Contacts of the strand formed by residues 37 - 43 (chain N) in PDB entry 5X6E
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 TYR 37 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N ILE 3.4 25.8 - - - -
29N PHE* 4.0 17.7 - - + -
35N GLN* 2.6 55.7 + - + +
36N GLU* 1.3 71.8 - - - +
38N CYS* 1.3 67.1 + - - +
39N ILE* 3.9 15.4 - - + +
69N ILE 4.1 0.3 - - - +
70N MET* 3.7 0.3 - - - -
71N SER* 2.3 54.1 + - - +
96N VAL* 3.5 28.3 - - + -
97N ILE 3.5 5.2 - - - +
98N LYS* 3.8 14.8 - - + -
99N ILE* 3.4 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 38 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N PHE* 6.5 1.3 - - - -
37N TYR* 1.3 68.9 - - - +
39N ILE* 1.3 65.3 + - - +
40N PHE* 4.9 1.3 - - - -
68N VAL* 3.8 15.5 - - - -
69N ILE 3.6 4.0 - - - -
70N MET* 3.5 30.5 - - + -
95N TYR 3.7 0.2 - - - +
97N ILE* 2.3 69.2 + - + +
99N ILE* 3.7 3.8 - - + +
102N LEU* 3.6 30.3 - - + -
116N VAL* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N ILE* 3.6 24.2 - - + -
29N PHE* 3.4 37.0 - - + -
37N TYR* 3.9 19.5 - - + -
38N CYS* 1.3 82.8 - - - +
40N PHE* 1.3 61.6 + - - +
41N LEU* 3.5 12.1 + - + +
68N VAL* 3.2 7.6 - - - -
69N ILE* 2.6 49.8 + - + +
85N LEU* 4.1 12.3 - - + -
94N ALA* 4.3 16.2 - - + -
95N TYR 3.5 7.6 - - - +
96N VAL* 4.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N ALA* 4.0 16.2 - - + -
8N PHE* 3.4 32.1 - + + -
9N LYS* 4.4 16.4 - - + -
12N LEU* 4.0 25.1 - - + -
38N CYS* 4.3 1.3 - - - -
39N ILE* 1.3 70.5 - - - +
41N LEU* 1.3 66.5 + - - +
42N TYR* 3.4 35.4 + + + -
66N ALA* 4.5 8.1 - - + -
67N PHE 3.5 9.0 - - - -
68N VAL* 4.3 12.6 - - + +
93N THR 4.3 0.2 - - - +
95N TYR* 3.0 41.4 + + + +
97N ILE* 4.6 4.1 - - + +
115N TYR* 3.5 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N ILE* 4.5 9.2 - - + -
39N ILE* 3.5 5.3 + - + +
40N PHE* 1.3 74.3 - - - +
42N TYR* 1.3 58.9 + - - +
43N ASP 3.9 14.1 - - - +
44N GLY 3.5 22.2 - - - +
46N THR* 3.8 24.5 - - + -
63N TYR* 3.7 22.4 - - + +
64N LYS* 3.8 4.5 - - - +
65N GLY 2.8 17.3 - - - +
66N ALA* 3.1 1.2 - - - -
67N PHE* 2.7 44.4 + - + +
69N ILE* 4.2 11.7 - - + -
85N LEU* 5.5 0.2 - - + -
87N VAL* 6.3 0.4 - - + -
92N ALA* 5.2 7.4 - - + -
93N THR 4.4 2.2 - - - +
94N ALA* 4.4 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N GLU* 3.1 46.9 + - + +
9N LYS* 4.2 27.1 - - + -
40N PHE* 3.4 25.7 + + + -
41N LEU* 1.3 73.7 - - - +
43N ASP* 1.3 67.8 + - + +
65N GLY* 2.9 19.8 - - - -
66N ALA* 3.0 11.1 + - + +
93N THR* 3.4 23.6 + - - +
95N TYR* 5.5 4.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N LEU* 3.9 13.4 - - - +
42N TYR* 1.3 84.6 - - + +
44N GLY* 1.3 64.7 + - - +
65N GLY* 4.1 5.2 - - - -
91N GLN* 4.7 11.7 + - - +
92N ALA* 3.8 3.8 - - - -
93N THR* 2.2 53.9 + - - +
----------------------------------------------------------
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