Contacts of the helix formed by residues 44 - 57 (chain O) in PDB entry 5GSE
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 GLY 44 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J C 3.5 6.6 + - - -
83J G 3.2 12.6 + - - -
42O ARG 3.1 0.8 + - - -
43O PRO* 1.3 73.5 - - - +
45O THR* 1.3 62.9 + - - +
47O ALA* 4.1 11.0 - - - -
48O LEU* 3.2 18.0 + - - +
44P LYS* 3.2 30.6 + - - -
45P ARG* 5.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I T 4.7 15.3 - - - +
247I C 3.0 36.1 + - - +
117M PRO* 6.0 6.1 - - + -
41O TYR* 4.0 8.3 - - - +
42O ARG* 3.0 17.5 + - + +
43O PRO 5.1 1.1 - - - +
44O GLY* 1.3 79.9 - - - +
46O VAL* 1.3 61.7 + - - +
47O ALA 3.0 1.1 - - - -
48O LEU* 3.1 12.6 - - + +
49O ARG* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J G 3.1 24.3 + - + +
84J C 3.6 25.1 - - - +
41O TYR* 3.6 31.0 - - + -
45O THR* 1.3 80.8 + - - +
47O ALA* 1.3 56.0 + - - +
49O ARG* 3.3 28.9 - - - +
50O GLU* 2.9 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J C 4.7 2.9 - - - +
83J G 3.0 18.1 + - - +
44O GLY* 4.1 15.0 - - - +
45O THR 3.0 0.4 - - - -
46O VAL* 1.3 76.7 - - - +
48O LEU* 1.3 59.1 + - - +
50O GLU* 2.8 22.4 + - - +
51O ILE* 2.9 12.6 + - - +
39P ARG* 3.2 37.9 - - - +
44P LYS* 3.6 13.0 - - + +
45P ARG* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M ILE* 4.7 7.2 - - + -
115M LEU* 3.5 24.7 - - + +
116M LEU* 3.7 20.9 - - + -
117M PRO* 4.6 6.7 - - + -
44O GLY 3.2 20.2 + - - +
45O THR* 3.1 34.3 - - + +
47O ALA* 1.3 76.1 - - - +
49O ARG* 1.3 64.5 + - - +
51O ILE* 3.4 21.8 - - + +
52O ARG* 2.9 56.5 + - - +
44P LYS* 4.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J A 3.4 37.0 + - - -
9J T 3.5 25.8 + - - +
84J C 4.9 2.4 + - - -
41O TYR* 3.3 33.7 - - - -
45O THR 2.9 16.2 + - - +
46O VAL* 3.3 38.4 + - - +
47O ALA 3.2 0.2 - - - -
48O LEU* 1.3 77.3 - - - +
50O GLU* 1.3 58.8 + - - +
52O ARG* 3.3 14.8 + - - +
53O ARG* 3.0 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J G 4.3 5.4 + - - -
46O VAL* 2.9 37.8 + - + +
47O ALA* 2.8 10.3 + - - +
49O ARG* 1.3 75.0 - - + +
51O ILE* 1.3 58.8 + - - +
53O ARG* 4.2 13.7 - - - +
54O TYR* 2.9 52.3 + - + +
35P ARG* 5.1 5.7 + - - +
36P ARG* 6.0 0.7 - - - +
39P ARG* 3.3 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M ILE* 3.6 29.4 - - + -
115M LEU* 5.2 2.7 - - + -
47O ALA 2.9 14.7 + - - +
48O LEU* 3.1 21.5 + - + +
50O GLU* 1.3 76.6 - - - +
52O ARG* 1.3 62.2 + - - +
55O GLN* 2.9 43.0 + - - +
39P ARG* 3.4 25.4 - - - +
42P GLY* 3.6 12.6 - - - +
43P VAL 3.1 36.3 - - - +
44P LYS* 3.9 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I T 5.1 8.3 + - - -
111M ILE* 3.5 24.2 - - + +
116M LEU* 4.1 14.5 - - - +
117M PRO* 5.5 2.4 - - - +
48O LEU* 2.9 50.1 + - - +
49O ARG* 3.6 12.3 - - - +
51O ILE* 1.3 75.8 - - - +
53O ARG* 1.3 62.4 + - - +
55O GLN* 3.9 4.5 - - - +
56O LYS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J T 5.4 9.1 + - - +
49O ARG* 3.0 17.4 + - + +
50O GLU* 3.7 11.7 - - - +
51O ILE 3.3 0.2 - - - -
52O ARG* 1.3 77.2 - - - +
54O TYR* 1.3 96.3 + - + +
56O LYS* 3.3 5.2 + - - +
57O SER* 2.9 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O GLU* 2.9 41.7 + - + +
53O ARG* 1.3 111.8 + - + +
55O GLN* 1.3 63.7 + - - +
57O SER* 3.1 15.2 + - - +
59O GLU* 4.2 7.4 - - - -
61O LEU* 3.6 27.4 - - + -
36P ARG* 3.1 42.7 + - + +
39P ARG* 4.2 10.8 - - + -
40P ARG* 2.8 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M ARG* 3.4 19.4 + - - -
107M VAL* 3.5 13.5 + - + +
108M LEU 4.3 3.4 + - - -
109M PRO* 3.2 15.5 - - + +
110M ASN* 2.7 50.0 + - - +
111M ILE* 4.3 3.3 - - - +
51O ILE* 2.9 28.9 + - - +
52O ARG* 4.0 3.6 - - - +
54O TYR* 1.3 77.1 - - - +
56O LYS* 1.3 60.8 + - - +
57O SER 3.4 5.4 - - - +
39P ARG 4.2 0.4 - - - +
40P ARG* 3.2 35.5 + - - +
41P GLY 4.4 1.0 - - - -
42P GLY* 3.7 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J C 4.0 21.9 + - - +
81M ARG* 4.1 19.9 + - - +
109M PRO* 5.2 8.0 - - + +
52O ARG 2.9 19.8 + - - +
53O ARG* 3.7 4.9 - - - +
55O GLN* 1.3 72.3 - - - +
57O SER* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M ARG* 3.8 6.4 + - - -
106M GLY* 4.6 1.4 - - - -
53O ARG* 2.9 19.5 + - - -
54O TYR* 3.1 15.9 + - - +
55O GLN 3.3 9.8 - - - +
56O LYS* 1.3 82.6 - - - +
58O THR* 1.3 61.1 + - - +
59O GLU* 3.0 25.4 + - - -
40P ARG* 2.4 38.3 + - - -
----------------------------------------------------------
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