Contacts of the helix formed by residues 43 - 55 (chain B) in PDB entry 1URP
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 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASN 3.9 5.2 - - - +
42B ASN* 1.3 87.4 - - - +
44B ALA* 1.3 55.4 + - - +
46B GLU* 3.4 11.0 + - + +
47B LEU* 2.9 29.5 + - - +
66B THR* 3.5 22.4 - - - +
67B ASP* 5.3 2.9 - - + -
70B ALA* 3.9 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASN* 2.8 21.6 + - - +
43B PRO* 1.3 73.4 - - - +
45B LYS* 1.3 54.7 + - - +
47B LEU* 3.2 11.0 + - - +
48B ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP 3.8 16.6 - - - +
39B SER 3.5 22.7 - - - +
40B GLN* 3.1 24.0 + - - +
42B ASN* 3.0 20.0 + - - +
44B ALA* 1.3 73.4 - - - +
46B GLU* 1.3 60.1 - - - +
48B ALA* 3.1 11.5 + - + +
49B ASN* 2.8 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.3 2.9 - - + +
39B SER* 3.1 25.4 + - - +
42B ASN 3.0 11.2 + - - +
43B PRO* 3.5 12.9 - - + +
45B LYS* 1.3 74.9 - - - +
47B LEU* 1.3 64.0 + - - +
49B ASN* 3.2 4.4 + - - +
50B VAL* 3.0 27.8 + - - +
63B ILE* 4.0 16.3 - - + +
64B ASN 3.9 3.6 - - - +
65B PRO* 3.3 7.3 - - - +
66B THR* 2.7 41.6 + - + +
70B ALA 4.6 1.0 - - - -
71B VAL* 3.3 37.2 + - + +
74B ALA* 4.5 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO 2.9 15.1 + - - +
44B ALA* 3.4 13.0 - - - +
46B GLU* 1.3 76.7 - - - +
48B ALA* 1.3 61.3 + - - +
50B VAL* 3.3 3.1 + - - -
51B GLN* 3.0 36.0 + - - +
73B ASN* 4.0 14.8 - - + +
74B ALA* 3.6 38.6 - - + +
77B MET* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 2.9 14.0 + - - +
45B LYS* 3.1 17.0 + - + +
47B LEU* 1.3 73.3 - - - +
49B ASN* 1.3 67.2 + - - +
51B GLN* 3.2 14.2 + - - +
52B ASP* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.0 9.8 - - + +
37B LEU* 3.5 37.5 + - + +
38B ASP 3.1 33.3 + - - +
39B SER* 3.5 13.1 + - - +
45B LYS* 2.8 28.9 + - - +
46B GLU 3.5 7.2 - - - +
48B ALA* 1.3 74.5 - - - +
50B VAL* 1.3 62.1 + - - +
52B ASP* 3.3 6.2 + - - +
53B LEU* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.2 12.8 - - + -
46B GLU 3.0 16.0 + - - +
47B LEU 3.8 4.0 - - - +
49B ASN* 1.3 76.7 - - - +
51B GLN* 1.3 61.5 + - - +
53B LEU* 3.3 8.6 + - + +
54B THR* 3.0 32.7 + - + +
61B LEU* 4.4 18.8 - - + -
63B ILE* 3.8 28.3 - - + -
74B ALA* 3.4 32.5 - - + +
77B MET* 4.5 5.4 - - + -
78B ALA* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.0 32.6 + - - +
48B ALA* 3.2 13.7 + - - +
50B VAL* 1.3 74.6 - - - +
52B ASP* 1.3 63.5 + - - +
54B THR* 2.6 27.2 + - - +
55B VAL* 3.4 11.3 + - - +
77B MET* 3.5 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.8 10.2 - - + +
48B ALA 3.0 12.8 + - - +
49B ASN* 3.4 12.9 - - - +
50B VAL 3.3 0.2 - - - -
51B GLN* 1.3 75.4 - - - +
53B LEU* 1.3 62.0 + - - +
55B VAL* 3.1 25.8 - - - +
56B ARG* 3.2 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA* 3.5 29.4 - - + -
6B LEU 5.2 0.2 - - - +
7B VAL* 3.5 32.1 - - + -
35B VAL* 4.3 7.2 - - + -
37B LEU* 3.9 10.8 - - + -
49B ASN 3.0 14.6 + - - +
50B VAL* 3.6 8.1 - - + +
51B GLN 3.3 0.2 - - - -
52B ASP* 1.3 76.6 - - - +
54B THR* 1.3 62.7 + - + +
56B ARG* 3.2 37.4 + - - +
57B GLY 3.6 0.3 + - - -
58B THR* 2.9 40.8 + - + +
61B LEU* 3.8 11.9 - - + -
83B ILE* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.0 24.0 + - + +
51B GLN* 2.6 24.1 + - - +
53B LEU* 1.3 74.3 - - - +
55B VAL* 1.3 69.7 + - - +
57B GLY* 3.2 14.7 + - - -
77B MET* 3.9 31.4 - - + +
78B ALA* 4.3 4.5 - - + +
81B ALA* 4.0 9.8 - - + +
83B ILE* 3.7 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN 3.6 8.1 - - - +
52B ASP* 3.1 23.8 - - - +
54B THR* 1.3 87.6 + - - +
56B ARG* 1.3 61.1 + - + +
57B GLY 3.3 3.3 + - - -
----------------------------------------------------------
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