Contacts of the helix formed by residues 53 - 67 (chain B) in PDB entry 4EOZ
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 SER 53 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A MET* 4.3 1.6 - - - -
234A GLU* 4.0 16.8 - - - +
235A GLU* 2.4 29.4 + - - -
51B GLY 4.2 0.2 + - - -
52B LEU* 1.3 75.0 - - - +
54B PHE* 1.3 61.7 + - - +
55B GLU* 3.9 1.9 - - - +
56B GLU* 3.5 30.7 + - - +
57B LEU* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 3.9 19.1 - - + -
227A ALA* 3.7 7.4 - - + -
228A MET* 3.6 35.7 - - + +
231A HIS* 4.5 11.2 - + + -
233A MET* 3.8 25.1 - - + -
235A GLU* 2.9 17.3 + - - +
52B LEU 4.1 0.2 + - - -
53B SER* 1.3 72.5 - - - +
55B GLU* 1.3 62.9 + - - +
57B LEU* 3.3 1.9 + - - +
58B TYR* 2.9 47.4 + + + +
118B MSE 4.6 0.4 - - - -
121B ASP* 3.3 34.3 - - + -
122B ILE* 3.5 30.1 - - + -
124B MSE 3.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 3.6 24.3 - - + +
235A GLU* 3.2 17.2 + - - +
241A VAL* 3.7 17.9 - - + -
242A GLU 3.8 18.8 - - - +
243A ILE* 3.9 10.1 - - + -
279A LYS* 2.8 15.8 + - - -
280A TYR* 2.8 29.5 + - - -
53B SER* 3.9 1.8 - - - +
54B PHE* 1.3 79.5 - - - +
56B GLU* 1.3 56.8 + - - +
58B TYR* 3.9 5.1 - - - +
59B ARG* 2.9 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.1 34.6 - - + +
53B SER* 3.5 25.1 + - - +
54B PHE 3.3 0.4 - - - -
55B GLU* 1.3 78.0 + - - +
57B LEU* 1.3 66.6 + - + +
59B ARG* 3.2 25.6 + - - +
60B ASN* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A MET* 4.6 3.1 - - + -
36B LEU* 3.8 22.4 - - + -
37B LEU* 3.5 16.0 - - + +
40B ALA* 3.6 35.4 - - + -
41B ILE* 6.5 0.2 - - + -
44B ILE* 4.8 1.8 - - + -
52B LEU* 4.3 22.4 - - + -
53B SER 3.1 22.2 + - - +
54B PHE 3.9 1.8 - - - +
56B GLU* 1.3 81.7 - - + +
58B TYR* 1.3 64.9 + - - +
60B ASN 3.1 2.4 + - - -
61B ALA* 3.0 20.4 + - - +
122B ILE* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 3.3 28.5 - - + +
228A MET* 6.1 0.9 - - + -
279A LYS* 2.8 49.3 + - + -
280A TYR* 5.2 0.7 - + - -
54B PHE* 2.9 39.8 + + + +
55B GLU* 4.0 7.0 - - - +
57B LEU* 1.3 73.1 - - - +
59B ARG* 1.3 61.2 + - - +
61B ALA* 3.3 0.7 + - - +
62B TYR* 2.8 33.0 + - + +
121B ASP 4.0 8.5 - - - -
122B ILE* 3.5 22.4 - - - +
124B MSE 4.0 20.9 - - + +
125B TYR* 3.9 31.3 - - + +
128B ARG* 4.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU 4.8 5.5 + - - -
244A ASN* 3.5 30.2 + - - +
245A ASP* 3.9 31.6 - - - +
279A LYS* 4.0 13.7 - - - +
55B GLU* 2.9 37.8 + - - +
56B GLU* 3.7 27.4 + - - +
57B LEU 3.2 0.2 - - - -
58B TYR* 1.3 80.5 - - - +
60B ASN* 1.3 68.5 + - - +
62B TYR* 3.7 7.1 - - + +
