Contacts of the helix formed by residues 59 - 73 (chain A) in PDB entry 1UPX
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 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 4.1 1.6 - - - +
58A VAL* 1.3 78.2 - - - +
60A HIS* 1.3 62.9 + - - +
61A ARG* 3.0 32.8 + - + +
62A ILE* 3.0 33.2 + - + +
63A ASP* 3.8 2.5 + - - +
98A LEU* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL 3.7 1.4 + - - -
59A ASP* 1.3 77.3 + - - +
61A ARG* 1.3 61.7 + - - +
62A ILE 3.1 0.2 - - - -
63A ASP* 2.8 42.6 + - + +
64A ARG* 3.0 52.6 + - + +
161A ASP* 2.8 29.7 + - + -
166A HIS* 3.5 48.5 - + + +
171A ASP* 4.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.0 18.2 + - + +
60A HIS* 1.3 76.6 - - - +
62A ILE* 1.3 61.9 + - + +
64A ARG* 3.4 13.9 + - + +
65A LEU* 3.0 27.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
44A LEU* 4.1 24.2 - - + -
48A ALA* 4.6 1.3 - - + -
58A VAL* 3.8 23.8 - - + -
59A ASP* 3.0 21.2 + - + +
61A ARG* 1.3 80.5 - - + +
63A ASP* 1.3 65.0 + - - +
65A LEU* 3.2 7.7 + - + +
66A VAL* 3.0 24.5 + - + +
94A ALA* 4.1 26.0 - - + +
98A LEU* 4.0 26.9 - - + -
175A GLN* 4.4 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.4 14.7 + - - -
58A VAL* 4.6 2.3 - - - +
59A ASP 4.1 4.6 - - - +
60A HIS* 2.8 43.4 + - + +
62A ILE* 1.3 75.6 - - - +
64A ARG* 1.3 57.6 + - - +
66A VAL* 3.3 2.6 + - - +
67A THR* 3.0 34.1 + - - +
166A HIS* 5.1 1.4 - - - -
168A ASN* 5.2 5.5 - - - +
171A ASP* 3.4 31.6 - - - +
175A GLN* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 3.0 37.7 + - + +
61A ARG* 3.7 15.1 - - + +
62A ILE 3.2 0.2 - - - -
63A ASP* 1.3 73.2 - - - +
65A LEU* 1.3 61.1 + - - +
67A THR* 3.6 7.0 - - - +
68A GLY* 2.9 23.4 + - - -
158A LYS* 3.1 15.7 + - - +
161A ASP* 2.7 45.5 + - - +
164A GLY* 6.2 0.2 - - - -
166A HIS* 5.6 1.0 + - - -
337A GLU* 3.5 7.5 - - - +
338A ILE* 3.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.8 15.5 - - + -
61A ARG* 3.0 13.7 + - + +
62A ILE* 3.5 12.3 - - + +
64A ARG* 1.3 77.4 - - - +
66A VAL* 1.3 55.5 + - - +
69A ASN* 2.9 55.5 + - - +
87A ARG* 3.4 11.9 + - - +
90A MET* 4.0 25.1 - - + +
91A THR* 3.9 17.0 - - - +
94A ALA* 3.6 31.0 - - + -
337A GLU* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.9 16.8 - - + +
44A LEU* 3.8 25.8 - - + -
45A GLY 5.3 0.7 - - - +
62A ILE* 3.0 15.0 + - + +
63A ASP 3.6 7.2 - - - +
65A LEU* 1.3 76.1 - - - +
67A THR* 1.3 66.1 + - + +
69A ASN* 3.3 3.2 + - - +
70A LEU* 3.0 30.3 + - + +
174A MET* 5.2 6.3 - - + -
175A GLN* 4.2 28.0 - - + +
178A LEU* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP 3.0 18.2 + - - +
64A ARG* 3.2 6.9 + - - +
66A VAL* 1.3 77.0 - - + +
68A GLY* 1.3 59.7 + - - +
70A LEU* 3.4 1.9 + - - +
71A PHE* 3.0 30.7 + - - +
154A ALA* 3.9 30.6 - - + +
157A ALA* 4.5 5.6 - - + -
158A LYS* 3.2 27.2 + - - +
161A ASP* 5.5 0.9 + - - +
171A ASP* 4.2 5.6 - - - +
174A MET* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG 2.9 14.1 + - - -
67A THR* 1.3 76.5 + - - +
69A ASN* 1.3 58.2 + - - +
71A PHE* 3.4 0.4 + - - -
72A ALA* 2.9 30.8 + - - +
87A ARG* 3.4 19.0 + - - -
158A LYS* 3.5 19.5 - - - +
325A ILE* 3.7 10.2 - - - +
337A GLU* 3.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 21.8 - - + +
38A ILE* 5.1 1.1 - - + -
41A THR* 2.9 31.4 + - + +
44A LEU* 5.3 0.4 - - - +
65A LEU* 2.9 31.7 + - - +
66A VAL* 3.3 4.4 + - - +
68A GLY* 1.3 76.6 - - - +
70A LEU* 1.3 64.4 + - - +
72A ALA* 3.3 10.0 + - - +
73A THR* 3.4 19.1 - - - +
87A ARG* 2.7 37.9 + - - +
91A THR* 2.8 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.5 24.0 - - + -
41A THR* 4.6 9.0 - - + -
66A VAL* 3.0 23.7 + - + +
67A THR 3.9 0.2 - - - +
69A ASN* 1.3 76.8 - - - +
71A PHE* 1.3 63.1 + - - +
73A THR* 2.8 23.0 + - - -
74A ILE* 3.5 9.6 + - - +
147A THR* 5.1 2.9 - - + +
150A LEU* 3.9 14.1 - - + +
151A LYS* 3.9 21.0 - - + +
154A ALA* 3.7 29.2 - - + -
174A MET* 4.6 5.4 - - + -
178A LEU* 4.1 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR 3.0 17.1 + - - +
68A GLY* 3.8 3.1 - - - +
70A LEU* 1.3 77.2 - - - +
72A ALA* 1.3 63.1 + - - +
74A ILE* 3.0 32.9 + - + +
77A ALA* 3.4 5.9 - - + +
151A LYS 5.1 0.4 - - - -
154A ALA* 5.0 0.6 - - - +
155A ALA* 3.6 41.3 - - + +
158A LYS* 4.0 18.2 - - + -
159A HIS* 3.8 28.7 - + - -
306A THR* 3.8 15.7 - - + -
307A ASN* 3.5 23.3 - - + -
325A ILE* 3.6 31.2 - - + -
489A LYS* 4.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.9 7.6 + - - -
37A LEU* 4.6 1.3 - - + -
68A GLY 2.9 19.0 + - - +
69A ASN* 3.6 6.3 - - - +
70A LEU 3.2 0.2 - - - -
71A PHE* 1.3 75.5 - - - +
73A THR* 1.3 60.5 + - - +
74A ILE 3.5 0.2 - - - -
77A ALA* 4.2 0.4 - - - -
78A ASN* 3.4 27.9 + - + +
84A LEU* 4.3 17.6 - - + +
87A ARG* 4.3 15.9 - - - -
325A ILE* 4.2 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 2.9 22.2 + - - -
34A GLN* 3.5 41.0 - - + +
37A LEU* 4.0 14.6 - - + -
38A ILE* 3.4 19.8 - - + +
69A ASN 3.4 13.9 - - - +
70A LEU 2.8 13.7 + - - -
72A ALA* 1.3 78.8 - - - +
74A ILE* 1.3 60.3 + - - +
151A LYS* 2.9 27.7 + - - -
----------------------------------------------------------
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