - + +
71G LEU* 3.7 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 2.9 33.4 + - + +
25G GLU* 3.3 15.1 - - - +
27G ILE* 1.3 80.2 - - - +
29G SER* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLU 3.1 14.6 + - - -
26G MET* 3.6 19.9 - - - +
27G ILE 4.7 2.2 - - - +
28G GLU* 1.3 80.2 - - - +
----------------------------------------------------------
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