Contacts of the strand formed by residues 102 - 107 (chain D) in PDB entry 3E5X
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 THR 102 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG 4.1 0.5 - - - +
36D ASP* 3.3 5.2 - - - +
37D PHE* 2.8 41.7 + - + +
43D VAL* 5.1 1.3 - - + -
56D LEU* 3.8 17.9 - - + -
58D GLU* 3.2 11.9 - - - +
60D LYS 3.1 25.2 + - - +
61D ILE* 4.0 15.3 - - + -
98D ALA* 3.9 12.0 - - + +
100D GLU 2.8 18.0 + - - -
101D PRO* 1.3 70.4 - - - +
103D ARG* 1.3 60.5 + - - +
104D THR* 3.9 19.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 3.7 25.4 - - + +
36D ASP* 2.9 38.3 + - - +
56D LEU* 3.8 1.9 - - - +
57D VAL* 2.8 50.5 + - + -
58D GLU* 2.9 24.3 + - + +
101D PRO 4.4 0.2 - - - -
102D THR* 1.3 71.9 - - - +
104D THR* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 3.3 10.2 - - - +
35D ARG 2.7 46.1 + - - +
37D PHE* 3.4 13.6 - - + -
43D VAL* 4.5 0.9 - - + -
54D ILE* 3.6 26.0 - - + -
55D PHE 3.2 6.5 - - - +
56D LEU* 4.8 2.2 - - + -
57D VAL* 4.1 3.6 - - - -
61D ILE* 4.2 11.7 - - + -
102D THR* 3.9 18.6 - - + -
103D ARG* 1.3 78.5 - - - +
105D CYS* 1.3 59.8 + - - +
106D TRP* 2.8 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR* 3.4 41.7 - - + -
32D GLY* 3.7 14.1 - - - -
33D LEU 3.4 6.3 - - - -
34D ILE* 4.0 11.4 - - + -
54D ILE* 3.7 0.2 - - - -
55D PHE* 2.8 41.9 + - + +
57D VAL* 4.0 4.0 - - + +
104D THR* 1.3 74.5 - - - +
106D TRP* 1.3 64.0 + - - +
107D PHE* 3.5 32.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLY* 3.4 2.9 - - - -
33D LEU* 2.7 51.7 + - + +
35D ARG* 3.4 49.7 - - + +
37D PHE* 4.1 3.4 - + - -
43D VAL* 3.5 31.9 - - + -
48D GLU* 4.6 3.6 - - - -
50D ILE* 3.6 32.3 - - + -
52D SER* 3.5 25.8 - - - +
53D MET 3.4 4.7 - - - +
54D ILE* 3.7 28.0 - - + +
104D THR* 2.8 32.1 + - - -
105D CYS* 1.3 73.7 - - - +
107D PHE* 1.3 61.6 + - - +
108D SER 4.0 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 4.3 24.0 - - + -
28D TYR* 3.3 30.7 - - + -
29D THR* 4.1 1.8 - - - -
32D GLY* 3.9 15.5 - - - -
52D SER* 3.3 5.3 - - - -
53D MET* 2.7 43.8 + - + +
55D PHE* 3.7 24.9 - + + -
83D LEU* 5.3 0.7 - - + -
87D LEU* 3.8 3.1 - - - +
105D CYS* 3.5 29.2 - - + -
106D TRP* 1.3 70.5 - - - +
108D SER* 1.3 63.9 + - - +
111D SER* 3.4 17.9 - - - +
112D LEU* 3.6 23.1 - - + +
115D VAL* 4.0 22.7 - - + -
----------------------------------------------------------
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