Contacts of the helix formed by residues 43 - 53 (chain B) in PDB entry 4XZC
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 LEU 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 4.1 12.8 - - + -
42B ASP* 1.3 81.1 + - - +
44B SER* 1.3 64.9 + - - +
45B ILE* 3.1 3.6 - - - -
46B PHE* 2.8 24.9 + - + +
47B GLU* 3.2 10.6 + - - +
66B ALA 3.9 22.4 - - - +
69B GLU* 4.4 7.4 - - + -
70B ALA* 4.2 4.5 - - + +
430B GLU* 4.0 20.9 - - - +
433B GLN* 3.2 37.8 + - + +
434B LEU* 3.9 25.1 - - + +
437B ILE* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 2.1 37.0 + - - -
43B LEU* 1.3 73.2 - - - +
45B ILE* 1.3 56.3 + - - +
47B GLU* 2.9 15.7 + - - +
48B VAL* 2.8 44.9 + - - +
433B GLN* 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 3.5 31.6 - - + +
43B LEU* 4.1 1.1 - - - -
44B SER* 1.3 83.2 - - - +
46B PHE* 1.3 74.5 + - + +
48B VAL* 3.6 7.0 + - - +
49B LYS* 3.1 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP 4.8 3.8 - - - -
43B LEU* 2.8 26.0 + - + +
45B ILE* 1.3 89.0 - - + +
47B GLU* 1.3 58.4 + - - +
49B LYS* 4.3 9.4 - - - -
50B MET* 2.7 36.8 + - - +
62B ILE* 3.5 23.4 - - + +
65B CYS* 3.6 30.7 - - + -
66B ALA* 3.7 18.8 - - + -
69B GLU* 3.5 36.1 - - + -
437B ILE* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU 3.2 6.1 + - - +
44B SER* 2.9 18.5 + - - +
46B PHE* 1.3 78.0 - - - +
48B VAL* 1.3 63.8 + - + +
50B MET* 3.4 5.1 - - - +
51B GLY* 3.0 19.9 + - - -
433B GLN* 4.6 4.2 - - - +
436B ARG* 3.2 47.5 + - - +
437B ILE* 3.9 26.3 - - + +
440B ALA* 4.4 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 2.8 30.4 + - - +
45B ILE* 3.9 7.2 - - - +
47B GLU* 1.3 73.4 - - + +
49B LYS* 1.3 63.0 + - + +
51B GLY* 3.1 4.4 + - - -
52B LEU* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.1 25.8 + - + +
46B PHE* 3.7 12.1 - - - +
48B VAL* 1.3 78.4 - - + +
50B MET* 1.3 52.6 + - - +
52B LEU* 3.0 12.1 + - - +
53B ALA* 2.7 34.3 + - - +
58B GLU* 4.7 9.8 + - - +
62B ILE* 3.8 36.2 - - + +
65B CYS* 6.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE 2.7 22.3 + - - +
47B GLU* 3.4 8.3 - - - +
49B LYS* 1.3 73.3 - - - +
51B GLY* 1.3 63.1 + - - +
53B ALA* 3.1 17.0 + - - +
59B LYS* 3.3 55.8 - - + +
62B ILE* 3.8 11.4 - - + +
63B TYR* 3.8 17.0 - - + +
437B ILE* 3.2 43.7 - - + +
440B ALA* 3.5 15.0 - - + +
441B GLY* 3.6 13.7 - - - +
442B PHE* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 3.0 14.0 + - - -
48B VAL* 3.1 4.6 + - - -
50B MET* 1.3 75.0 - - - +
52B LEU* 1.3 64.3 + - - +
53B ALA 3.3 4.5 + - - +
440B ALA* 4.4 15.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
48B VAL* 3.0 30.2 + - + +
49B LYS* 3.0 12.8 + - - +
51B GLY* 1.3 76.2 - - - +
53B ALA* 1.3 65.8 + - - +
54B THR* 3.5 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS 2.7 15.3 + - - +
50B MET 3.1 16.3 + - - +
51B GLY 4.0 4.7 - - - +
52B LEU* 1.3 75.6 - - - +
54B THR* 1.3 64.4 + - - +
58B GLU* 4.3 14.8 - - + -
59B LYS* 3.5 33.3 + - + +
62B ILE* 3.8 17.7 - - + -
----------------------------------------------------------
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