Contacts of the strand formed by residues 43 - 52 (chain B) in PDB entry 4LHZ
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 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.1 23.7 - - - +
38B ILE* 4.3 1.1 - - - -
41B ILE* 3.3 6.7 - - + +
42B GLY* 1.3 82.0 - - - +
44B ASP* 1.3 66.6 + - - +
62B TRP* 3.4 35.7 - - + -
63B ASP 3.3 8.5 - - - +
64B THR* 5.0 2.7 - - - -
67B GLN* 6.3 0.2 - - + -
70B PHE* 4.0 27.8 - - + -
73B ILE* 4.4 2.2 - - + -
74B THR* 3.6 31.9 - - + -
77B TYR* 4.0 14.1 - - + -
201C PHE* 3.9 16.1 - - + -
196D LEU* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 5.2 2.2 - - + -
25B LEU* 5.8 1.1 - - + -
26B PHE* 4.1 9.2 - - + -
36B THR* 2.8 16.6 + - - +
37B PHE* 2.7 36.2 + - - -
38B ILE* 4.3 8.7 - - + +
43B ILE* 1.3 79.2 - - - +
45B PHE* 1.3 68.6 + - - +
62B TRP* 3.5 6.6 - - - -
63B ASP* 2.6 51.5 + - + +
201C PHE* 4.2 4.8 - - - -
205C HIS* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.9 2.8 - - - +
44B ASP* 1.3 89.3 + - - +
46B LYS* 1.3 78.1 + - - +
47B ILE* 3.2 39.7 - - + -
60B GLN* 4.1 19.5 - - + -
61B ILE 3.4 13.7 - - - -
62B TRP* 3.2 57.7 - + + -
198C ALA* 3.4 27.1 - - + -
201C PHE* 3.8 23.8 - - + -
202C GLU* 3.3 10.8 - - + +
205C HIS* 3.9 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.4 25.8 - - + +
26B PHE* 4.4 11.9 - - + -
29B SER* 3.3 31.9 - - - +
31B ASP* 2.5 34.3 + - - +
35B SER 5.0 0.4 + - - -
45B PHE* 1.3 94.0 - - - +
47B ILE* 1.3 63.5 + - - +
60B GLN* 4.0 0.5 - - - -
61B ILE* 3.0 35.1 + - - +
202C GLU* 4.8 1.3 - - - -
205C HIS* 3.0 47.6 + - + +
209C ARG* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 3.9 9.8 + - - +
45B PHE* 3.2 22.4 - - + -
46B LYS* 1.3 75.0 - - - +
48B ARG* 1.3 75.7 + - - +
49B THR* 4.6 5.4 - - - +
58B LYS* 5.1 5.2 - - + -
59B LEU 3.2 14.8 - - - +
60B GLN* 3.9 22.9 - - + +
61B ILE* 5.3 0.4 - - - -
198C ALA* 5.5 0.4 - - + -
202C GLU* 2.7 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG 4.9 1.0 + - - -
28B PHE* 2.5 69.8 + - + +
29B SER* 4.2 13.0 - - - +
30B GLU* 3.2 31.8 + - - +
46B LYS 4.4 0.2 + - - -
47B ILE* 1.3 82.4 - - - +
49B THR* 1.3 73.5 + - - +
50B ILE* 4.2 13.3 - - + +
59B LEU* 2.6 47.3 + - - +
61B ILE* 4.9 1.8 - - + +
159B GLU* 3.2 35.5 + - - -
163B PHE* 4.0 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 5.1 5.0 - - + +
47B ILE* 4.6 3.8 - - - +
48B ARG* 1.3 83.5 + - - +
50B ILE* 1.3 78.5 + - - +
56B ARG* 4.6 10.8 - - + -
57B ILE 3.3 13.7 - - - +
58B LYS* 3.3 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 5.3 0.4 - - + -
48B ARG* 4.2 17.5 - - + +
49B THR* 1.3 85.5 - - - +
51B GLU* 1.3 70.7 - - + +
52B LEU* 5.2 4.5 - - + -
56B ARG* 3.6 1.8 - - - -
57B ILE* 2.7 58.1 + - + +
59B LEU* 4.5 17.9 - - + -
163B PHE* 3.1 48.9 - - + -
166B ALA* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 1.3 92.4 - - + +
52B LEU* 1.3 64.9 + - - +
53B ASP 4.2 0.7 - - - -
54B GLY* 2.9 43.5 - - - +
55B LYS 3.3 6.3 - - - +
56B ARG* 4.1 6.6 - - + +
163B PHE* 4.3 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 5.6 1.1 - - + -
50B ILE* 4.0 2.2 + - + -
51B GLU* 1.3 77.0 - - - +
53B ASP* 1.3 81.2 + - - +
55B LYS* 3.0 24.0 + - + +
57B ILE* 4.3 15.5 - - + -
163B PHE* 4.3 11.2 - - + +
166B ALA* 4.0 18.4 - - + +
167B ARG* 3.1 70.4 - - + +
170B LYS* 4.2 19.7 - - + -
----------------------------------------------------------
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