Contacts of the helix formed by residues 50 - 60 (chain G) in PDB entry 4KYI
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 TYR 50 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 4.2 15.4 - - + +
41G SER 3.2 24.4 + - - -
45G ALA* 4.9 3.4 - - + +
46G LYS 4.3 9.9 - - - -
47G GLY* 3.6 5.5 + - - +
48G ILE 3.2 0.6 - - - -
49G SER* 1.3 78.5 - - - +
51G LEU* 1.3 65.8 + - - +
52G GLY 3.3 2.7 - - - -
53G MET* 3.3 28.7 + - + +
54G ILE* 3.3 18.3 + - - +
73G SER* 6.1 0.2 - - - -
74G ALA* 3.8 11.4 - - + +
75G GLY* 3.6 26.3 + - - -
78G THR* 3.4 40.2 - - + +
95G ILE* 6.1 0.7 - - + -
309G VAL* 4.1 18.8 - - + -
311G ALA* 3.9 24.3 + - + +
374G ILE* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLY 3.9 2.2 + - - -
48G ILE* 3.3 16.6 + - + +
50G TYR* 1.3 79.0 - - - +
52G GLY* 1.3 61.9 + - - +
54G ILE* 3.6 5.3 + - + +
55G GLN* 3.4 53.1 + - + +
91G ILE* 4.2 9.6 - - + +
92G LYS* 4.0 20.0 - - + -
95G ILE* 3.6 41.3 - - + -
96G GLU* 4.1 22.4 - - + +
395G VAL* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE 4.4 0.8 + - - -
49G SER 4.3 3.8 + - - -
50G TYR 3.3 0.4 - - - -
51G LEU* 1.3 77.6 - - - +
53G MET* 1.3 59.9 + - - +
55G GLN* 3.4 8.2 + - - +
56G ALA* 3.0 26.7 + - - +
395G VAL* 3.7 34.7 - - - +
398G GLY* 3.7 8.3 - - - -
399G TYR* 3.6 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU* 4.5 13.2 - - + -
40G LEU* 3.9 28.7 - - + -
50G TYR* 3.3 33.2 + - + +
52G GLY* 1.3 73.6 - - - +
54G ILE* 1.3 69.7 + - + +
56G ALA* 3.1 4.4 + - - +
57G LEU* 2.9 51.7 + - + +
78G THR* 5.0 0.4 - - + -
82G LEU* 5.5 0.2 - - + -
309G VAL* 4.5 15.0 - - + -
372G ILE* 4.7 0.9 - - + -
374G ILE* 4.0 14.4 - - + -
398G GLY* 3.4 14.9 + - - +
402G THR* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR 3.3 13.1 + - - +
51G LEU* 3.8 8.5 - - + +
52G GLY 3.3 0.2 - - - -
53G MET* 1.3 92.3 - - + +
55G GLN* 1.3 57.8 + - + +
57G LEU* 3.2 5.3 + - + +
58G GLN* 2.9 29.9 + - + +
63G ILE* 4.0 16.1 - - + +
78G THR* 4.0 23.6 - - + +
81G ILE* 5.1 2.0 - - + -
82G LEU* 4.0 23.6 - - + -
88G ILE* 4.8 11.2 - - + -
91G ILE* 3.9 41.7 - - + -
95G ILE* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 3.4 33.8 + - + +
52G GLY* 3.4 9.0 + - - +
53G MET 3.3 0.4 - - - -
54G ILE* 1.3 77.4 - - + +
56G ALA* 1.3 61.1 + - - +
58G GLN* 4.1 1.4 - - - +
59G GLU* 3.2 25.6 + - - +
88G ILE* 4.3 24.0 - - + +
92G LYS* 3.4 38.8 - - + +
395G VAL* 4.2 13.2 - - - +
399G TYR* 4.3 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLY 3.0 13.2 + - - +
53G MET 3.1 9.4 + - - +
55G GLN* 1.3 74.5 - - - +
57G LEU* 1.3 65.6 + - - +
59G GLU* 3.3 4.5 + - - +
60G ARG* 3.3 19.1 + - - +
399G TYR* 4.0 13.7 - - + +
402G THR* 3.7 23.6 - - + -
403G MET* 3.5 31.9 - - - +
406G LEU* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU* 4.1 26.0 - - + -
53G MET* 2.9 43.2 + - + +
54G ILE* 3.7 4.5 - - + +
56G ALA* 1.3 74.1 - - - +
58G GLN* 1.3 57.8 + - - +
60G ARG 3.1 3.1 + - - -
61G GLY 2.8 9.0 + - - -
62G LYS* 2.8 52.4 + - + +
63G ILE* 3.8 19.5 - - + -
66G LEU* 5.0 1.8 - - + -
82G LEU* 6.3 0.2 - - + -
307G LEU* 4.0 17.3 - - + -
372G ILE* 5.4 1.3 - - + -
402G THR* 4.2 9.0 - - + -
406G LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ILE 2.9 17.1 + - - +
55G GLN 4.1 1.1 - - - +
57G LEU* 1.3 76.8 - - - +
59G GLU* 1.3 60.3 + - - +
61G GLY* 3.0 19.1 + - - +
63G ILE* 3.8 25.0 - - + +
87G ASP* 5.9 0.2 + - - -
88G ILE* 3.6 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G GLN 3.2 15.0 + - - +
56G ALA 3.5 6.3 - - - +
57G LEU 3.2 0.8 - - - -
58G GLN* 1.3 79.3 - - - +
60G ARG* 1.3 62.0 + - + +
61G GLY 3.7 0.3 + - - -
399G TYR* 2.7 36.0 + - - -
403G MET* 3.5 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ALA 3.3 5.6 + - - +
57G LEU 3.1 4.0 + - - +
59G GLU* 1.3 78.9 + - - +
61G GLY* 1.3 63.3 + - - +
62G LYS* 3.2 23.5 + - + +
403G MET* 3.5 45.3 - - + +
406G LEU* 3.7 28.0 - - + +
407G ASP* 3.1 30.8 + - - -
----------------------------------------------------------
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