Contacts of the strand formed by residues 54 - 59 (chain G) in PDB entry 4N3E
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 VAL 54 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ILE* 3.8 5.2 - - - +
45G ILE* 3.2 48.6 + - + -
46G GLU* 3.7 26.9 + - + +
52G GLY 3.0 13.4 + - - +
53G THR* 1.3 75.9 - - - +
55G THR* 1.3 72.5 + - - +
69G LEU* 4.2 4.3 - - + -
70G HIS 3.2 5.4 - - - +
71G LYS* 3.7 22.4 - - + +
87G PHE* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G HIS* 3.9 37.6 - - + +
43G GLU 3.1 14.4 - - - +
44G ILE* 4.7 3.1 - - + -
45G ILE 4.2 0.9 - - - +
53G THR* 4.5 14.8 - - + -
54G VAL* 1.3 81.5 - - - +
56G LYS* 1.3 60.8 + - - +
57G ILE* 4.6 3.8 - - - +
68G MET 3.9 0.2 - - - +
69G LEU* 3.2 9.5 - - - +
70G HIS* 3.0 43.8 + - - +
72G PHE* 4.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G SER* 4.2 0.7 + - - +
42G GLY* 3.2 3.3 - - - -
43G GLU* 2.9 41.2 + - - +
45G ILE* 3.6 27.0 - - + +
55G THR* 1.3 75.2 - - - +
57G ILE* 1.3 63.6 + - - +
58G THR* 3.9 20.6 - - - +
67G TYR* 4.1 20.6 - - + -
68G MET 3.4 5.8 - - - +
69G LEU* 3.5 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ARG* 5.3 2.5 - - + -
28G HIS* 4.1 35.7 - - + +
31G LEU* 3.7 26.0 - - + -
32G VAL* 4.7 1.1 - - + -
39G PHE* 3.3 34.1 - - + -
41G SER 3.5 9.2 - - - +
42G GLY* 4.0 0.2 - - - -
55G THR* 4.6 4.7 - - - +
56G LYS* 1.3 77.2 - - - +
58G THR* 1.3 61.5 + - - +
59G PHE* 4.2 2.4 + - - -
67G TYR* 3.2 3.9 - - - -
68G MET* 2.9 52.8 + - + +
70G HIS* 4.2 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G PHE* 3.6 5.5 - - - +
40G LYS* 2.7 56.2 + - + +
41G SER* 2.6 30.3 + - - +
56G LYS* 3.9 23.6 - - - +
57G ILE* 1.3 74.2 - - - +
59G PHE* 1.3 69.2 + - - +
66G THR* 3.5 11.0 - - + +
67G TYR* 4.2 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 3.3 31.0 - - + +
39G PHE* 3.7 25.6 - + - +
40G LYS* 3.5 7.1 + - - +
57G ILE 4.6 0.9 - - - -
58G THR* 1.3 90.9 - - - +
60G VAL* 1.3 73.4 + - - +
61G ASP* 3.7 1.2 + - - +
63G HIS* 3.4 32.5 - + + -
65G LEU* 3.7 30.3 - - + +
66G THR* 2.8 28.9 + - - +
67G TYR* 3.9 7.2 - - - -
68G MET* 4.1 24.5 - - + -
91G VAL* 5.2 0.7 - - + -
201G 2AN 3.8 18.4 - + - -
----------------------------------------------------------
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