Contacts of the strand formed by residues 43 - 48 (chain D) in PDB entry 5J7C
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 43 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER* 6.2 1.1 - - - -
44C LEU 3.3 10.5 - - - -
45C VAL* 5.3 2.0 - - - -
37D GLY* 4.1 11.4 - - - -
38D GLU 4.5 4.3 + - - +
41D GLY* 3.5 3.4 - - - -
42D ASN* 1.3 92.6 + - - +
44D LEU* 1.3 70.8 + - - +
45D VAL* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 4.4 21.8 - - + -
43C SER* 3.2 8.8 - - - -
44C LEU* 2.9 47.5 + - + +
46C GLN* 3.9 34.1 - - + +
35D ILE* 3.6 27.6 - - + -
36D TYR* 3.6 15.3 - - - +
37D GLY* 4.5 6.7 - - - +
38D GLU 6.0 0.9 - - - +
41D GLY 5.8 0.2 - - - -
43D SER* 1.3 82.7 - - - +
45D VAL* 1.3 66.0 + - - +
70D THR* 5.6 7.0 - - + +
72D THR* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ASN* 3.5 11.7 - - + +
43C SER* 5.6 1.8 - - - -
44C LEU* 4.5 2.2 - - - -
34D ILE 3.5 1.2 - - - +
35D ILE* 3.2 4.5 - - - +
36D TYR* 2.9 75.1 + - + +
43D SER* 5.9 0.7 - - - +
44D LEU* 1.3 78.5 - - - +
46D GLN* 1.3 66.2 + - - +
47D GLU* 4.0 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLU 4.5 2.2 + - - -
40C GLY* 3.7 9.7 - - - +
41C GLY 2.5 41.6 + - - +
42C ASN* 2.9 26.4 + - - +
44C LEU* 3.9 22.1 - - + +
34D ILE 3.2 5.8 - - - +
35D ILE* 3.6 18.9 - - + +
45D VAL* 1.3 74.1 - - - +
47D GLU* 1.3 72.1 + - - +
48D PHE* 3.6 15.3 - - + -
74D TYR* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLY* 3.3 5.0 - - - -
34D ILE* 2.8 45.3 + - + +
36D TYR* 3.1 32.6 + - + -
45D VAL* 4.0 9.9 - - + +
46D GLN* 1.3 80.3 - - - +
48D PHE* 1.3 68.8 + - - +
59D THR 5.1 6.4 - - - +
60D ILE* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.9 14.1 - - + -
61B ARG* 3.5 43.5 - - - -
62B TRP* 3.4 25.7 - - + -
40C GLY* 3.7 13.2 - - - -
41C GLY 4.2 2.2 - - - -
31D TYR* 3.9 18.2 - + + -
32D TYR 3.2 8.1 - - - +
33D GLY* 3.6 16.8 - - - -
34D ILE* 5.5 0.7 - - - -
46D GLN* 3.6 26.2 - - + -
47D GLU* 1.3 79.3 - - - +
49D THR* 1.3 68.1 + - - +
74D TYR* 3.2 27.4 - - - -
76D VAL* 4.0 3.1 - - + -
----------------------------------------------------------
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