Contacts of the strand formed by residues 53 - 60 (chain B) in PDB entry 1UUG
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 GLU 53 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 3.6 5.3 - - - -
48B ASP* 2.9 38.6 + - + +
51B THR* 3.1 36.0 + - - +
52B ASP* 1.3 78.8 - - - +
54B ASN* 1.3 62.7 + - - +
55B VAL* 3.9 4.5 + - + +
72B ILE* 3.9 25.3 - - + +
73B GLN 3.0 20.4 - - - +
74B ASP* 4.0 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 4.2 15.6 - - - +
190A PRO* 4.1 30.4 - - + +
45B THR* 4.4 6.2 - - + +
46B ALA 3.6 4.9 - - - +
47B TYR* 3.5 26.1 - - - +
53B GLU* 1.3 75.2 - - - +
55B VAL* 1.3 62.2 + - - +
56B MET* 4.3 6.9 - - + +
71B VAL 3.8 1.2 - - - +
72B ILE* 3.6 2.9 - - - +
73B GLN* 2.9 46.2 + - + +
74B ASP 5.6 2.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
8B ILE* 4.2 19.2 - - + +
12B THR* 4.1 24.9 - - + -
16B LEU* 3.6 26.0 - - + -
44B HIS 3.7 1.2 - - - +
45B THR* 3.6 2.4 - - - -
46B ALA* 2.9 38.9 + - + +
48B ASP* 4.6 8.3 - - + +
53B GLU* 4.4 10.5 - - + +
54B ASN* 1.3 77.2 - - - +
56B MET* 1.3 61.3 + - - +
70B LEU* 4.3 15.9 - - + -
71B VAL 3.8 4.3 - - - +
72B ILE* 4.6 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 4.9 0.4 - - - -
190A PRO* 4.1 11.2 - - + -
191A LEU* 3.6 38.1 - - + +
43B VAL* 4.1 16.6 - - + -
44B HIS 3.4 3.1 - - - +
45B THR* 3.7 21.5 - - + +
54B ASN* 4.3 4.5 - - + +
55B VAL* 1.3 77.8 - - - +
57B LEU* 1.3 61.0 + - - +
58B LEU* 3.9 6.9 + - + +
70B LEU* 3.5 6.8 - - - +
71B VAL* 2.8 66.2 + - + +
73B GLN* 3.8 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.0 36.8 - - + +
7B ILE* 4.1 22.0 - - + -
8B ILE* 4.3 18.3 - - + +
44B HIS* 2.9 47.2 + - + +
55B VAL 4.2 0.6 - - - -
56B MET* 1.3 71.9 - - - +
58B LEU* 1.3 63.5 + - - +
59B THR* 4.1 19.7 - - + -
67B PRO* 5.0 2.2 - - + -
69B ALA 3.8 6.7 - - - +
70B LEU* 4.0 12.8 - - + -
84B LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 4.6 7.9 - - + -
29B VAL* 4.4 3.8 - - + -
33B ILE* 4.4 18.8 - - + -
41B ILE* 3.9 22.2 - - + -
42B LEU 3.3 3.8 - - - -
43B VAL* 3.7 35.4 - - + -
56B MET* 4.3 11.2 - - + +
57B LEU* 1.3 77.0 - - - +
59B THR* 1.3 63.2 + - - +
67B PRO* 3.8 0.9 - - - +
68B TRP* 2.9 50.4 + - + -
69B ALA* 2.9 30.3 + - + +
71B VAL* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.7 5.8 - - + -
41B ILE* 3.2 10.2 - - - +
42B LEU* 2.9 28.8 + - - +
44B HIS* 2.8 34.5 + - + +
57B LEU* 4.1 17.0 - - + -
58B LEU* 1.3 79.1 - - - +
60B SER* 1.3 70.0 + - - +
65B TYR* 3.6 23.0 - - - +
66B LYS 3.0 12.1 - - - -
67B PRO* 3.9 11.9 - - + -
68B TRP* 4.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 4.2 14.6 - - - -
40B ASP 3.8 7.9 - - - -
41B ILE* 4.5 2.7 - - - +
42B LEU* 4.0 6.8 - - - +
59B THR* 1.3 89.4 + - - +
61B ASP* 1.3 67.2 + - - +
64B GLU* 3.9 6.2 - - - +
65B TYR* 3.7 8.5 + - - -
66B LYS* 2.7 45.9 + - - +
68B TRP* 5.3 0.6 - - - +
----------------------------------------------------------
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