Contacts of the strand formed by residues 33 - 38 (chain I) in PDB entry 3UF2
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 ILE 33 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I GLN* 1.3 79.5 - - - +
34I THR* 1.3 66.1 + - - +
35I PHE* 3.9 19.5 - - + -
64I THR* 4.1 15.3 - - + -
106I PHE 3.5 0.7 - - - +
107I TYR* 3.4 5.9 - - - +
108I GLU 3.0 39.0 + - - +
110I PRO* 4.1 30.3 - - + -
113I LEU* 4.0 16.4 - - + -
27J MET* 5.1 4.0 - - + -
29J THR* 4.4 12.6 - - + -
30J SER* 5.1 6.5 - - - +
31J CYS* 4.1 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ILE* 1.3 81.3 - - - +
35I PHE* 1.3 69.7 + - - +
64I THR* 5.1 4.3 + - - +
105I THR* 3.4 28.9 - - + -
106I PHE 3.2 5.2 - - - +
107I TYR* 3.6 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ILE* 3.9 13.5 - - + -
34I THR* 1.3 84.4 - - - +
36I GLU* 1.3 63.5 + - - +
37I PHE* 4.2 15.3 - - + -
60I ILE* 4.4 9.9 - - + -
64I THR* 4.6 13.0 - - + +
105I THR* 3.6 2.5 - - - -
106I PHE* 2.8 63.3 + + + +
108I GLU* 3.9 39.5 - - + -
113I LEU* 3.6 52.0 - - + -
116I LYS* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I THR* 6.4 0.2 - - + -
35I PHE* 1.3 76.6 - - - +
37I PHE* 1.3 62.7 + - - +
56I LEU* 4.5 17.9 - - + +
60I ILE* 3.4 21.3 - - - +
100I LYS* 3.6 34.1 + - - +
103I VAL* 4.6 7.5 - - + +
104I ARG 3.5 8.5 - - - +
105I THR* 4.0 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I PHE* 4.2 9.6 - + + -
36I GLU* 1.3 73.8 - - - +
38I VAL* 1.3 81.0 + - + +
49I TYR* 3.4 22.7 - + - -
53I ALA* 4.1 13.7 - - + -
56I LEU* 3.8 16.8 - - + -
57I VAL* 4.0 21.8 - - + -
60I ILE* 3.8 20.9 - - + -
103I VAL* 3.3 3.5 - - - +
104I ARG 3.0 31.7 + - - +
106I PHE* 3.5 17.6 - - + -
113I LEU* 5.3 1.3 - - + -
116I LYS* 3.7 40.6 - - + -
117I VAL* 5.4 4.3 - - + -
120I VAL* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 1.3 85.1 - - + +
39I ASP* 1.3 68.9 + - - +
40I GLN* 3.6 2.5 + - - +
43I LEU* 4.1 15.3 - - + -
49I TYR* 3.3 39.4 + - + +
52I LYS* 3.7 5.2 - - + -
53I ALA* 3.3 33.7 - - + +
56I LEU* 3.3 23.3 - - + -
102I CYS 3.7 13.7 - - - +
106I PHE* 3.3 19.3 - - - -
116I LYS* 5.4 0.9 - - - -
----------------------------------------------------------
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