Contacts of the helix formed by residues 58 - 70 (chain A) in PDB entry 1UU1
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 ASP 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 2.6 38.8 + - + -
55A ASP* 3.6 11.4 - - - +
56A SER 2.5 8.3 + - - -
57A PRO* 1.3 76.5 - - - +
59A GLU* 1.3 74.3 + - - +
60A GLU* 3.5 8.6 + - - +
61A LEU* 3.4 7.3 + - + +
62A ILE* 3.2 21.5 + - - +
238A GLN* 2.7 22.4 - - - +
242A LYS* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.7 0.2 - - - +
57A PRO 3.8 1.0 + - - -
58A ASP* 1.3 80.8 + - - +
60A GLU* 1.3 63.1 + - - +
62A ILE* 3.4 8.3 + - - +
63A GLU* 3.1 43.1 + - + +
76A LYS* 4.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 3.0 25.6 + - - -
58A ASP* 3.5 5.2 + - - +
59A GLU* 1.3 76.8 - - - +
61A LEU* 1.3 59.5 + - - +
63A GLU* 3.3 14.5 + - - +
64A LYS* 2.9 68.2 + - + +
242A LYS* 3.1 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER 4.6 1.8 - - - +
57A PRO* 5.5 0.9 - - + -
58A ASP* 3.4 11.7 + - + +
59A GLU 3.2 0.6 - - - -
60A GLU* 1.3 79.1 - - - +
62A ILE* 1.3 65.1 + - + +
64A LYS* 3.4 1.5 + - + +
65A ILE* 2.8 49.8 + - + +
81A VAL* 4.5 23.1 - - + -
200A PHE* 4.9 0.7 - - + -
211A VAL* 5.0 3.1 - - + -
238A GLN* 3.6 40.8 - - + +
241A ALA* 3.9 23.6 - - + -
242A LYS* 3.8 30.9 - - + +
245A LEU* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.5 21.3 - - + +
58A ASP 3.2 16.8 + - - +
59A GLU* 3.7 9.0 - - - +
60A GLU 3.2 0.2 - - - -
61A LEU* 1.3 80.6 - - + +
63A GLU* 1.3 67.8 + - + +
65A ILE* 3.3 6.0 + - + +
66A LEU* 2.9 27.6 + - + +
76A LYS* 3.7 43.1 - - + +
79A VAL* 3.7 38.1 - - + +
80A SER* 4.7 4.7 - - - +
81A VAL* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.1 41.4 + - + +
60A GLU* 3.3 16.7 + - - +
62A ILE* 1.3 78.8 - - + +
64A LYS* 1.3 67.0 + - + +
66A LEU* 3.3 11.4 - - + +
67A SER* 2.9 22.5 + - - -
76A LYS* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 4.4 0.2 - - - +
60A GLU* 2.9 59.8 + - + +
61A LEU* 3.7 6.1 - - + +
63A GLU* 1.3 79.9 - - + +
65A ILE* 1.3 62.9 + - - +
67A SER* 3.0 10.5 + - - -
68A TYR* 2.8 22.5 + - - +
242A LYS* 4.1 12.5 + - + +
245A LEU* 3.6 24.9 - - + -
246A ASP* 2.7 45.4 + - - +
248A ARG* 3.8 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 2.8 36.4 + - + +
62A ILE* 3.6 6.7 - - + +
64A LYS* 1.3 73.2 - - - +
66A LEU* 1.3 65.9 + - - +
68A TYR* 2.8 5.3 + - + +
69A LEU* 2.7 49.6 + - + +
79A VAL* 3.8 17.9 - - + -
200A PHE* 3.7 35.4 - - + -
213A TYR* 3.7 32.5 - - + -
245A LEU* 3.6 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 2.9 16.1 + - + +
63A GLU* 3.3 14.8 - - + +
65A ILE* 1.3 74.1 - - - +
67A SER* 1.3 58.5 + - - +
69A LEU* 3.1 10.6 + - + +
70A ASP* 2.9 24.9 + - - -
71A THR 4.5 2.1 + - - -
74A LEU* 4.0 26.0 - - + +
75A SER* 3.7 12.8 - - - +
76A LYS* 3.6 28.7 - - + +
79A VAL* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU 2.9 13.4 + - - -
64A LYS* 3.2 12.3 - - - -
66A LEU* 1.3 78.4 - - - +
68A TYR* 1.3 60.4 + - - +
70A ASP* 3.2 20.0 + - - +
248A ARG* 3.6 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS 2.8 11.1 + - - +
65A ILE* 2.8 11.8 + - - +
67A SER* 1.3 69.2 - - - +
69A LEU* 1.3 71.4 + - + +
70A ASP* 3.0 7.0 + - - +
177A TYR* 4.4 7.2 - + - -
178A GLU* 2.7 39.1 + - - +
198A ARG* 4.1 6.9 + - - -
200A PHE* 6.2 0.2 - + - -
204A PHE* 3.6 22.7 - + - -
213A TYR* 3.4 27.8 - + - -
245A LEU* 4.0 18.6 - - + -
248A ARG* 3.7 40.8 - - + +
252A GLU* 5.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 2.7 44.4 + - + +
66A LEU* 3.5 11.7 - - + +
68A TYR* 1.3 90.2 - - + +
70A ASP* 1.3 69.2 + - - +
71A THR* 3.2 20.5 + - + +
74A LEU* 4.0 16.6 - - + -
79A VAL* 4.4 6.3 - - + -
185A VAL* 5.4 6.4 - - + +
198A ARG* 4.1 14.8 - - - +
213A TYR* 3.8 13.9 - - + +
215A VAL* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 2.9 11.6 + - - -
67A SER* 3.5 17.1 - - - +
68A TYR 3.0 6.0 - - - +
69A LEU* 1.3 78.9 - - - +
71A THR* 1.3 60.7 + - - +
----------------------------------------------------------
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