Contacts of the strand formed by residues 36 - 42 (chain D) in PDB entry 1EFX
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 HIS 36 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.3 3.7 - - - +
35D GLU* 1.3 89.2 + - + +
37D PHE* 1.3 66.9 + - - +
38D LEU* 4.3 5.2 - - + -
50D HIS* 3.1 33.4 + + + +
51D LEU 3.4 7.4 - - - +
52D ILE* 4.0 15.4 - - + +
53D GLY 4.2 0.9 - - - +
81D GLY* 3.0 4.7 - - - -
82D SER* 3.0 34.0 + - - +
84D THR 3.6 15.0 - - - -
85D HIS* 3.0 56.3 + + - +
88D TYR* 3.8 11.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.2 5.4 - - + -
28D CYS* 3.2 42.2 - - + -
29D TRP* 4.0 3.8 - - - -
30D SER 4.4 0.9 - - - -
34D PHE* 4.0 37.2 - + + -
36D HIS* 1.3 77.1 - - - +
38D LEU* 1.3 65.1 + - - +
49D LEU 3.6 0.2 - - - +
51D LEU 2.8 30.4 + - - +
53D GLY* 3.8 14.1 - - - -
60D SER* 3.3 26.9 - - - -
61D LYS 3.6 16.2 - - - -
62D ALA* 3.5 27.6 - - + -
64D PHE* 3.5 15.7 - - + -
80D TYR 3.2 9.4 - - - -
81D GLY* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D HIS* 4.5 7.0 - - + +
37D PHE* 1.3 83.1 - - - +
39D LEU* 1.3 60.6 + - - +
48D THR* 4.1 18.4 - - + -
49D LEU 3.6 3.4 - - - +
50D HIS* 3.6 30.1 - - + +
64D PHE* 4.2 0.2 - - - -
79D CYS* 2.9 6.6 - - - -
80D TYR* 2.7 43.2 + - + +
82D SER* 5.1 3.8 - - - +
88D TYR* 3.7 44.0 - - + -
90D LEU* 4.2 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.7 8.3 - - + -
26D LEU* 3.9 10.8 - - + -
38D LEU* 1.3 72.5 - - - +
40D HIS* 1.3 72.1 + - - +
48D THR* 3.1 3.3 - - - -
49D LEU* 2.7 44.1 + - + +
64D PHE* 3.6 52.2 - - + -
66D ILE* 4.2 6.1 - - + -
77D TYR* 3.3 45.1 - - + -
78D ARG 3.4 17.9 - - - +
79D CYS* 3.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 1.3 78.1 - - - +
41D ARG* 1.3 68.1 + - - +
42D GLU* 2.9 42.3 + - + +
46D LYS* 4.0 11.2 - - + -
47D ASP* 2.5 31.2 + - - -
48D THR* 2.7 22.3 + - + +
76D THR 3.7 1.0 - - - +
77D TYR* 3.3 3.1 - - - -
78D ARG* 2.7 45.5 + - + +
80D TYR* 4.5 19.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 4.9 3.0 - - - +
40D HIS* 1.3 76.3 - - - +
42D GLU* 1.3 62.9 + - - +
45D PHE* 3.0 32.8 + - - +
46D LYS* 3.0 4.2 - - - +
47D ASP* 3.0 52.6 + - - +
49D LEU* 4.8 5.5 - - - +
66D ILE* 5.9 0.2 - - - +
72D ASP* 3.3 31.3 + - - +
73D LEU* 3.5 23.6 - - - +
74D ALA 4.1 9.1 + - - -
75D GLY* 4.7 2.5 - - - -
76D THR 3.0 11.9 - - - +
77D TYR* 3.4 51.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D HIS* 2.9 36.5 + - + +
41D ARG* 1.3 75.6 - - - +
43D GLY* 1.3 61.7 + - - +
45D PHE 5.3 0.2 - - - -
46D LYS* 4.1 20.2 - - - +
75D GLY* 4.6 5.0 - - - -
76D THR* 3.0 31.1 + - + +
78D ARG* 6.4 1.8 - - + -
186D TYR* 5.0 2.6 - - - -
----------------------------------------------------------
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