Contacts of the strand formed by residues 62 - 70 (chain E) in PDB entry 3CII
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 62 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR* 3.6 31.4 - - + -
94D THR* 4.1 5.8 - - + -
96D GLN* 3.4 37.0 - - - -
29E GLY 2.9 25.5 + - - -
30E PHE* 2.4 44.2 + + + +
31E HIS* 3.0 33.2 - - - -
33E SER* 3.3 31.4 - - - -
54E LEU* 3.6 21.5 - - + -
55E SER 3.7 2.0 - - - -
56E PHE* 3.5 16.4 - - + -
60E TRP 4.0 1.1 - - - -
61E SER* 1.3 73.5 - - - +
63E TYR* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PHE* 5.0 2.4 - - - -
27D TYR* 2.9 26.6 + + - -
235D PRO* 6.2 0.2 - - + -
26E TYR* 3.8 32.3 - + + +
27E VAL 3.3 15.0 - - - +
28E SER* 4.0 4.7 - - - -
29E GLY 4.9 0.4 - - - +
30E PHE* 4.1 1.6 - - - -
52E SER* 4.4 4.3 + - - -
53E ASP 4.9 0.3 - - - +
54E LEU* 4.4 0.2 - - - +
55E SER* 2.7 67.6 + - - +
56E PHE 3.8 6.2 + - - -
57E SER* 3.4 28.7 - - - -
62E PHE* 1.3 77.8 - - - +
64E LEU* 1.3 71.7 + - - +
65E LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E CYS 3.8 0.5 - - - +
26E TYR* 3.5 6.6 - - - -
27E VAL* 3.0 44.5 + - + +
30E PHE* 4.6 4.3 - - + -
33E SER 5.7 0.4 - - - +
35E ILE* 3.7 27.8 - - + +
51E HIS* 4.8 5.8 - - - +
52E SER* 3.2 28.5 - - - +
54E LEU* 3.7 37.5 - - + +
63E TYR* 1.3 78.1 - - - +
65E LEU* 1.3 60.9 + - - +
66E TYR* 3.8 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D PRO* 3.7 26.9 - - + +
237D GLY* 4.1 23.6 - - - +
10E TYR* 3.7 20.0 - - - +
24E ASN* 3.9 17.3 - - + +
25E CYS 3.4 17.5 - - - +
26E TYR* 3.8 13.7 - - + -
50E GLU 3.7 0.9 - - - +
51E HIS* 3.3 7.3 - - - -
52E SER* 2.8 45.1 + - - +
63E TYR* 6.5 0.2 - - + -
64E LEU* 1.3 75.7 - - - +
66E TYR* 1.3 64.4 + - - +
67E TYR* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU 3.4 4.2 - - - +
24E ASN* 3.5 1.4 - - - -
25E CYS* 2.8 46.2 + - + +
27E VAL* 5.2 0.7 - - + -
35E ILE 5.0 5.2 + - - -
36E GLU* 5.4 0.5 - - - -
37E VAL* 3.4 61.6 + - + +
39E LEU* 3.5 8.8 - - + +
49E VAL* 3.7 26.9 - - + -
50E GLU 3.6 1.8 - - - -
51E HIS* 3.5 33.7 + + + +
64E LEU* 3.8 33.7 - - + +
65E LEU* 1.3 79.1 - - - +
67E TYR* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ARG* 5.9 0.7 + - - -
237D GLY* 5.0 14.6 - - - -
12E ARG* 5.0 3.4 - - - +
22E PHE* 3.8 33.4 - + + -
23E LEU 3.2 6.5 - - - +
24E ASN* 3.4 17.3 - - - +
39E LEU* 4.3 1.8 - - - +
48E LYS 4.3 0.3 - - - +
49E VAL* 3.7 3.1 - - - +
50E GLU* 3.1 73.0 + - + +
51E HIS 4.9 7.3 + - - -
52E SER* 5.0 3.4 - - - -
65E LEU* 4.5 20.9 - - + -
66E TYR* 1.3 76.2 - - - +
68E THR* 1.3 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E PHE* 3.5 9.2 - - - -
23E LEU* 3.1 34.2 + - + -
39E LEU* 3.9 19.5 - - + -
46E ILE* 4.2 29.2 - - + +
48E LYS* 4.0 18.1 + - - +
49E VAL* 4.9 3.6 - - + -
67E TYR* 1.3 82.6 - - - +
69E GLU* 1.3 75.3 + - - +
70E PHE* 3.6 2.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E SER* 4.1 19.6 + - - +
21E ASN 3.7 10.5 - - - +
22E PHE* 4.5 23.2 - - + -
46E ILE* 5.9 0.9 - - - +
68E THR* 1.3 85.9 + - - +
70E PHE* 1.3 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E SER* 4.9 5.8 - - - -
20E SER* 4.3 2.4 - - - -
21E ASN* 3.1 49.0 + - + +
22E PHE 3.4 9.2 - - - -
23E LEU* 3.4 43.5 - - + -
46E ILE* 5.8 2.0 - - + -
68E THR* 4.0 5.8 - - + +
69E GLU* 1.3 80.9 - - - +
71E THR* 1.3 69.9 + - - +
72E PRO* 4.2 22.7 - - + -
78E TYR* 3.5 57.0 - + + +
95E TRP* 4.4 15.0 - + - -
----------------------------------------------------------
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