Contacts of the strand formed by residues 79 - 84 (chain D) in PDB entry 3CJC
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 ARG 79 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 4.6 4.4 - - - +
60A SER 4.9 3.6 + - - -
61A LYS* 5.8 2.2 - - - +
37D ILE 4.1 2.4 - - - +
38D GLN* 4.4 0.9 - - - -
39D GLU 4.2 4.9 + - - -
40D VAL* 2.9 48.5 + - + +
42D ASP 2.9 20.3 + - - +
43D SER* 3.2 26.3 + - - +
45D LEU* 3.5 39.6 - - - +
67D VAL* 4.2 4.9 - - + +
68D SER* 3.3 36.8 + - - +
69D GLU* 4.0 8.3 + - - +
70D PRO* 3.4 38.9 - - + +
71D LEU* 4.3 0.4 - - - -
78D GLU* 1.3 80.9 - - - +
80D TYR* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.3 0.7 - - + +
36D LEU* 4.5 7.9 - - + -
37D ILE 3.9 2.9 - - - -
38D GLN* 4.9 13.2 - - + -
66D VAL 3.9 1.0 - - - +
67D VAL* 3.4 8.0 - - - +
68D SER* 3.4 29.6 + - - +
71D LEU* 4.1 18.2 - - + -
78D GLU* 5.2 4.5 - - + -
79D ARG* 1.3 75.6 - - - +
81D LEU* 1.3 59.7 + - - +
82D PHE* 4.3 4.0 - - + -
111D ARG* 3.0 33.2 + - + +
112D GLU 3.4 24.0 - - - -
113D PRO* 4.5 0.2 - - + -
114D ALA* 3.9 30.5 - - + -
132D ALA* 4.1 11.2 - - + -
133D LEU* 3.4 17.6 - - - +
134D HIS* 3.3 40.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 4.9 5.2 - - + -
35D VAL 3.6 1.0 - - - +
36D LEU* 3.4 4.6 - - - +
37D ILE* 2.8 53.8 + - + +
40D VAL* 4.2 16.2 - - + -
48D VAL* 3.7 39.3 - - + -
51D LEU* 4.9 3.6 - - + -
65D TYR* 4.4 9.4 - - + -
66D VAL 3.6 4.0 - - - +
67D VAL* 3.5 29.4 - - + -
80D TYR* 1.3 76.2 - - - +
82D PHE* 1.3 73.2 + - - +
83D LEU* 4.4 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.6 1.3 - - + -
34D ILE* 4.8 6.7 - - + -
35D VAL 3.2 6.3 - - - -
36D LEU* 3.9 25.4 - - + -
65D TYR* 3.2 7.2 - - - +
66D VAL* 2.8 54.7 + - + +
80D TYR* 4.9 3.1 - - + -
81D LEU* 1.3 75.7 - - - +
83D LEU* 1.3 67.5 + - - +
84D PHE* 4.1 6.5 - - + -
114D ALA* 3.9 20.4 - - + -
116D VAL* 3.5 33.9 - - + -
118D PHE* 4.6 13.5 - + + -
130D ILE* 4.0 27.4 - - + -
132D ALA* 3.5 24.0 - - + -
166D MET* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.9 19.3 - - + -
33D ASP 3.7 1.7 - - - +
34D ILE* 3.5 1.6 - - - -
35D VAL* 2.7 47.4 + - + +
37D ILE* 4.3 12.8 - - + -
51D LEU* 3.6 30.5 - - + -
52D LEU* 3.6 29.4 - - + -
55D LEU* 4.0 7.2 - - + -
63D TYR* 3.9 17.5 - - + -
64D HIS 3.5 4.3 - - - +
65D TYR* 3.9 9.6 - - + -
81D LEU* 4.4 16.8 - - + +
82D PHE* 1.3 82.5 - - - +
84D PHE* 1.3 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ASP 3.3 6.7 - - - +
34D ILE* 4.2 12.1 - - + -
63D TYR* 3.5 6.0 - - - -
64D HIS* 2.9 65.5 + - + -
65D TYR* 4.0 3.1 - - - -
66D VAL* 3.9 18.6 - - + -
82D PHE* 4.9 3.8 - - + -
83D LEU* 1.3 75.9 - - - +
85D ARG* 1.3 70.6 + - - +
86D PRO* 3.6 1.3 - - + -
89D VAL* 3.9 8.7 - - + -
91D VAL* 3.4 29.8 - - + -
118D PHE* 3.8 27.4 - + + -
275D SO4 3.3 39.5 - - - -
----------------------------------------------------------
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