Contacts of the strand formed by residues 43 - 51 (chain E) in PDB entry 5MEN
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 LEU 43 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 4.8 11.7 - - + -
86D PHE* 5.0 6.7 - - + -
99D TYR 5.4 0.7 - - - +
100D ILE* 5.5 0.2 - - - -
101D PHE* 3.4 56.2 + - + +
35E TYR* 3.7 21.3 - - + -
36E ARG 3.4 2.7 - - - +
37E GLN* 3.8 29.4 - - + +
42E GLY* 1.3 80.7 - - - -
44E ARG* 1.3 59.2 + - - +
90E PHE* 3.7 19.1 - - + -
102E PHE* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D TYR 6.1 0.2 - - - -
35E TYR* 3.6 3.1 - - - -
36E ARG* 2.8 52.9 + - + +
41E MET* 5.7 12.3 - - + -
42E GLY 5.2 0.9 - - - +
43E LEU* 1.3 75.1 - - - +
45E LEU* 1.3 81.6 + - - +
46E ILE* 3.4 8.9 + - - +
60E VAL* 6.3 1.2 - - - +
61E PRO 5.9 1.4 + - - -
64E TYR* 6.3 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LYS* 3.4 37.9 - - + +
99D TYR 4.9 2.3 + - - +
31E TYR* 4.7 0.2 - - - +
33E SER* 4.1 7.2 - - - -
34E TRP 3.7 13.2 - - - +
35E TYR* 3.4 39.7 - - + +
44E ARG* 1.3 96.8 + - - +
46E ILE* 1.3 64.0 + - - +
47E HIS* 3.8 20.6 - - - +
48E TYR* 3.6 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TRP* 2.8 14.7 + - + +
35E TYR 3.9 8.1 - - - +
36E ARG* 3.5 38.1 - - + -
44E ARG* 3.4 5.8 + - - +
45E LEU* 1.3 80.7 - - - +
47E HIS* 1.3 80.6 + - + +
64E TYR* 3.6 42.6 - - + -
76E LEU* 4.1 15.3 - - + -
89E TYR* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E SER* 3.5 1.0 - - - -
34E TRP* 2.9 27.0 + - + +
45E LEU* 3.8 8.0 - - - +
46E ILE* 1.3 103.2 + - + +
48E TYR* 1.3 59.5 + - - +
56E ASP 4.1 2.3 + - - -
57E GLN* 3.2 43.7 - - + +
58E GLY 3.9 10.8 - - - -
59E GLU* 5.7 2.6 + - - -
62E ASN 5.8 0.8 + - - -
64E TYR* 3.9 27.6 + + + +
65E ASN* 5.5 0.2 - - - -
66E VAL* 3.7 36.1 - - + +
74E PHE* 3.7 5.7 - - + -
76E LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLY 4.3 1.0 + - - -
96D THR* 3.5 22.4 - - + +
97D TYR* 3.0 59.1 + + + -
98D LYS* 4.5 1.6 - - + -
31E TYR* 3.1 28.5 - + + +
32E MET 3.4 7.6 - - - +
33E SER* 4.0 5.6 - - - +
45E LEU* 3.6 24.7 - - + -
47E HIS* 1.3 74.5 - - - +
49E SER* 1.3 62.6 + - - +
50E VAL* 3.8 14.8 - - + -
55E THR* 3.6 5.2 - - - -
56E ASP* 3.1 56.2 + - + +
74E PHE* 3.9 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLU 3.4 0.9 - - - +
31E TYR* 3.2 4.3 - - - -
32E MET 2.7 36.1 + - - -
48E TYR* 1.3 75.7 - - - +
50E VAL* 1.3 63.6 + - - +
51E GLY 3.1 1.6 + - - -
54E ILE 2.7 19.5 + - - -
55E THR* 4.1 2.5 - - - +
68E ARG* 2.7 34.4 + - - +
74E PHE* 3.7 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 5.4 1.3 - - + -
72A GLN* 5.0 9.9 - - + +
73A THR* 5.8 0.2 - - + -
6C LEU* 3.4 48.1 - - + +
8C TRP* 3.4 20.0 + - + -
97D TYR* 3.8 13.0 - - + -
30E GLU* 3.7 9.4 - - - +
31E TYR* 4.1 10.5 + - + +
48E TYR* 3.8 28.1 - - + -
49E SER* 1.3 73.2 - - - +
51E GLY* 1.3 56.9 + - - +
54E ILE* 3.4 28.5 + - + +
55E THR* 5.1 0.2 - - - +
56E ASP* 5.5 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TRP* 4.5 13.2 - - - -
30E GLU* 3.2 17.3 - - - -
49E SER* 3.1 2.7 + - - -
50E VAL* 1.3 82.2 - - - +
52E ALA* 1.3 70.0 + - - -
53E GLY 3.1 0.3 + - - -
54E ILE* 2.8 27.0 + - - +
68E ARG* 3.4 6.3 - - - -
----------------------------------------------------------
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