Contacts of the strand formed by residues 32 - 38 (chain T) in PDB entry 5EEY
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 PHE 32 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S GLU* 4.6 1.1 - - - -
22T ILE* 3.5 48.5 - - + -
23T GLY 3.5 3.6 - - - -
24T LEU* 4.2 13.2 - - + -
25T THR* 4.4 0.7 - - - -
31T ARG* 1.3 85.4 + - - +
33T HIS* 1.3 60.6 + - - +
34T HIS 4.5 3.1 - - - +
35T SER* 5.0 0.7 - - - +
56T LYS* 4.4 3.4 - - - -
58T ARG* 4.4 7.6 - - - -
143W G 2.9 83.7 + + - +
144W U 3.2 51.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T GLY* 2.9 31.7 + - - -
24T LEU 3.9 6.3 - - - -
25T THR* 3.7 14.8 - - + -
31T ARG* 3.7 2.4 + - - +
32T PHE* 1.3 74.8 - - - +
34T HIS* 1.4 68.2 + - + +
51T HIS* 3.5 25.7 + - + +
52T THR* 2.5 33.6 + - - -
28U ALA* 4.6 17.7 + - - +
30U THR* 4.6 2.4 + - - -
101U TRP* 3.9 35.4 - + - -
144W U 5.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T VAL 3.9 0.5 - - - +
22T ILE* 3.4 4.5 - - - +
23T GLY 2.8 30.2 + - - -
32T PHE* 3.6 3.0 - - - -
33T HIS* 1.4 94.6 + - + +
35T SER* 1.3 73.2 + - - +
36T GLU* 2.7 42.1 + - + -
24U LEU* 5.6 0.2 - - + -
30U THR* 3.4 42.8 + - + +
101U TRP* 3.9 14.1 - + + -
144W U 5.7 4.3 - - - -
147W A 4.1 9.6 - + - -
148W G 3.5 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T ASN* 3.9 7.0 - - - -
21T VAL 3.4 4.7 - - - -
22T ILE* 3.6 19.7 - - - +
32T PHE* 4.3 0.3 - - - -
34T HIS* 1.3 80.8 + - - +
36T GLU* 1.3 61.1 + - - +
37T LYS* 3.5 26.7 - - - -
144W U 3.0 29.2 + - - -
146W G 4.9 1.1 + - - -
147W A 3.3 18.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T VAL 3.6 1.0 - - - +
20T ASN* 3.4 5.0 - - - -
21T VAL* 2.8 39.7 + - + +
34T HIS* 2.7 24.5 + - + +
35T SER* 1.3 73.9 - - - +
37T LYS* 1.3 61.5 + - - +
38T LEU* 4.0 19.5 + - + -
44T LEU* 4.3 20.9 - - + -
24U LEU* 3.9 11.3 - - + +
32U PHE* 4.4 0.7 - - - -
56U LYS* 2.4 36.9 + - + +
101U TRP* 5.6 1.3 - - + -
147W A 3.8 2.9 - - - +
148W G 2.4 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T GLY* 5.1 0.9 - - - +
19T VAL 3.4 2.7 - - - +
20T ASN* 3.0 41.0 + - - +
35T SER* 3.5 30.7 - - - -
36T GLU* 1.3 70.5 - - - +
38T LEU* 1.3 62.4 + - - +
42T GLU* 4.1 2.1 - - - +
56U LYS* 3.8 11.6 + - - -
144W U 3.9 11.1 + - - -
146W G 3.1 82.2 + - + +
147W A 2.9 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T ILE* 4.1 26.9 - - + +
14T ALA* 3.7 16.6 - - + -
16T GLU 3.9 1.4 - - - +
17T ASP 3.9 0.2 - - - -
18T GLY 3.1 5.6 + - - -
19T VAL* 2.8 38.7 + - + +
21T VAL* 3.9 26.7 - - + -
36T GLU* 4.1 11.9 - - + +
37T LYS* 1.3 80.3 - - - +
39T ASP* 1.3 64.4 + - - +
42T GLU* 3.3 21.3 - - + +
44T LEU* 4.1 13.9 - - + +
56U LYS* 3.9 25.8 - - + -
146W G 4.9 0.2 - - - -
----------------------------------------------------------
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