Contacts of the strand formed by residues 228 - 234 (chain E) in PDB entry 3M4D
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 228 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ILE 3.8 0.3 - - - +
56E ARG* 3.2 7.2 - - - +
57E THR* 2.9 40.6 + - - +
85E LYS* 6.1 0.4 - - - -
86E VAL* 3.8 31.2 - - + -
102E TYR 3.5 2.9 - - - -
103E PRO* 3.7 15.3 - - + -
155E THR* 4.2 17.7 - - + -
167E TRP* 3.6 57.4 - + + -
169E VAL* 4.1 8.5 - - + -
224E PHE* 3.7 27.6 - + - -
226E PRO* 3.8 10.3 - - + -
227E ASP* 1.3 87.9 - - + +
229E ALA* 1.3 62.2 + - - +
230E THR* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 4.8 11.7 - - + -
54E VAL* 4.7 8.5 - - + -
55E ILE 3.5 4.0 - - - -
56E ARG* 4.1 22.4 - - + +
101E TYR* 3.1 5.2 - - - -
102E TYR* 2.8 47.3 + - + +
167E TRP* 3.4 5.6 - - - -
228E PHE* 1.3 74.7 - - - +
230E THR* 1.3 62.1 + - - +
231E VAL* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E LEU 3.5 1.6 - - - +
54E VAL* 3.5 3.2 - - - -
55E ILE* 2.8 42.6 + - - +
57E THR* 5.7 0.5 + - - +
88E LEU* 3.5 30.3 - - + +
98E ILE* 4.4 7.6 - - + -
100E ASP 3.7 7.6 - - - +
101E TYR* 4.4 0.9 - - + +
165E VAL* 3.8 18.9 - - + +
167E TRP* 3.4 21.7 - - - -
228E PHE 5.4 0.2 - - - -
229E ALA* 1.3 71.6 - - - +
231E VAL* 1.3 66.2 + - - +
232E ILE* 4.1 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 3.8 47.6 - - + +
7D ILE* 5.1 0.9 - - + -
52E LEU* 3.8 34.8 - - + -
53E LEU 3.6 6.3 - - - +
54E VAL* 4.5 8.1 - - + -
98E ILE* 3.6 4.2 - - - +
99E SER* 2.7 42.3 + - - +
100E ASP* 2.8 27.5 + - + +
230E THR* 1.3 75.7 - - - +
232E ILE* 1.3 57.3 + - - +
24F ASP* 5.9 0.2 - - - +
37F LYS* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E LEU* 3.6 3.6 - - - +
53E LEU* 3.0 35.4 + - + +
55E ILE* 3.4 32.1 - - + -
90E LEU* 4.3 12.1 - - + -
96E ALA* 3.8 25.8 - - + -
97E GLN 3.1 14.8 - - - +
98E ILE* 4.5 8.1 - - + -
230E THR* 4.1 13.7 - - + -
231E VAL* 1.3 79.4 - - - +
233E THR* 1.3 63.3 + - - +
245E ILE* 3.6 20.6 - - + -
284E ILE* 4.6 6.5 - - + -
286E TRP* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E LYS* 3.8 24.5 + - + +
51E LYS 3.4 5.4 - - - -
52E LEU* 3.1 27.8 - - + -
95E VAL 4.8 0.3 - - - +
96E ALA* 3.3 6.1 - - - +
97E GLN* 2.8 47.0 + - - +
99E SER* 3.5 28.0 - - - +
232E ILE* 1.3 72.6 - - - +
234E MET* 1.3 62.0 + - - +
286E TRP* 4.3 0.7 - - - -
24F ASP* 4.1 15.5 - - + +
26F VAL* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E LYS* 3.6 5.2 - - - +
51E LYS* 3.0 34.8 + - + +
95E VAL* 3.4 37.5 - - + -
96E ALA* 3.7 13.9 - - + +
233E THR* 1.3 76.8 - - - +
235E ASP* 1.3 78.2 + - - +
236E ARG 3.4 0.3 + - - -
238E ALA* 4.3 1.1 - - - -
240E LYS 3.6 13.5 - - - +
241E GLN* 4.1 7.9 - - - +
242E GLN 4.8 1.3 - - - +
243E THR* 3.2 27.1 - - - +
286E TRP* 3.3 50.0 - - + +
----------------------------------------------------------
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