Contacts of the helix formed by residues 104 - 118 (chain N) in PDB entry 2DYS
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 LEU 104 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N MET* 3.0 26.3 + - + +
102N PHE 3.1 0.6 - - - -
103N TRP* 1.3 78.6 - - - +
105N LEU* 1.3 59.6 + - - +
107N PRO* 3.3 5.4 - - + +
108N SER* 3.0 28.6 + - - -
152N LEU* 4.0 21.3 - - + +
155N VAL* 3.9 18.2 - - + -
156N SER* 3.7 39.0 - - - +
159N LEU* 4.2 10.1 - - + -
609N PGV 4.5 7.9 - - + -
21P ALA* 3.9 13.2 - - - +
24P ALA* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N TYR* 3.8 24.9 - - + -
22N PHE* 3.6 23.3 - - + -
67N PHE 4.9 3.4 - - - +
68N PHE* 4.4 10.2 - - + -
72N PRO* 3.7 29.4 - - + -
101N SER 3.8 0.4 - - - +
102N PHE* 3.0 14.7 + - + +
104N LEU* 1.3 77.6 - - - +
106N PRO* 1.3 64.4 - - + +
108N SER* 3.2 2.3 + - - -
109N PHE* 2.7 31.7 + - - +
153N ALA* 4.3 19.1 - - + +
156N SER* 3.6 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N PHE* 3.9 15.7 - - + -
102N PHE* 3.3 20.0 - - + +
103N TRP* 3.5 28.0 - - + +
105N LEU* 1.3 91.1 - - + +
107N PRO* 1.4 62.1 - - + +
109N PHE* 3.2 2.8 + - - +
110N LEU* 2.8 34.6 + - - +
606N TGL 3.8 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 107 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N TRP* 2.8 30.3 - - + +
104N LEU* 3.3 8.3 - - - +
106N PRO* 1.4 87.1 - - + +
108N SER* 1.3 65.0 + - - +
110N LEU* 3.0 8.0 + - + +
111N LEU* 2.9 26.5 + - - +
152N LEU* 4.0 11.9 - - + -
21P ALA* 4.2 16.2 - - + +
22P LEU* 4.9 10.3 - - + -
25P LEU* 3.9 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N PHE* 3.5 14.8 - - - -
104N LEU 3.0 16.8 + - - -
105N LEU* 3.4 9.0 - - - -
107N PRO* 1.3 79.8 - - - +
109N PHE* 1.3 60.6 + - - +
111N LEU* 3.4 1.1 + - - -
112N LEU 3.3 6.4 + - - -
149N SER* 2.5 51.5 + - - +
152N LEU* 3.7 21.5 - - - -
153N ALA* 3.6 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N PHE* 3.6 25.1 - + + -
25N TRP* 3.5 29.2 - + - -
26N ALA* 4.0 17.3 - - + -
29N VAL* 3.9 27.6 - - + -
64N VAL* 4.0 8.1 - - + -
68N PHE* 3.6 32.9 - + + -
105N LEU 2.7 19.8 + - - +
106N PRO* 3.5 4.9 - - + +
108N SER* 1.3 71.3 - - - +
110N LEU* 1.3 66.9 - - - +
112N LEU* 3.1 20.1 + - + -
113N LEU* 3.0 33.5 + - + +
606N TGL 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N PRO 2.8 13.2 + - - +
107N PRO* 3.2 11.0 - - + +
109N PHE* 1.3 78.0 - - - +
111N LEU* 1.3 57.2 + - + +
113N LEU* 3.2 6.1 + - + +
114N ALA* 2.9 29.3 + - + +
606N TGL 3.8 25.7 - - + +
25P LEU* 4.0 30.1 - - + -
43W THR* 5.9 0.9 - - + -
46W SER* 5.5 3.4 - - - +
47W LEU* 3.9 31.9 - - + -
50W LEU* 5.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N PRO 2.9 14.0 + - - +
108N SER 3.7 6.5 - - - +
