Contacts of the strand formed by residues 41 - 47 (chain J) in PDB entry 2ZHX
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 41 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ILE 3.3 1.7 - - - +
23J LEU* 3.4 6.4 - - - -
24J MET* 2.8 44.6 + - - +
25J LEU 5.1 0.4 - - - -
29J VAL* 4.3 13.0 - - + -
37J PRO* 3.5 23.8 - - + -
39J SER 3.7 7.8 + - - +
40J ASP* 1.3 77.7 - - - +
42J LEU* 1.3 66.3 + - - +
43J VAL* 3.8 3.5 + - + +
58J LEU* 3.6 31.0 - - + -
59J THR 3.3 15.5 - - - +
60J SER* 4.9 1.6 - - - +
68J TRP* 3.3 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I PRO* 5.0 2.9 - - + +
138I ALA* 4.6 17.7 - - + -
141I ARG* 4.7 3.1 - - - +
21J SER* 4.1 14.6 - - - +
22J ILE 3.2 1.3 - - - -
23J LEU* 3.8 37.5 - - + +
41J ILE* 1.3 72.8 - - - +
43J VAL* 1.3 60.4 + - - +
44J HIS* 3.2 39.0 + - + +
57J LEU 3.3 1.6 - - - +
58J LEU* 3.4 1.6 - - - -
59J THR 2.8 25.7 + - - +
60J SER 3.6 17.5 - - - +
61J ASP* 4.1 10.1 - - - -
62J ALA* 4.3 2.2 - - - +
65J TYR* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I SER* 4.5 4.5 - - - +
195I LEU* 3.7 35.0 - - + -
20J GLU 3.4 4.7 - - - +
22J ILE* 2.5 45.0 + - + +
24J MET* 3.6 32.3 - - + -
29J VAL* 5.4 0.2 - - + -
41J ILE* 4.4 4.0 - - + +
42J LEU* 1.3 72.6 - - - +
44J HIS* 1.3 60.9 + - - +
45J THR* 3.5 11.8 + - - +
56J MET* 4.2 17.5 - - + -
57J LEU 4.1 1.3 - - - -
58J LEU* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I PRO* 3.8 17.5 - - + +
4J LEU* 4.1 15.6 - - + +
8J ILE* 5.6 0.2 - - - +
18J ILE* 3.5 34.1 - - + -
20J GLU 3.2 6.3 - - - +
21J SER* 3.0 25.9 + - - -
42J LEU* 3.2 24.7 + - + +
43J VAL* 1.3 70.5 - - - +
45J THR* 1.3 59.6 + - - +
46J ALA 4.2 0.2 - - - -
55J VAL 3.9 0.5 - - - +
56J MET* 3.0 6.2 - - - +
57J LEU* 2.7 58.7 + - + +
59J THR* 3.3 34.3 - - + +
65J TYR* 4.7 1.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ARG* 3.9 31.0 - - + -
193I SER* 3.9 8.0 + - - -
194I PRO* 4.0 9.9 - - + -
18J ILE* 4.6 2.0 - - - +
19J GLN* 3.0 28.0 + - - +
20J GLU* 2.9 33.5 + - + +
43J VAL* 3.5 11.1 + - - +
44J HIS* 1.3 76.5 + - - +
46J ALA* 1.3 66.8 + - - +
54J ASN* 4.6 3.8 - - + -
55J VAL 3.8 2.0 - - - -
56J MET* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 4.8 8.5 - - + +
16J LEU* 4.1 20.2 - - + -
17J VAL 3.3 28.0 - - - +
18J ILE* 4.1 9.0 - - + +
19J GLN* 4.6 1.3 - - - +
45J THR* 1.3 78.6 - - - +
47J TYR* 1.3 60.8 + - - +
54J ASN* 3.9 1.4 - - - -
55J VAL* 2.9 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I PRO* 4.7 14.9 - - + +
90I TRP 5.4 0.2 - - - +
92I ARG* 3.1 47.1 - - + +
16J LEU* 3.7 16.2 - - - +
17J VAL 4.4 3.9 + - - +
19J GLN* 4.3 15.9 + - - +
46J ALA* 1.3 74.4 - - - +
48J ASP* 1.3 74.2 + - - +
49J GLU* 3.6 30.8 + - + +
52J ASP* 2.8 34.0 + - - +
53J GLU 3.7 7.4 - - - -
54J ASN* 3.1 27.8 - - - -
----------------------------------------------------------
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