63B THR* 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.4 44.9 + - + +
36B LEU* 4.0 34.7 - - - +
37B LEU* 3.8 11.9 - - + -
56B GLU* 2.9 24.0 + - - +
57B LEU 3.7 7.0 - - - +
59B ARG* 1.3 92.6 + - - +
61B ALA* 1.3 64.4 + - - +
63B THR* 3.3 5.2 + - - -
64B MSE 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.9 15.2 - - + +
57B LEU 3.0 11.9 + - - +
58B TYR* 3.7 0.4 - - + +
60B ASN* 1.3 76.2 - - - +
62B TYR* 1.3 62.5 + - - +
64B MSE 3.4 9.6 + - - +
65B VAL* 3.4 22.5 + - - +
73B LEU* 3.8 6.1 - - + +
122B ILE* 3.5 25.1 - - + +
123B LEU* 3.6 26.0 - - + -
125B TYR* 5.4 1.6 - - + -
126B MSE 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 4.7 8.1 - - - -
275A ALA* 4.0 20.8 + - - +
278A ASP* 4.1 5.7 + - - -
279A LYS* 3.8 47.5 - - + +
58B TYR* 2.8 26.3 + - + +
59B ARG* 3.7 6.3 - - - +
61B ALA* 1.3 77.4 - - - +
63B THR* 1.3 69.5 + - - +
65B VAL 3.4 1.0 + - - -
66B LEU* 2.9 63.3 + - + +
125B TYR* 3.7 54.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 5.1 2.4 + - - -
29B TYR* 3.7 17.3 - - - +
33B ILE* 4.2 11.4 - - + -
59B ARG* 2.7 29.1 + - - +
60B ASN* 3.3 8.0 + - - -
62B TYR* 1.3 86.4 - - - +
64B MSE 1.3 64.2 + - - +
66B LEU* 4.2 5.6 - - + -
67B HIS* 3.2 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.6 31.0 - - + +
33B ILE* 3.7 24.7 - - + -
34B TRP* 3.8 19.5 - - + -
37B LEU* 4.1 9.4 - - - -
60B ASN 3.2 11.1 + - - +
61B ALA 3.7 6.5 - - - +
62B TYR 3.3 0.2 - - - -
63B THR* 1.3 80.7 - - - +
65B VAL* 1.3 59.7 + - - +
67B HIS* 3.4 4.9 + - - +
69B HIS* 2.8 37.0 + - + +
72B LYS* 3.7 16.2 - - + -
73B LEU* 3.7 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.4 15.3 - - - +
62B TYR 3.4 0.8 + - - -
64B MSE 1.3 73.8 - - - +
66B LEU* 1.3 58.6 + - - +
68B LYS* 2.8 24.9 + - - -
70B GLY* 4.2 15.7 - - - +
73B LEU* 3.8 19.5 - - + -
125B TYR* 3.7 14.4 - - + -
126B MSE 4.1 20.4 - - + +
129B VAL* 3.5 31.6 - - + +
130B TYR* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASP* 5.0 2.5 - - - +
62B TYR* 2.9 55.7 + - + +
63B THR* 3.9 6.3 - - + +
64B MSE 3.4 0.2 - - - -
65B VAL* 1.3 76.3 - - - +
67B HIS* 1.3 79.1 + - + +
68B LYS* 3.5 7.8 + - - +
125B TYR* 4.0 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 6.0 1.6 - - - +
29B TYR* 4.3 21.6 - + - -
33B ILE* 5.8 0.2 - - - +
63B THR* 3.2 41.2 + - + +
64B MSE 4.0 2.7 - - - +
65B VAL 3.0 1.0 + - - -
66B LEU* 1.3 97.4 - - + +
68B LYS* 1.3 72.9 + - - +
69B HIS* 3.3 23.1 + - + +
----------------------------------------------------------
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