Contacts of the strand formed by residues 67 - 75 (chain E) in PDB entry 2CPK
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 ASN 67 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LYS* 3.5 1.8 - - - -
62E HIS* 2.9 28.0 + - - +
65E SER* 3.4 26.1 + - - +
66E GLY* 1.3 79.6 - - - +
68E HIS* 1.3 66.8 + - - +
69E TYR* 4.1 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE* 3.4 25.6 - - + +
59E LEU* 3.6 24.2 - - + +
60E VAL 3.4 9.3 + - - +
61E LYS* 3.9 26.6 + - + +
66E GLY 4.7 2.5 - - - -
67E ASN* 1.3 81.2 + - - +
69E TYR* 1.3 73.1 + - - +
121E GLU* 5.1 0.2 - - - -
122E TYR* 4.0 19.5 + - + +
321E PRO* 4.3 13.0 + - + +
322E GLY* 4.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PHE* 4.2 4.5 - + - -
59E LEU* 3.4 6.6 - - - +
60E VAL* 2.8 35.9 + - + -
62E HIS* 3.6 35.0 - + + -
65E SER* 4.3 3.6 + - - -
67E ASN* 4.1 26.2 + - + +
68E HIS* 1.3 80.1 - - - +
70E ALA* 1.3 57.8 + - - +
107E GLU* 4.1 26.3 - - + +
108E PHE* 3.7 27.5 - + - -
119E VAL* 3.3 23.8 - - + -
120E MET 3.6 16.4 - - - +
121E GLU* 4.4 7.4 - - + -
122E TYR* 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 4.7 10.1 - - + -
57E VAL* 3.8 19.1 - - + -
58E MET 3.5 6.5 - - - -
59E LEU* 4.7 0.4 - - - +
69E TYR* 1.3 72.5 - - - +
71E MET* 1.3 59.4 + - - +
119E VAL* 3.2 3.1 - - - +
120E MET* 2.8 47.8 + - + +
121E GLU 4.2 9.6 - - - +
122E TYR* 4.0 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E LEU* 4.9 9.6 - - + -
43E PHE* 3.8 22.2 - - + -
56E ARG 3.5 1.7 - - - +
57E VAL* 3.1 5.4 - - - -
58E MET* 2.9 42.6 + - + +
60E VAL* 4.3 19.5 - - + -
69E TYR 4.1 0.2 + - - -
70E ALA* 1.3 73.9 - - - +
72E LYS* 1.3 60.3 + - - +
73E ILE* 3.6 12.6 + - + -
110E PHE* 3.6 22.7 - - + -
117E TYR* 3.8 29.2 - - + -
118E MET 3.3 9.0 - - - +
119E VAL* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PHE* 6.3 0.8 - - - -
55E GLY 6.5 0.7 - - - -
56E ARG 3.4 8.7 - - - +
57E VAL* 4.2 16.4 - - + +
70E ALA 4.2 0.2 - - - -
71E MET* 1.3 70.2 - - - +
73E ILE* 1.3 63.9 + - - +
74E LEU* 3.6 26.0 - - + +
91E GLU* 3.0 39.7 + - - +
116E LEU 3.6 4.2 - - - +
118E MET* 2.7 37.5 + - + +
120E MET* 3.8 25.8 - - + +
184E ASP* 3.7 26.2 + - - +
186E GLY* 5.1 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E GLY* 3.5 4.4 - - - -
56E ARG* 2.7 60.1 + - - +
58E MET* 3.7 26.2 - - + -
71E MET* 4.2 11.0 - - + +
72E LYS* 1.3 73.7 - - - +
74E LEU* 1.4 64.4 + - - +
115E ASN* 3.9 32.1 - - + +
116E LEU 3.6 4.0 - - - -
117E TYR* 3.9 21.8 - - + -
335E ILE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PHE* 3.9 34.3 - - + +
55E GLY* 4.4 2.5 - - - +
72E LYS* 3.6 35.7 - - + +
73E ILE* 1.4 77.3 - - - +
75E ASP* 1.3 60.0 + - - +
76E LYS 3.5 0.3 + - - -
79E VAL* 4.1 12.1 - - + -
88E THR* 4.4 17.0 - - + +
91E GLU* 5.6 0.9 - - - +
115E ASN* 3.1 7.0 - - - -
116E LEU* 2.8 53.8 + - + +
118E MET* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PHE 4.0 7.6 + - - +
55E GLY* 5.1 1.9 - - - -
73E ILE* 5.2 0.2 - - - +
74E LEU* 1.3 71.9 - - - +
76E LYS* 1.3 64.3 + - - +
77E GLN* 3.2 15.0 + - - +
78E LYS* 2.9 40.0 + - + +
79E VAL* 3.0 20.9 + - - +
114E SER* 4.3 7.5 - - - +
115E ASN* 3.8 16.5 - - - +
----------------------------------------------------------
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