109N PHE 3.3 0.2 - - - -
110N LEU* 1.3 75.7 - - + +
112N LEU* 1.3 57.0 + - - +
114N ALA* 3.5 5.6 - - + +
115N SER* 3.0 29.3 + - - -
145N LEU* 3.6 41.6 - - + +
148N PHE* 3.6 27.1 - - + -
149N SER* 3.7 4.3 - - - +
152N LEU* 3.6 31.4 - - + -
25P LEU* 4.3 12.6 - - + -
28P THR* 3.7 18.4 - - - +
29P SER* 4.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 6.0 0.2 - - + -
60N ALA* 4.7 14.6 - - + +
63N PHE* 3.5 36.6 - - + -
64N VAL* 4.0 12.3 - - + -
68N PHE* 3.5 23.3 - - + -
108N SER 3.3 3.3 + - - +
109N PHE* 3.1 30.1 + - + +
111N LEU* 1.3 76.7 - - - +
113N LEU* 1.3 77.7 + - + +
115N SER* 3.3 15.7 + - - -
116N SER* 3.4 12.4 + - - +
146N THR* 5.6 2.5 - - - +
149N SER* 3.7 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TRP* 4.7 6.1 - - + -
29N VAL* 5.1 10.5 - - + -
109N PHE* 3.0 29.0 + - + +
110N LEU* 3.8 9.4 - - + +
112N LEU* 1.3 87.7 - - + +
114N ALA* 1.3 60.3 + - - +
116N SER* 2.6 22.5 + - - +
117N MET* 3.1 16.3 - - + +
606N TGL 3.1 54.1 - - + -
35Y ALA* 5.2 4.5 - - + -
36Y PRO* 6.1 0.7 - - + -
39Y ILE* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N LEU* 2.9 19.5 + - + +
111N LEU* 3.5 10.3 - - + +
113N LEU* 1.3 76.5 - - - +
115N SER* 1.3 57.4 + - - +
117N MET* 2.8 22.4 + - - +
118N VAL* 3.0 17.0 + - - +
145N LEU* 4.1 19.5 - - + -
50W LEU* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU 3.0 17.9 + - - -
112N LEU* 3.4 8.8 + - - -
114N ALA* 1.3 76.7 - - - +
116N SER* 1.3 59.4 + - - +
118N VAL 3.5 1.7 - - - +
121N GLY* 3.2 6.1 - - - -
122N ALA* 3.9 8.8 + - - +
142N SER* 2.7 39.0 + - - +
145N LEU* 3.8 14.8 - - - +
146N THR* 2.9 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N VAL* 4.3 18.7 - - - +
60N ALA* 5.9 5.8 - - - -
112N LEU* 3.4 7.5 + - - +
113N LEU* 2.6 27.1 + - - +
115N SER* 1.3 79.2 - - - +
117N MET* 1.3 58.3 + - - +
118N VAL 4.2 1.1 - - - -
121N GLY* 4.0 10.8 - - - -
39Y ILE* 3.6 26.4 - - - +
43Y GLN* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113N LEU* 3.1 27.4 + - + +
114N ALA* 2.8 10.8 + - - +
116N SER* 1.3 79.2 - - - +
118N VAL* 1.3 59.7 + - - +
50W LEU* 4.1 14.6 - - + -
54W SER* 3.1 32.6 - - - +
55W PHE* 5.7 2.0 - - + -
39Y ILE* 4.0 32.3 - - + -
42Y HIS* 3.1 38.5 + - + +
43Y GLN* 3.1 5.1 + - - +
46Y LYS* 2.9 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N ALA 3.0 17.6 + - - +
115N SER 3.5 2.1 - - - +
117N MET* 1.3 77.7 - - - +
119N GLU* 1.3 74.8 + - + +
121N GLY* 3.1 6.2 + - - -
141N ALA* 4.1 5.6 - - + -
142N SER* 3.0 45.6 + - - +
145N LEU* 4.0 16.8 - - + -
37P PHE* 5.8 0.9 - - + -
50W LEU* 4.1 14.6 - - + -
53W ALA* 3.7 39.9 - - + +
----------------------------------------------------------
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