Contacts of the helix formed by residues 102 - 111 (chain N) in PDB entry 2DFS
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 ALA 102 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N ILE 3.7 1.0 + - - -
101N SER* 1.3 71.9 - - - +
103N ALA* 1.3 55.8 + - - +
105N LEU* 3.7 9.8 - - + +
106N ARG* 2.9 32.6 + - - +
125N ILE* 5.8 11.2 - - + -
130N ILE* 3.9 25.4 - - + +
134N GLY 3.1 11.9 + - - +
136N VAL* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N SER* 3.9 10.0 - - - +
102N ALA* 1.3 76.7 - - - +
104N GLU* 1.4 58.8 + - + +
106N ARG* 3.9 4.0 - - - +
107N HIS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N PHE* 3.8 36.6 - - + +
93N ASP 4.5 4.3 + - - -
100N ILE* 3.8 12.8 - - + +
101N SER* 2.8 45.2 + - - +
103N ALA* 1.4 76.6 - - - +
105N LEU* 1.4 57.6 + - - +
107N HIS* 3.2 8.2 + - - +
108N VAL* 2.9 32.5 + - - +
135N GLN* 4.9 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
774M ILE* 6.6 0.4 - - + -
90N ARG* 6.1 1.8 - - - +
100N ILE* 3.9 23.7 - - + +
101N SER 3.0 16.9 + - - +
102N ALA* 3.7 7.0 - - + +
104N GLU* 1.4 76.7 - - - +
106N ARG* 1.3 63.0 + - - +
108N VAL* 3.1 26.0 - - + +
109N MET* 3.1 38.1 + - + +
121N VAL* 5.8 0.7 - - + -
125N ILE* 4.6 11.2 - - + -
136N VAL* 3.7 25.6 - - + -
138N TYR* 6.0 0.4 - - + -
141N PHE* 3.5 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N ALA 2.9 21.6 + - - +
103N ALA* 4.0 5.4 - - - +
105N LEU* 1.3 72.4 - - - +
107N HIS* 1.4 53.1 + - - +
109N MET* 3.3 1.7 + - - -
110N THR* 2.8 48.6 + - + +
118N ASP* 2.7 43.2 + - - +
121N VAL* 4.0 20.6 - - + +
122N ASP* 2.6 48.0 + - - +
125N ILE* 3.4 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N PHE* 5.0 7.0 - + - -
103N ALA 3.0 15.8 + - - +
104N GLU* 3.2 11.9 + - - +
106N ARG* 1.4 75.6 - - - +
108N VAL* 1.3 60.4 + - + +
110N THR* 4.4 2.2 - - - -
111N ASN* 2.8 63.2 + - + +
112N LEU* 3.3 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767M LEU 4.6 0.2 - - - +
771M CYS* 3.1 54.6 - - + +
774M ILE* 5.7 7.9 - - + -
90N ARG* 6.2 2.7 - - - -
92N PHE* 3.4 43.1 - - + -
100N ILE* 5.6 3.1 - - + -
104N GLU 2.9 18.0 + - - +
105N LEU* 3.1 31.9 - - + +
107N HIS* 1.3 77.7 - - - +
109N MET* 1.3 62.2 + - + +
112N LEU* 3.5 11.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 109 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771M CYS* 5.1 0.4 - - - -
774M ILE* 5.3 5.2 - - + -
775M GLN* 2.8 30.4 + - + +
778M ILE* 3.6 30.1 - - + -
105N LEU* 3.1 39.4 + - + +
106N ARG 3.7 2.7 - - - +
108N VAL* 1.3 79.0 - - + +
110N THR* 1.3 58.2 + - - +
115N LYS* 3.5 1.2 - - - -
116N LEU* 2.9 21.2 + - + +
121N VAL* 3.7 34.5 - - + -
124N MET* 3.8 15.9 - - - +
141N PHE* 4.2 9.6 - - + -
145N MET* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N ARG* 2.8 32.6 + - + +
107N HIS* 4.4 2.6 - - - -
109N MET* 1.3 72.7 - - - +
111N ASN* 1.3 62.2 + - - +
115N LYS* 3.2 26.3 - - - +
116N LEU 3.4 21.0 - - - +
117N THR 4.1 1.1 - - - +
118N ASP* 3.8 31.3 + - - +
121N VAL* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M TYR* 4.5 14.4 - - - +
41M ARG* 5.9 0.7 + - - -
107N HIS* 2.8 45.4 + - + +
110N THR* 1.3 81.4 + - - +
112N LEU* 1.3 65.6 + - + +
115N LYS* 2.7 34.5 + - - +
----------------------------------------------------------
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