Contacts of the helix formed by residues 48 - 56 (chain I) in PDB entry 6C6U
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 GLY 48 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LYS 3.8 8.3 - - - -
38I PHE* 3.5 22.0 - - - -
40I GLU 5.8 1.1 - - - -
42I ASP* 5.5 1.1 - - - -
47I TYR* 1.3 79.7 - - - +
49I LEU* 1.3 66.7 + - - -
50I GLU 3.2 2.0 - - - -
51I ALA* 3.5 5.6 + - - +
52I ALA 4.1 0.3 + - - -
461I GLU* 3.4 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I PHE* 3.4 42.9 + - + +
39I ILE* 5.0 3.8 - - + -
40I GLU 5.6 0.4 + - - -
48I GLY* 1.3 70.2 - - - -
50I GLU* 1.3 60.6 + - - +
51I ALA 3.2 0.7 - - - -
52I ALA* 3.1 8.4 + - + +
53I PHE* 3.0 36.3 + - + +
73I TYR* 3.7 41.7 + - + +
75I LEU* 4.9 1.1 - - + -
96I LEU* 4.3 14.6 - - + -
127I ILE* 4.4 16.4 - - + -
461I GLU* 5.5 1.6 - - - -
464I PHE* 3.7 35.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I GLU 5.3 0.4 - - - +
41I GLN* 4.5 6.2 - - - +
42I ASP* 3.4 32.3 + - + +
45I GLY* 3.4 16.8 - - - +
47I TYR 4.7 4.3 - - - +
48I GLY* 3.2 0.8 - - - -
49I LEU* 1.3 78.1 - - - +
51I ALA* 1.3 57.0 + - - +
53I PHE* 4.5 3.8 - - - +
54I ARG* 2.9 67.5 + - - +
70I TYR* 3.5 18.2 + - - -
72I SER* 4.9 3.1 + - - -
73I TYR* 3.3 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I GLY 3.5 12.0 + - - +
46I GLN* 4.7 12.1 - - + -
47I TYR* 4.8 2.9 - - + -
48I GLY 3.5 11.2 + - - +
49I LEU 3.2 1.0 - - - -
50I GLU* 1.3 77.8 - - - +
52I ALA* 1.3 57.1 + - - +
54I ARG* 3.8 1.8 - - - +
55I SER* 2.9 33.4 + - - -
461I GLU* 3.4 21.5 - - - +
465I ARG* 3.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I GLY 4.1 0.8 + - - -
49I LEU* 3.1 10.4 + - - +
51I ALA* 1.3 78.4 - - - +
53I PHE* 1.3 59.0 + - - +
55I SER* 3.3 6.4 + - - -
56I VAL* 3.0 36.0 + - - +
461I GLU* 4.8 9.2 - - + -
464I PHE* 4.3 13.9 - - + -
465I ARG* 3.7 26.3 - - + +
468I LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LEU* 3.0 22.2 + - + +
50I GLU* 4.2 3.1 - - - +
52I ALA* 1.3 76.4 - - - +
54I ARG* 1.3 58.3 + - - +
57I PHE* 3.3 43.5 - + - +
70I TYR* 3.3 49.7 - + + +
73I TYR* 4.1 16.2 - + + -
96I LEU* 4.5 5.6 - - + -
98I VAL* 3.8 32.1 - - + -
124I MET* 4.1 6.3 - - - -
464I PHE* 3.6 35.7 - + - -
468I LEU* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I GLY* 4.5 21.1 - - - +
50I GLU* 2.9 44.5 + - - +
51I ALA* 4.4 2.0 - - - +
53I PHE* 1.3 80.4 - - - +
55I SER* 1.3 59.8 + - - +
56I VAL 3.6 0.2 - - - -
57I PHE 3.4 14.6 - - - +
70I TYR* 4.5 16.3 + - + -
71I VAL 4.3 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ALA 2.9 15.9 + - - -
52I ALA 3.3 2.8 + - - -
54I ARG* 1.3 78.8 - - - +
56I VAL* 1.3 62.7 + - - +
57I PHE 3.5 1.9 - - - +
180I ARG* 6.0 2.2 - - - -
393I ASP* 5.6 1.6 - - - +
465I ARG* 2.3 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ALA 3.0 20.4 + - - +
55I SER* 1.3 78.9 - - - +
57I PHE* 1.3 81.3 + - + +
58I PRO 4.3 3.3 - - - +
59I ILE* 4.0 9.6 - - + +
465I ARG* 5.7 3.8 - - + -
468I LEU* 3.7 40.2 - - + +
469I VAL* 4.1 15.7 - - + -
472I GLU* 3.3 39.6 - - + +
----------------------------------------------------------
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