Contacts of the strand formed by residues 49 - 54 (chain E) in PDB entry 1QG1
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 ASP 49 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LYS* 3.1 7.4 - - - +
46E PHE* 3.1 30.4 + - + +
48E ASN* 1.3 87.9 + - - +
50E VAL* 1.3 63.9 + - - +
51E GLN* 3.9 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ALA 3.5 0.7 - - - +
16E GLU* 2.6 71.5 + - + +
19E LEU* 3.0 48.9 - - + +
20E SER* 3.9 9.4 - - - +
43E SER* 3.6 12.1 - - - -
44E VAL 3.3 2.5 - - - +
48E ASN 4.5 0.7 - - - +
49E ASP* 1.3 82.8 + - - +
51E GLN* 1.3 57.3 + - - +
52E HIS* 3.3 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E VAL* 2.8 59.8 + - - +
46E PHE* 2.5 38.3 - - + +
49E ASP* 3.9 3.5 - - + +
50E VAL* 1.3 74.8 - - - +
52E HIS* 1.3 62.3 + - - +
53E PHE* 2.7 40.8 - - - -
6I VAL* 2.9 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ARG* 4.1 9.4 - - + +
16E GLU* 2.4 42.5 + - + +
31E ARG* 5.1 1.8 - - - -
42E LEU 2.6 27.6 - - - +
43E SER* 3.6 20.2 - - - +
50E VAL 3.3 12.3 + - - -
51E GLN* 1.3 74.1 - - - +
53E PHE* 1.3 50.3 + - - +
3I PRO* 3.8 16.2 - - + -
4I SER 2.7 29.0 + - - -
5I PTR 2.5 46.2 - + + +
6I VAL* 2.6 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E SER* 3.4 2.6 - - - -
42E LEU* 2.7 57.5 + - + -
44E VAL* 4.0 7.2 - - + -
46E PHE* 3.7 11.0 - + - -
51E GLN* 2.7 24.2 - - - -
52E HIS* 1.3 72.1 - - - +
54E LYS* 1.3 62.2 + - - +
55E VAL* 4.2 1.0 - - - +
65E LEU* 3.2 25.8 - - + +
66E TRP* 2.7 42.6 - + - -
80E HIS* 5.0 1.1 - - - -
85E VAL* 3.7 19.7 - - + -
93E LEU* 4.6 2.9 - - + -
5I PTR 3.3 5.4 - - - -
6I VAL* 2.8 36.6 - - + -
7I ASN* 3.1 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E SER* 4.0 11.4 + - - -
39E ASP* 4.1 21.4 + - - -
40E PHE 3.9 14.1 - - - -
41E SER* 4.0 6.5 - - - +
53E PHE* 1.3 71.9 - - - +
55E VAL* 1.3 60.9 + - - +
56E LEU* 3.3 22.7 - - + +
65E LEU* 2.9 11.1 - - - +
5I PTR 2.9 47.1 + - + +
7I ASN* 2.7 36.8 + - - +
8I VAL* 4.0 11.7 - - + +
----------------------------------------------------------
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