Contacts of the strand formed by residues 50 - 58 (chain H) in PDB entry 2ZJQ
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 ILE 50 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 2.8 40.0 + - + +
27H SER* 2.9 26.7 - - - -
28H GLY 4.5 2.9 - - - +
34H LEU* 3.7 34.3 - - + -
49H ASP* 1.3 72.3 - - - +
51H ILE* 1.3 76.5 + - - +
71H LYS* 4.5 14.4 - - + +
72H ALA 3.1 16.2 - - - +
73H VAL* 4.2 1.1 - - + -
99H ILE* 4.2 5.6 - - + -
123H PHE* 3.4 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H ILE* 4.3 2.9 - - + -
8H LEU* 3.9 27.6 - - + -
19H ILE* 5.1 1.3 - - + -
21H CYS* 3.8 28.3 - - + -
23H ARG 3.5 6.3 - - - +
24H VAL* 4.2 9.4 - - - -
25H LEU* 3.0 10.3 - - - +
45H ALA* 3.7 29.2 - - + -
50H ILE* 1.3 82.7 - - - +
52H VAL* 1.3 64.5 + - - +
53H ALA* 4.7 6.3 - - + -
71H LYS* 3.3 3.3 - - - -
72H ALA* 2.8 45.2 + - + +
74H VAL* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ILE* 3.1 41.8 + - + -
23H ARG* 3.0 10.8 + - - +
25H LEU* 3.3 33.4 - - + -
51H ILE* 1.3 77.8 - - - +
53H ALA* 1.3 69.2 + - - +
69H VAL* 4.2 16.4 - - + -
70H VAL 3.7 7.4 - - - +
71H LYS* 4.1 10.8 - - + +
2540X A 3.6 21.1 - - - +
2541X U 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ILE* 3.9 28.0 - - + -
20H MET 3.1 17.5 - - - +
21H CYS* 4.3 2.7 - - - -
22H ILE* 3.9 8.0 - - - +
51H ILE* 4.7 6.5 - - + -
52H VAL* 1.3 77.2 - - - +
54H SER* 1.3 64.1 + - - +
69H VAL* 3.5 9.4 - - - +
70H VAL* 2.5 39.4 + - + +
72H ALA* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ILE* 4.5 2.5 - - - -
20H MET* 2.9 27.9 + - - -
22H ILE* 3.9 12.1 - - - -
53H ALA* 1.3 79.4 - - - +
55H VAL* 1.3 68.2 + - - +
56H LYS* 3.2 8.6 + - - +
67H GLY* 5.0 0.3 - - - -
68H ASP 3.8 5.6 + - - -
69H VAL* 4.4 1.8 - - - +
1935X A 2.6 50.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ALA* 4.2 8.5 - - + -
18H GLU 4.1 6.7 - - - +
19H ILE* 4.2 4.9 - - + -
54H SER* 1.3 75.5 + - - +
56H LYS* 1.3 63.5 + - - +
57H ASP 3.6 15.5 - - - +
58H ALA* 3.7 20.9 - - + +
64H VAL* 3.6 23.6 - - + -
65H LYS 3.5 20.6 - - - +
66H ALA* 3.9 2.9 - - - -
67H GLY* 3.1 21.3 + - - +
68H ASP* 3.0 20.1 + - + +
70H VAL* 3.9 15.5 - - + -
1935X A 4.7 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ARG* 3.7 31.8 - - - +
18H GLU* 3.4 11.7 + - - +
20H MET* 3.7 40.7 - - + +
54H SER* 3.2 14.3 + - - +
55H VAL* 1.3 74.8 - - - +
57H ASP* 1.3 77.3 + - - +
66H ALA* 4.9 7.4 - - - +
1934X U 3.3 15.6 + - - -
1935X A 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ARG* 2.8 31.5 + - + +
18H GLU* 3.1 35.5 + - + +
55H VAL* 3.5 3.4 - - - +
56H LYS* 1.3 94.7 - - - +
58H ALA* 1.3 64.1 + - - +
66H ALA* 4.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H GLY 3.4 8.1 - - - +
16H ALA* 3.9 3.8 - - - -
17H ARG* 3.7 7.3 - - - +
55H VAL* 3.7 18.8 - - + +
57H ASP* 1.3 76.7 - - - +
59H ALA* 1.3 64.4 + - - +
60H PRO* 4.7 0.2 - - - +
64H VAL 3.1 28.3 - - - +
65H LYS* 3.7 11.4 - - - -
66H ALA* 3.7 8.7 - - - +
----------------------------------------------------------
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