Contacts of the strand formed by residues 67 - 76 (chain S) 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 TYR 67 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S LYS* 4.8 7.6 - - + -
57S ILE 2.8 19.3 - - - +
58S THR* 4.3 8.1 - - + +
59S PHE* 3.6 3.2 - - - -
66S THR* 1.3 93.1 - - + +
68S MET* 1.3 70.1 + - - +
69S LEU* 3.5 37.5 - - + -
88S GLU* 2.4 26.6 + - - +
89S GLY* 3.3 23.4 - - - -
90S ASP* 3.1 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S LEU* 4.8 2.7 - - + -
39S PHE* 3.8 33.9 - - + -
55S THR 3.6 0.5 - - - +
56S LYS* 3.5 4.7 - - - -
57S ILE* 2.9 54.8 + - + +
59S PHE* 3.8 17.9 - - + -
67S TYR* 1.3 77.0 - - - +
69S LEU* 1.3 63.5 + - - +
70S HIS* 4.2 10.5 - - + -
86S LEU* 3.8 10.1 - - + -
88S GLU 3.6 5.8 - - - -
91S VAL* 3.3 31.6 - - + -
201S 2AN 4.2 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S ILE* 3.8 18.2 - - + -
54S VAL* 4.6 0.4 - - + -
55S THR 3.1 12.6 - - - +
56S LYS* 3.4 33.4 - - + -
67S TYR* 3.5 19.7 - - + -
68S MET* 1.3 74.6 - - - +
70S HIS* 1.3 61.6 + - - +
86S LEU* 3.8 5.0 - - - +
87S PHE* 3.2 48.4 + - + -
88S GLU* 2.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 70 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S ARG* 5.6 4.2 - - - -
31S LEU* 5.3 4.5 - - + +
53S THR 3.3 1.3 - - - +
54S VAL* 3.1 9.4 - - - +
55S THR* 3.0 41.9 + - + +
57S ILE* 3.4 32.2 - - + +
68S MET* 4.2 12.3 - - + -
69S LEU* 1.3 72.9 - - - +
71S LYS* 1.3 61.2 + - - +
72S PHE* 4.2 7.2 - - + -
84S TYR* 3.9 30.8 - + + -
85S THR 3.4 1.8 - - - -
86S LEU* 3.6 47.9 - - + +
87S PHE* 4.0 1.8 - - - -
101S TYR* 4.4 8.1 + - - -
201S 2AN 4.5 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S GLU* 5.4 3.8 + - - -
52S GLY* 5.0 6.3 - - - +
53S THR 3.3 4.3 - - - +
54S VAL* 4.2 16.0 - - + +
70S HIS* 1.3 73.4 - - - +
72S PHE* 1.3 65.3 + - - +
73S ASP* 3.0 25.9 - - - +
84S TYR* 3.3 0.5 - - - -
85S THR* 2.9 37.0 + - + +
87S PHE* 3.4 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S VAL* 4.1 21.8 - - + -
25S LEU* 5.2 11.0 - - + -
27S ARG* 6.2 1.1 - - + -
28S HIS* 4.7 11.9 - + - -
49S GLY* 4.8 5.8 - - - -
51S VAL* 3.4 2.0 - - - +
52S GLY* 2.8 30.2 + - - +
53S THR* 3.0 41.0 + - + +
55S THR* 4.2 20.6 - - + -
70S HIS* 5.0 5.6 - - + -
71S LYS* 1.3 71.7 - - - +
73S ASP* 1.3 61.7 + - - +
74S GLU 3.6 0.7 - - - -
75S ILE* 3.8 33.4 - - + -
82S CYS* 4.7 7.9 - - - -
83S LYS 4.3 0.4 - - - -
84S TYR* 3.7 32.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S VAL* 2.7 23.5 - - - +
52S GLY* 5.7 0.4 - - - -
71S LYS* 3.0 41.2 - - - +
72S PHE* 1.3 69.0 - - - +
74S GLU* 1.3 70.2 + - + +
83S LYS* 3.0 16.0 + - + +
84S TYR* 3.4 4.0 - - - -
85S THR* 2.8 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S VAL* 3.6 6.9 - - + +
72S PHE 3.6 0.2 - - - -
73S ASP* 1.3 85.2 - - + +
75S ILE* 1.3 65.3 + - - +
81S TYR* 4.0 24.7 + - + -
82S CYS* 3.5 3.7 - - - -
83S LYS* 3.0 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S PHE* 4.6 0.4 - - + -
25S LEU* 4.0 26.7 - - + -
49S GLY 4.0 10.5 - - - +
51S VAL* 4.0 35.4 - - + +
72S PHE* 3.8 39.7 - - + -
74S GLU* 1.3 80.2 - - - +
76S ASP* 1.3 62.1 + - - +
77S ALA* 3.8 12.9 + - + +
81S TYR* 3.5 13.2 - - - +
82S CYS* 4.2 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S ILE* 1.3 73.3 - - - +
77S ALA* 1.3 66.2 + - - +
78S ALA* 3.1 10.7 + - - +
79S ASN* 2.8 31.9 + - - +
80S PHE 3.2 3.5 + - - -
81S TYR* 3.0 42.9 + - + +
----------------------------------------------------------
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