Contacts of the strand formed by residues 45 - 51 (chain D) in PDB entry 4PAR
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 VAL 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 3.8 11.7 - - - +
16D GLN* 3.8 12.1 - - - +
19D ARG* 4.7 3.8 - - - +
43D LYS* 4.9 5.4 - - - -
44D PHE* 1.3 81.5 - - - +
46D THR* 1.3 75.7 + - - +
47D GLN 4.2 0.2 + - - -
48D GLN* 3.4 32.8 - - + +
62D LEU* 3.4 3.0 - - - -
63D TYR* 2.7 51.3 + - + +
65D PRO* 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 2.6 52.6 + - + +
17D LEU* 4.2 6.7 - - + -
19D ARG* 2.9 26.2 + - - -
21D LYS* 5.1 6.5 - - - +
26D GLU* 5.3 1.1 - - - -
30D VAL* 4.1 15.0 - - + -
44D PHE* 4.6 1.6 - - + -
45D VAL* 1.3 77.1 - - - +
47D GLN* 1.3 76.3 + - - +
48D GLN 3.3 1.8 - - - -
61D ASP 3.3 13.7 - - - +
62D LEU* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ARG* 3.7 30.1 + - - +
20D THR* 2.8 31.6 + - - +
21D LYS* 4.1 1.8 - - - +
22D ASN* 3.3 28.8 + - - +
26D GLU* 3.4 26.0 + - - +
46D THR* 1.3 76.5 - - - +
48D GLN* 1.3 63.0 + - - +
49D PHE* 3.3 16.4 + - + -
59D LEU* 4.5 12.5 - - + +
60D THR 3.2 16.6 + - - -
61D ASP* 3.3 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D VAL* 3.4 26.8 - - + +
46D THR 3.3 2.4 - - - -
47D GLN* 1.3 75.7 - - - +
49D PHE* 1.3 84.7 + - - +
50D VAL* 3.5 11.7 + - + +
59D LEU* 3.2 2.5 - - - -
60D THR* 2.9 41.7 + - - +
63D TYR* 3.9 40.0 - - + -
70D HIS* 4.4 2.2 - - + -
111D ASP* 3.4 27.1 + - - +
112D ILE* 4.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN 3.3 11.4 + - - -
48D GLN* 1.3 94.0 + - - +
50D VAL* 1.3 59.7 + - - +
57D ILE* 3.9 13.2 - - + -
58D ALA 3.4 13.7 - - - -
59D LEU* 4.3 22.0 - - + -
99D ILE* 4.6 11.2 - - + -
107D MET* 3.9 33.4 - - + -
110D GLU* 3.8 37.5 - - + -
111D ASP 3.6 16.0 + - - +
112D ILE* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLN* 3.7 13.0 - - + +
49D PHE* 1.3 79.3 - - - +
51D ARG* 1.3 64.4 + - - +
52D LEU* 4.6 1.3 - - + -
57D ILE* 3.7 4.0 - - - +
58D ALA* 2.9 43.2 + - + +
59D LEU* 4.4 0.9 - - - +
60D THR* 4.4 4.7 - - + +
70D HIS* 3.9 28.3 - - + +
95D PRO* 3.8 33.2 - - + -
112D ILE* 3.5 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D VAL* 1.3 78.5 - - - +
52D LEU* 1.3 73.9 + - - +
54D ASN 3.9 8.3 - - - +
55D LYS* 4.2 18.1 + - - +
56D LYS 3.9 7.9 - - - +
57D ILE* 4.8 11.4 - - + +
108D ARG 5.8 2.2 + - - -
112D ILE* 3.6 40.8 + - + +
----------------------------------------------------------
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