Contacts of the helix formed by residues 103 - 110 (chain I) in PDB entry 6RAR
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 THR 103 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLU* 5.0 1.2 + - - -
61I LYS* 4.2 1.3 - - - -
64I GLU 6.1 0.4 - - - -
65I LYS 5.3 0.2 - - - -
66I SER* 4.0 22.0 - - - +
67I GLN 5.9 0.4 - - - +
101I SER 4.0 0.4 + - - +
102I ALA* 1.3 76.5 - - - +
104I LYS* 1.3 65.4 + - - +
105I GLU* 3.6 14.7 + - - +
106I GLU* 3.0 38.6 + - - +
107I TRP* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I LYS* 3.6 28.5 - - - +
62I GLU* 2.4 38.6 + - - +
63I SER 3.7 13.2 - - - +
64I GLU* 4.0 28.4 + - + +
65I LYS 5.5 0.2 + - - -
102I ALA 3.9 1.6 + - - -
103I THR* 1.3 71.9 - - - +
105I GLU* 1.3 68.8 + - + +
108I ASN* 3.0 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLU* 3.6 20.2 - - + +
64I GLU* 3.1 27.9 - - - +
103I THR* 3.6 17.9 + - - +
104I LYS* 1.3 83.0 + - + +
106I GLU* 1.3 58.4 + - - +
108I ASN* 5.2 1.3 - - - -
109I GLY* 2.8 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LYS* 5.6 4.0 - - + -
9I GLU* 3.6 27.3 - - - +
69I PHE* 3.9 19.2 + - - +
101I SER 4.9 0.2 - - - +
102I ALA* 3.4 15.0 - - + +
103I THR* 3.0 50.0 + - - +
105I GLU* 1.3 75.6 - - - +
107I TRP* 1.3 66.7 + - - +
110I PHE* 3.1 7.7 + - + +
111I TYR* 3.0 48.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I VAL* 4.0 11.9 - - + -
59I PRO 3.0 21.4 + - - -
61I LYS* 3.8 8.7 - - + -
69I PHE* 4.8 2.9 - + - -
74I PHE* 4.7 5.2 - + - -
77I LEU* 5.1 0.2 - - + -
95I ILE* 3.6 36.3 - - + -
98I ALA* 3.9 22.0 - - + -
99I MET* 3.3 37.3 - - + -
102I ALA* 4.1 15.0 - - + -
103I THR 2.9 17.8 + - - +
104I LYS 3.9 2.2 - - - +
106I GLU* 1.3 81.1 - - - +
108I ASN* 1.3 77.7 + - - +
109I GLY 3.3 0.2 + - - -
111I TYR* 3.4 22.2 + + + -
112I ARG* 2.8 36.9 + - + +
115I LEU* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I GLU* 3.4 22.9 - - + +
61I LYS* 2.8 47.5 + - - +
104I LYS* 3.0 31.2 + - - +
105I GLU* 4.6 1.1 - - - +
107I TRP* 1.3 77.9 - - - +
109I GLY* 1.3 57.4 + - - +
110I PHE 3.5 0.6 + - - -
112I ARG* 4.3 10.8 + - - +
113I ARG* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLU* 3.6 21.1 - - - +
12I ILE* 3.6 21.1 - - - +
105I GLU 2.8 20.1 + - - -
108I ASN* 1.3 78.0 - - - +
110I PHE* 1.3 60.9 + - - +
113I ARG* 3.9 13.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LYS* 3.8 29.2 - - + -
9I GLU* 4.2 12.1 - - + +
12I ILE* 3.9 19.1 - - + -
39I PHE* 3.6 48.5 - + - -
42I GLY* 4.0 4.9 - - - -
43I ILE* 4.3 11.0 - - + -
71I TRP* 4.2 9.9 - + - -
106I GLU* 3.1 9.6 + - + +
108I ASN 3.5 2.2 + - - -
109I GLY* 1.3 79.5 - - - +
111I TYR* 1.3 88.1 + + + +
112I ARG 3.3 1.3 - - - -
113I ARG* 2.9 11.8 + - - +
114I VAL* 2.9 48.1 + - + +
119I LEU* 5.6 1.6 - - + -
----------------------------------------------------------
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