Contacts of the helix formed by residues 114 - 132 (chain A) in PDB entry 6DWY
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 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER 3.3 8.4 + - - -
111A ALA* 3.3 10.7 + - - -
112A VAL 3.2 2.9 - - - +
113A SER* 1.3 78.6 - - - +
115A SER* 1.3 67.3 + - - -
116A GLY 3.3 2.5 - - - -
117A PHE* 3.1 6.9 + - - +
118A ILE* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER 3.5 3.9 + - - -
114A GLY* 1.3 70.5 - - - -
116A GLY* 1.3 66.9 + - - +
118A ILE* 3.2 17.7 + - - +
119A ASP* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLY 3.3 0.6 - - - -
115A SER* 1.3 84.6 + - - +
117A PHE* 1.3 61.0 + - - +
118A ILE 3.4 0.2 + - - -
119A ASP* 3.5 8.5 + - - +
120A MET* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A CYS* 6.0 4.3 - - - -
101A TRP* 4.0 32.1 - + - -
111A ALA* 3.3 27.1 - - + +
112A VAL* 3.3 35.4 - - + -
114A GLY* 3.1 6.2 + - - +
116A GLY* 1.3 74.5 - - - +
118A ILE* 1.3 66.0 + - - +
120A MET* 3.3 30.4 + - + +
121A ILE* 3.4 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL 3.9 18.2 - - - +
113A SER* 4.9 8.7 - - - +
114A GLY 2.9 11.4 + - - +
115A SER* 3.2 10.5 + - - +
117A PHE* 1.3 78.0 - - + +
119A ASP* 1.3 76.9 + - - +
121A ILE* 3.3 15.0 + - - +
122A LYS* 3.4 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.3 17.3 + - - +
116A GLY* 4.0 7.2 - - - +
117A PHE 3.3 0.4 - - - -
118A ILE* 1.3 91.4 - - - +
120A MET* 1.3 62.3 + - - +
122A LYS* 3.3 32.0 + - + +
123A PHE* 3.5 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLY 3.3 11.6 + - - +
117A PHE* 3.7 37.0 - - + +
118A ILE 3.2 0.6 - - - -
119A ASP* 1.3 79.3 - - - +
121A ILE* 1.3 67.4 + - + +
123A PHE* 3.4 18.5 + - + +
124A PHE* 3.5 43.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.4 48.2 - - + +
118A ILE* 3.3 9.1 + - - +
119A ASP 3.2 0.6 - - - -
120A MET* 1.3 86.0 - - + +
122A LYS* 1.3 65.5 + - - +
123A PHE 3.1 2.0 - - - -
124A PHE* 2.9 25.4 + - + +
125A ILE* 3.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 3.4 28.6 + - - +
119A ASP* 3.5 20.6 + - + +
121A ILE* 1.3 77.6 - - - +
123A PHE* 1.3 57.4 + - - +
125A ILE* 3.1 33.3 - - + +
126A LYS* 3.2 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP 3.5 7.2 + - - +
120A MET* 3.4 14.7 + - + +
121A ILE 3.1 0.8 - - - -
122A LYS* 1.3 79.9 - - - +
124A PHE* 1.3 88.9 + + - +
125A ILE 3.4 0.2 - - - -
126A LYS* 3.2 25.2 + - + +
127A VAL* 3.0 48.3 + - + +
140A LEU* 5.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 3.5 41.0 + - + -
121A ILE* 2.9 22.6 + - + +
123A PHE* 1.3 105.8 - + - +
125A ILE* 1.3 60.8 + - + +
126A LYS 3.2 0.2 - - - -
127A VAL* 3.5 6.9 + - + +
128A GLY* 3.1 22.0 + - - -
137A VAL* 6.1 1.1 - - + -
140A LEU* 3.8 22.4 - - + -
141A LEU* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.1 19.9 + - + +
122A LYS* 3.1 32.8 - - + +
124A PHE* 1.3 75.5 - - + +
126A LYS* 1.3 58.2 + - - +
128A GLY* 3.7 2.1 - - - +
129A ALA* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS 3.2 12.3 + - - +
123A PHE* 3.2 30.0 + - + +
124A PHE 3.2 0.2 - - - -
125A ILE* 1.3 83.0 - - - +
127A VAL* 1.3 60.4 + - + +
129A ALA* 3.6 4.2 + - - +
130A GLU* 2.8 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.0 51.8 + - + +
124A PHE* 4.0 8.5 - - + +
125A ILE 3.3 0.2 - - - -
126A LYS* 1.3 75.5 - - + +
128A GLY* 1.3 65.7 + - - +
129A ALA 3.2 0.2 - - - -
130A GLU* 3.4 0.8 + - - -
131A TYR* 3.0 50.0 + - + +
135A VAL* 5.2 12.1 - - + -
140A LEU* 5.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE 3.1 14.7 + - - -
125A ILE* 3.3 4.9 + - - -
127A VAL* 1.3 79.1 - - - +
129A ALA* 1.3 56.5 + - - +
131A TYR* 5.1 0.2 - - - -
132A GLY* 2.8 38.4 + - - -
135A VAL* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE 3.0 16.3 + - - +
126A LYS* 3.8 6.5 - - - +
127A VAL 3.2 0.4 - - - -
128A GLY* 1.3 80.1 - - - +
130A GLU* 1.3 77.3 + - - +
131A TYR 3.4 0.7 + - - -
132A GLY* 4.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 2.8 34.4 + - - +
127A VAL* 3.4 2.4 + - - -
129A ALA* 1.3 88.3 - - - +
131A TYR* 1.3 79.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.0 35.8 + - + +
129A ALA 4.5 0.4 - - - -
130A GLU* 1.3 97.6 - - + +
132A GLY* 1.3 60.7 + - - +
134A HIS 4.9 3.6 - - - +
135A VAL* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL 4.0 0.2 + - - -
128A GLY* 2.8 31.4 + - - -
129A ALA 4.3 1.8 + - - -
131A TYR* 1.3 74.3 - - - +
133A GLU* 1.3 54.9 + - - -
134A HIS 2.8 18.1 + - - -
135A VAL* 3.1 19.4 - - - +
----------------------------------------------------------
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