Contacts of the helix formed by residues 69 - 75 (chain R) in PDB entry 5CYT
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 GLU 69 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R MET 3.6 5.0 + - - +
66R GLU* 3.3 15.1 + - - +
67R TYR 3.1 1.0 + - - -
68R LEU* 1.3 78.2 - - - +
70R ASN* 1.3 63.9 + - + +
84R GLY* 3.4 9.2 - - - -
85R ILE 3.5 9.9 - - - +
86R LYS* 2.9 38.2 + - + +
91R ARG* 3.6 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R GLU 3.8 3.1 + - - +
67R TYR 3.0 5.7 + - - +
69R GLU* 1.3 89.6 - - + +
71R PRO* 1.3 68.6 - - - +
72R LYS* 3.5 23.6 + - - +
73R LYS* 3.2 44.9 + - + +
74R TYR* 3.2 12.6 + - - +
83R ALA* 3.9 4.9 - - - +
86R LYS* 4.0 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R TYR* 3.0 40.7 - - + +
68R LEU* 4.1 2.5 - - - +
70R ASN* 1.3 86.8 - - - +
72R LYS* 1.3 57.8 + - - +
74R TYR* 3.2 2.9 + - - +
75R ILE* 2.8 29.1 + - - +
78R THR* 4.4 3.4 - - + -
80R MET* 3.7 32.5 - - + +
82R PHE* 3.4 32.5 - - + +
83R ALA 3.8 6.7 - - - +
84R GLY* 3.8 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ASN* 3.5 26.5 + - - +
71R PRO* 1.3 78.6 - - - +
73R LYS* 1.3 68.1 + - - +
75R ILE 4.0 7.0 - - - +
76R PRO* 3.3 27.8 - - + +
77R GLY 5.6 1.8 - - - +
78R THR* 4.4 9.0 - - + +
80R MET 5.7 2.7 - - - +
82R PHE 5.1 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ASN* 3.2 35.2 + - + +
72R LYS* 1.3 89.5 - - - +
74R TYR* 1.3 63.5 + - - +
76R PRO* 3.9 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R LYS* 2.8 54.2 + - - +
57R ILE* 3.7 19.2 - - + +
59R TRP* 4.1 14.1 - + - -
63R THR* 3.4 32.7 - - - +
66R GLU* 3.5 43.3 + - + +
67R TYR* 3.7 39.5 - + + +
70R ASN 3.2 9.4 + - - +
71R PRO 3.2 7.0 + - - +
73R LYS* 1.3 82.2 - - - +
75R ILE* 1.3 63.8 + - + +
76R PRO* 3.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R THR* 4.8 0.4 - - + -
51R ALA* 3.6 36.3 - - + +
52R ASN* 3.8 18.2 - - + +
55R LYS* 4.0 24.9 - - + -
59R TRP* 4.2 21.8 - - + -
67R TYR* 4.0 19.5 - - + +
71R PRO 2.8 9.5 + - - +
72R LYS* 3.6 5.0 - - - +
74R TYR* 1.3 94.0 - - + +
76R PRO* 1.3 67.2 - - - +
77R GLY 3.2 0.2 + - - -
78R THR* 3.0 34.2 + - + +
----------------------------------------------------------
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