Contacts of the helix formed by residues 109 - 124 (chain A) in PDB entry 2DB9
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 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 4.3 17.3 + - - +
107A GLU 2.8 15.0 + - - +
108A PHE* 1.3 74.0 - - - +
110A GLU* 1.3 64.5 + - - +
111A SER* 2.8 11.0 + - - -
112A GLU* 2.8 39.4 + - - +
113A PHE* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 4.2 21.7 - - + +
108A PHE 3.5 1.4 + - - -
109A THR* 1.3 73.4 - - - +
111A SER* 1.3 57.7 + - - +
113A PHE* 4.0 1.2 - - - +
114A MET* 3.0 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 2.8 5.5 + - - -
110A GLU* 1.3 76.8 + - - +
112A GLU* 1.3 67.6 + - - -
113A PHE 3.1 1.3 - - - -
114A MET* 2.7 8.9 + - - +
115A LYS* 2.5 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 4.6 6.0 + - - +
61A TYR* 3.0 55.3 + - + +
62A ARG* 4.0 6.2 + - - +
63A VAL* 3.9 16.4 - - + -
108A PHE* 4.9 0.7 - - - -
109A THR* 2.8 35.4 + - - +
111A SER* 1.3 83.8 - - - +
113A PHE* 1.3 56.6 + - - +
115A LYS* 2.9 14.3 + - - +
116A TRP* 2.5 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.2 31.0 - - + -
15A SER 4.6 0.7 - - - -
16A LEU* 3.2 23.6 - - - -
17A PRO* 3.2 49.4 - - + -
20A LEU* 3.6 21.3 - - + -
63A VAL* 4.1 5.1 - - - +
108A PHE* 4.8 4.2 - - + +
109A THR 3.0 9.1 + - - +
110A GLU 4.0 2.7 - - - +
112A GLU* 1.3 78.1 - - - +
114A MET* 1.3 75.8 - - + +
116A TRP* 3.1 32.2 - + - -
117A LYS* 2.7 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER 5.6 2.7 - - - +
17A PRO* 5.3 3.6 - - + -
110A GLU* 3.0 26.7 + - + +
111A SER* 2.7 12.7 + - - +
113A PHE* 1.3 96.9 - - + +
115A LYS* 1.3 66.8 + - + +
117A LYS* 3.2 25.8 + - - +
118A GLU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.5 36.5 + - - +
111A SER* 2.5 31.6 + - - +
112A GLU* 3.4 15.0 - - - +
114A MET* 1.3 73.2 - - + +
116A TRP* 1.3 61.9 + - - +
118A GLU* 3.1 33.6 - - + +
119A ALA* 3.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.1 33.0 - - + -
47A PHE* 3.8 17.8 - + - -
62A ARG* 5.2 1.3 - - - +
63A VAL* 2.9 50.7 + - + +
64A ALA* 4.9 1.8 - - - +
65A GLU* 5.3 2.2 - - + +
90A ARG 4.9 6.1 + - - -
91A HIS* 4.9 12.8 - - + -
92A GLY 4.9 7.8 - - - +
112A GLU 2.5 20.3 + - - +
113A PHE* 3.1 38.6 - + - -
115A LYS* 1.3 70.4 - - - +
117A LYS* 1.3 70.1 + - + +
119A ALA* 2.8 25.4 + - + +
120A MET* 3.3 27.6 + - + +
127A LEU* 3.5 29.6 - - + -
128A PRO* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO 4.8 1.0 + - - -
14A VAL 4.3 4.9 + - - -
15A SER 5.1 3.4 + - - -
113A PHE* 2.7 55.5 + - + +
114A MET* 3.2 29.8 + - - +
116A TRP* 1.3 82.8 - - + +
118A GLU* 1.3 49.7 + - - +
120A MET* 2.6 10.8 + - - +
121A PHE* 2.5 68.6 + - + -
127A LEU* 3.5 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET 2.9 21.4 + - - +
115A LYS* 3.1 28.0 - - + +
116A TRP 3.0 0.2 - - - -
117A LYS* 1.3 74.7 - - - +
119A ALA* 1.3 52.3 + - - +
121A PHE* 2.9 11.0 + - - +
122A SER* 2.5 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 6.0 0.4 - - - +
91A HIS* 4.5 17.9 - - + +
92A GLY* 3.6 28.8 - - - +
93A ASN 4.9 0.2 + - - -
115A LYS 3.8 1.7 + - - +
116A TRP* 2.8 18.4 + - + +
118A GLU* 1.3 75.3 - - - +
120A MET* 1.3 57.6 + - - +
122A SER* 3.8 5.8 - - - -
123A ALA* 3.0 31.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
92A GLY* 4.6 4.0 - - - -
116A TRP* 3.7 38.4 - - + +
117A LYS* 2.6 13.7 + - - +
119A ALA* 1.3 71.5 - - + +
121A PHE* 1.3 59.3 + - + +
124A GLY 2.8 6.1 + - - -
125A MET* 2.7 68.8 + - + +
126A GLN 2.7 39.0 - - - +
127A LEU* 3.4 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 2.5 76.0 + - + +
118A GLU* 3.5 11.2 - - - +
120A MET* 1.3 75.8 - - + +
122A SER* 1.3 63.2 + - - +
124A GLY* 3.5 9.8 + - - -
125A MET 5.0 2.2 - - - -
127A LEU* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 2.5 22.0 + - - -
119A ALA* 3.8 6.1 - - - -
121A PHE* 1.3 72.1 - - - +
123A ALA* 1.3 60.4 + - - +
124A GLY* 3.1 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 3.8 24.6 + - + +
119A ALA 3.0 14.8 + - - +
122A SER* 1.3 75.6 - - - +
124A GLY* 1.3 59.1 + - - +
125A MET* 3.0 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET 2.8 6.9 + - - -
121A PHE* 3.5 9.2 + - - -
122A SER 3.1 5.2 - - - -
123A ALA* 1.3 80.4 - - - +
125A MET* 1.3 64.8 - - - +
126A GLN* 4.6 4.9 - - - +
----------------------------------------------------------
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