Contacts of the strand formed by residues 49 - 54 (chain A) in PDB entry 1QM7
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 ILE 49 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.8 18.4 - - + +
27A SER 3.3 4.9 - - - +
29A ARG* 4.4 6.7 - - - +
36A LEU* 3.3 34.1 - - + -
45A VAL* 3.1 45.3 - - + +
46A ALA* 3.5 17.4 + - + +
47A PRO 3.2 5.8 - - - +
48A GLY* 1.3 82.8 - - - +
50A LYS* 1.3 72.3 + - - +
51A LEU* 3.8 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS 3.7 1.2 - - - +
26A LYS* 3.5 2.4 - - - -
27A SER* 2.8 50.0 + - - +
28A ARG 4.9 0.7 - - - +
29A ARG* 4.2 19.8 - - + +
48A GLY 4.1 1.2 + - - -
49A ILE* 1.3 71.0 - - - +
51A LEU* 1.3 64.3 + - - +
52A ASN* 3.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.9 25.6 - - + -
25A LYS 3.5 11.4 - - - +
26A LYS* 4.6 3.6 - - + +
42A CYS* 3.9 4.7 - - - -
43A PRO* 3.2 27.4 - - + +
44A THR* 5.3 0.2 - - - -
45A VAL* 3.9 32.1 - - + +
49A ILE 3.8 1.2 + - - +
50A LYS* 1.3 77.6 + - - +
52A ASN* 1.3 77.9 + - - +
53A CYS* 3.8 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.2 6.4 - - - +
25A LYS* 2.8 54.2 + - + +
50A LYS* 3.9 26.1 - - - +
51A LEU* 1.3 88.0 + - - +
53A CYS* 1.3 61.0 + - - +
54A CYS* 4.3 3.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 3.9 13.5 + - - +
23A CYS 3.3 6.3 - - - +
24A TYR* 4.1 3.8 - - - -
42A CYS* 2.0 58.8 - - + -
51A LEU* 3.8 17.0 + - - -
52A ASN* 1.3 78.7 - - - +
54A CYS* 1.3 63.5 + - - +
55A THR* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 3.0 6.9 - - - +
23A CYS 2.7 40.3 + - - -
52A ASN* 5.4 2.5 - - + -
53A CYS* 1.3 77.2 - - - +
55A THR* 1.3 62.1 + - - +
59A CYS* 2.0 62.4 - - + -
60A ASN* 3.7 9.2 - - - -
----------------------------------------------------------
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