Contacts of the helix formed by residues 49 - 59 (chain A) in PDB entry 6UPQ
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 49 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY 3.3 2.8 + - - -
48A LEU* 1.3 78.1 - - - +
50A LYS* 1.3 57.8 + - - +
52A THR* 3.3 2.9 + - - -
53A LEU* 2.9 29.8 + - - +
152A PHE* 5.2 0.9 - - - -
183A LYS* 3.9 2.1 - - - +
1401A GDP 2.9 52.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.0 21.5 - - + -
43A VAL* 5.2 0.7 - - - +
44A GLY* 3.2 38.3 + - - +
45A GLU 2.9 21.1 + - - +
46A SER* 3.7 5.7 - - - +
48A LEU* 4.3 5.6 - - + -
49A GLY* 1.3 77.1 - - - +
51A SER* 1.3 64.2 + - - +
53A LEU* 3.2 2.6 + - - +
54A ILE* 2.9 29.0 + - - +
63A TYR* 5.3 0.2 - - - -
101A ASP* 5.4 3.8 - - - +
102A THR* 6.1 0.2 - - - -
152A PHE* 3.5 40.4 - - + -
1401A GDP 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 1.3 76.0 - - - +
52A THR* 1.3 62.2 + - - +
54A ILE* 3.5 0.4 + - - -
55A ASN* 3.0 31.7 + - - +
63A TYR* 3.5 39.0 - - - +
66A ARG* 3.4 24.1 + - - -
101A ASP* 5.9 0.4 + - - -
1401A GDP 2.8 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.6 1.3 - - - -
50A LYS 3.2 0.2 - - - -
51A SER* 1.3 80.4 + - - +
53A LEU* 1.3 59.9 + - - +
55A ASN* 3.9 4.9 - - - +
56A SER* 2.9 27.7 + - - -
241A GLY 3.6 6.7 - - - -
242A SER* 3.5 34.1 - - - +
243A ASN* 4.2 7.9 - - + +
1401A GDP 2.7 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 2.9 16.7 + - - +
50A LYS 3.8 3.6 - - - +
52A THR* 1.3 73.0 - - - +
54A ILE* 1.3 66.7 + - + +
56A SER* 3.0 6.3 + - - -
57A LEU* 3.0 28.8 + - + +
150A PHE* 5.0 1.6 - - + -
152A PHE* 3.4 34.1 - - + -
239A VAL* 3.6 24.0 - - + -
240A VAL 3.9 13.0 - - - +
241A GLY* 4.2 5.8 - - - +
273A PHE* 3.6 31.4 - - + -
276A LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.3 10.1 - - + -
42A VAL* 3.6 33.9 - - + -
50A LYS 2.9 21.7 + - - +
51A SER 3.9 1.8 - - - +
53A LEU* 1.3 75.6 - - + +
55A ASN* 1.3 63.3 + - - +
57A LEU* 3.2 19.3 + - + +
58A PHE* 3.3 21.8 - - + -
62A LEU* 3.8 22.4 - - + -
63A TYR* 3.7 23.3 - - + +
99A VAL* 4.2 11.4 - - + -
150A PHE* 4.2 20.9 - - + -
152A PHE* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER* 3.0 22.1 + - - +
52A THR* 4.0 5.7 - - - +
54A ILE* 1.3 75.9 - - - +
56A SER* 1.3 57.4 + - - +
59A LEU* 2.9 32.4 + - - +
60A THR* 2.9 36.7 + - - +
61A ASP* 4.0 8.7 + - - +
62A LEU* 3.2 25.0 + - - +
63A TYR* 3.6 18.2 - - - +
243A ASN* 6.1 5.4 - - + +
254A ARG* 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR 2.9 17.6 + - - -
53A LEU* 3.0 12.6 + - - -
55A ASN* 1.3 76.8 - - - +
57A LEU* 1.3 66.3 + - - +
58A PHE 3.4 0.5 + - - -
59A LEU* 3.8 0.6 + - - -
241A GLY* 3.8 2.6 - - - -
242A SER 3.1 33.2 + - - -
254A ARG* 2.2 38.7 + - - +
265A VAL* 5.1 1.8 - - - -
273A PHE* 3.5 21.7 - - - -
277A ARG* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.0 21.2 + - + +
54A ILE* 3.2 9.6 + - + +
56A SER* 1.3 78.5 - - - +
58A PHE* 1.3 96.2 + - + +
150A PHE* 3.8 29.8 - - + -
273A PHE* 3.7 22.7 - - + +
276A LEU* 4.7 9.4 - - + -
277A ARG* 3.1 66.6 + - + +
280A LEU* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.5 10.3 - - + -
54A ILE* 3.3 26.7 - - + -
55A ASN 3.7 1.4 + - - -
57A LEU* 1.3 103.4 - - + +
59A LEU* 1.3 71.8 + - - +
60A THR* 3.3 17.6 + - + +
62A LEU* 5.7 0.7 - - + -
88A ILE* 3.6 38.0 - - + +
90A GLU* 5.9 0.7 - - - -
95A LEU* 6.3 0.4 - - + -
97A LEU* 3.5 35.9 - - + -
99A VAL* 4.8 0.7 - - + -
277A ARG* 5.3 3.8 - - + +
280A LEU* 3.8 28.7 - - + -
281A ILE* 5.9 5.6 - - + -
284A MET* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN 2.9 9.3 + - - +
56A SER* 3.8 0.6 + - - -
57A LEU 3.7 1.6 - - - +
58A PHE* 1.3 80.8 - - - +
60A THR* 1.3 60.6 + - - +
254A ARG* 3.3 36.1 - - - +
----------------------------------------------------------
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