Contacts of the helix formed by residues 44 - 52 (chain K) in PDB entry 2GLJ
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 CYS 44 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K LYS 4.5 2.7 - - - -
40K THR* 3.1 33.3 - - - +
41K GLU 4.4 0.4 - - - -
42K ARG* 2.1 47.7 + - - +
43K GLU* 1.3 66.4 - - - +
45K VAL* 1.3 67.6 + - - +
46K THR* 2.8 3.4 - - - +
47K GLU* 2.8 38.6 + - - +
48K LEU 3.3 8.7 + - - -
82K GLY 5.4 0.2 - - - -
148K HIS* 6.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K SER* 5.0 10.3 - - - +
40K THR* 3.4 21.2 - - + +
42K ARG 5.1 0.7 - - - -
43K GLU* 3.0 17.9 - - - +
44K CYS* 1.3 80.3 - - - +
46K THR* 1.3 54.3 + - - +
48K LEU* 3.5 0.6 + - + +
49K ILE* 2.7 65.9 + - + +
106K ILE* 4.1 25.6 - - + -
267K ARG* 4.1 35.0 - - + +
270K ALA* 5.9 1.3 - - + -
271K TYR* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K GLU 4.0 3.5 + - - -
44K CYS* 2.8 0.9 - - - -
45K VAL* 1.3 78.5 - - - +
47K GLU* 1.3 56.7 + - + +
49K ILE* 3.6 3.4 - - - +
50K LYS* 2.5 65.9 + - + +
79K ASN* 3.4 22.2 - - - +
82K GLY* 3.2 28.1 + - - +
83K LYS 4.0 4.7 - - - -
84K GLY 4.0 9.3 - - - +
85K LEU* 4.2 6.9 - - + +
106K ILE* 4.0 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ARG* 4.9 5.0 + - - -
44K CYS* 2.8 35.0 + - + +
46K THR* 1.3 78.8 - - + +
48K LEU* 1.3 54.6 + - - +
50K LYS* 3.6 4.8 - - - +
51K THR* 2.8 40.0 + - - +
82K GLY 6.0 0.7 - - - +
160K ASN* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K SER* 5.7 7.9 - - - +
39K LYS* 4.8 18.8 - - + +
40K THR* 3.9 31.4 - - + +
44K CYS 3.3 3.0 + - - -
45K VAL* 4.1 1.6 - - + +
47K GLU* 1.3 77.7 - - - +
49K ILE* 1.3 62.6 + - + +
51K THR* 3.5 13.5 + - + +
52K ALA* 3.2 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K VAL* 2.7 47.2 + - + +
46K THR 3.7 1.1 - - - +
48K LEU* 1.3 74.7 - - + +
50K LYS* 1.3 65.9 + - - +
52K ALA* 3.0 25.7 + - - +
53K GLU* 4.0 3.0 - - + +
85K LEU* 3.4 24.5 - - + -
106K ILE* 5.7 0.2 - - + -
270K ALA 4.9 4.9 - - - +
271K TYR* 5.4 9.0 - - + -
274K PHE* 3.2 47.2 - - + -
291K LEU* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K THR* 2.5 38.8 + - + +
47K GLU* 3.6 5.4 - - - +
49K ILE* 1.3 72.3 - - - +
51K THR* 1.3 58.5 + - - +
52K ALA 2.5 16.0 - - - +
53K GLU* 4.6 4.1 - - - +
54K LYS* 4.6 2.9 + - - +
77K TYR* 3.4 59.9 - - + +
79K ASN* 3.2 29.8 - - + +
85K LEU* 3.3 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K GLU* 2.8 17.0 + - - +
48K LEU* 3.6 17.5 - - + +
50K LYS* 1.3 71.2 - - - +
52K ALA* 1.3 68.8 + - - +
54K LYS* 3.3 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K LEU* 3.2 12.4 + - + +
49K ILE* 3.0 12.7 + - - +
50K LYS 2.5 20.3 - - - +
51K THR* 1.3 77.9 - - - +
53K GLU* 1.3 67.4 + - - +
54K LYS* 2.8 7.4 - - - +
274K PHE* 4.0 17.7 - - + -
278K LEU* 4.9 2.2 - - + -
----------------------------------------------------------
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