Contacts of the helix formed by residues 105 - 112 (chain D) in PDB entry 3BUW
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 LYS 105 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ARG 3.1 26.2 + - - -
102D TYR* 3.3 36.9 - - + +
103D GLU 2.8 9.6 + - - +
104D GLY* 1.3 72.9 - - - +
106D MET* 1.3 61.9 + - - -
107D GLU* 3.1 6.0 + - - +
108D THR* 3.2 28.3 + - + +
109D LEU 3.7 2.6 + - - -
173D LEU* 4.6 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 4.5 7.8 - - + +
52D ASP* 4.7 3.8 - - - -
53D LYS* 4.1 38.8 - - + +
56D VAL* 5.2 1.3 - - + -
99D LEU* 3.4 42.6 - - + +
102D TYR 3.9 13.5 - - - +
103D GLU* 5.6 0.4 - - - -
104D GLY* 3.0 14.5 + - - +
105D LYS* 1.3 76.9 - - - +
107D GLU* 1.3 56.9 + - - +
109D LEU* 3.3 17.8 + - + +
110D GLY* 2.9 28.4 + - - -
115D PHE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D THR* 5.6 0.4 - - - +
104D GLY 4.7 1.0 + - - +
105D LYS* 3.1 2.6 - - - +
106D MET* 1.3 79.3 - - - +
108D THR* 1.3 60.9 + - - +
110D GLY* 3.5 1.8 + - - -
111D GLU* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TYR* 4.3 17.3 - - + -
105D LYS* 3.2 22.4 + - + +
107D GLU* 1.3 79.8 - - - +
109D LEU* 1.3 62.6 + - - +
111D GLU* 3.4 11.2 + - - +
112D ASN* 3.4 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL 5.9 0.2 - - - +
98D ILE* 3.8 29.2 - - + +
99D LEU* 3.7 29.8 - - + -
102D TYR* 3.8 37.0 - - + -
105D LYS 3.7 1.0 + - - -
106D MET* 3.3 13.6 + - + +
107D GLU 3.3 0.2 - - - -
108D THR* 1.3 77.0 - - - +
110D GLY* 1.3 62.8 + - - +
111D GLU 3.1 6.0 + - - -
112D ASN* 3.1 21.4 + - + +
115D PHE* 3.6 37.8 - - + +
169D PHE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D THR* 3.2 13.7 - - - +
51D VAL* 2.9 52.5 + - - -
106D MET* 2.9 17.4 + - - +
107D GLU* 4.0 2.0 - - - -
109D LEU* 1.3 74.1 - - - +
111D GLU* 1.3 56.8 + - - +
116D ARG* 3.2 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D THR* 4.7 11.2 - - + +
107D GLU* 2.9 45.9 + - + +
108D THR* 3.8 8.1 - - - +
109D LEU 3.1 1.0 - - - -
110D GLY* 1.3 82.2 - - - +
112D ASN* 1.3 64.3 + - - +
113D GLU 3.2 3.5 + - - -
116D ARG* 3.4 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D THR 3.4 10.2 + - - +
109D LEU* 3.1 19.3 + - + +
111D GLU* 1.3 74.0 - - - +
113D GLU* 1.3 65.6 + - - +
114D TYR* 2.9 13.4 + - - +
115D PHE* 2.8 33.7 + - + +
116D ARG* 3.0 26.0 + - - +
169D PHE* 4.6 2.4 - - - -
174D PHE* 3.4 48.1 - - - +
----------------------------------------------------------
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