Contacts of the helix formed by residues 105 - 127 (chain E) in PDB entry 5VOT
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 SER 105 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU* 5.4 14.8 - - - -
101E VAL 4.0 6.1 - - - -
102E ARG 4.2 5.8 + - - -
103E ALA* 2.9 10.2 + - - +
104E SER* 1.3 78.8 - - - +
106E ILE* 1.3 66.2 + - - +
107E PHE 3.5 1.8 - - - -
108E PRO* 3.2 25.2 - - - +
109E ILE* 3.2 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ALA 5.1 1.8 - - - +
101E VAL* 4.2 34.8 + - + +
103E ALA 4.5 2.9 - - - +
104E SER* 3.8 19.5 - - - +
105E SER* 1.3 77.3 - - - +
107E PHE* 1.3 65.3 + - - +
109E ILE* 3.8 3.4 - - - +
110E LEU* 2.9 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E VAL* 5.1 7.3 - - + +
106E ILE* 1.3 81.7 - - + +
108E PRO* 1.3 63.8 - - + +
110E LEU* 3.3 8.2 + - - +
111E SER* 2.9 27.3 + - - -
148E SER* 4.3 11.2 + - - +
151E ILE* 5.0 2.0 - - + -
152E GLY* 3.5 26.5 - - - +
155E VAL* 5.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E VAL* 5.3 11.9 - - + +
105E SER* 3.2 34.3 - - - +
107E PHE* 1.3 94.7 - - + +
109E ILE* 1.3 55.3 + - + +
111E SER* 3.0 10.0 + - - -
112E VAL* 2.9 27.2 + - - +
149E ASN* 5.1 7.6 - - - +
152E GLY* 4.6 13.4 - - - +
155E VAL* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E VAL* 5.6 13.5 - - + -
104E SER 3.2 27.1 - - - +
105E SER* 3.2 17.3 + - - +
106E ILE* 3.8 2.9 - - - +
108E PRO* 1.3 76.0 - - + +
110E LEU* 1.3 66.9 + - + +
112E VAL* 3.0 8.6 + - + +
113E ILE* 2.9 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ILE* 2.9 42.1 + - + +
107E PHE* 3.6 7.2 - - - +
109E ILE* 1.3 79.2 - - + +
111E SER* 1.3 56.4 + - - +
113E ILE* 4.7 9.9 - - + +
114E LEU* 2.8 34.0 + - - +
148E SER* 5.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E PHE 2.9 14.0 + - - -
108E PRO* 3.1 12.1 - - - -
110E LEU* 1.3 74.3 - - - +
112E VAL* 1.3 59.6 + - - +
114E LEU* 3.7 2.7 - - - +
115E LEU* 2.9 38.9 + - - +
145E ALA 4.3 2.7 - - - -
148E SER* 4.2 8.5 + - - -
149E ASN* 3.7 42.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E PHE* 3.4 20.4 - - + +
24E MET* 5.0 16.5 - - + +
25E THR* 5.6 4.3 - - - +
28E VAL* 5.0 12.3 - - + -
108E PRO 2.9 11.8 + - - +
109E ILE* 3.6 10.1 - - + +
111E SER* 1.3 77.6 - - - +
113E ILE* 1.3 66.4 + - + +
115E LEU* 3.2 6.5 + - - +
116E PHE 2.9 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ILE* 2.9 37.2 + - + +
110E LEU* 4.4 10.5 - - + +
112E VAL* 1.3 77.1 - - + +
114E LEU* 1.3 63.6 + - - +
116E PHE* 3.0 14.9 + - + +
117E MET* 2.9 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU 2.8 23.1 + - - +
111E SER* 3.7 1.1 - - - +
113E ILE* 1.3 77.8 - - - +
115E LEU* 1.3 57.8 + - - +
117E MET* 3.0 11.4 + - - +
118E GLY* 2.9 22.0 + - - -
141E PHE* 5.0 5.5 - - - +
142E PHE* 5.7 0.2 - - - -
145E ALA* 3.5 26.3 - - + +
148E SER* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ALA* 5.3 4.0 - - + +
21E PHE* 4.3 21.4 - - + +
24E MET* 4.8 17.5 - - + -
111E SER* 2.9 25.0 + - - +
112E VAL* 3.7 4.5 - - - +
114E LEU* 1.3 75.9 - - - +
116E PHE* 1.3 57.1 + - - +
118E GLY* 3.0 4.4 + - - +
119E GLY* 2.9 23.6 + - - -
142E PHE* 3.8 39.7 - - + +
145E ALA* 3.8 21.1 - - + -
146E GLY* 4.4 6.1 - - - +
149E ASN* 5.0 11.7 - - - +
186E SER* 5.7 2.0 - - - +
190E ALA* 4.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E PHE* 3.5 37.6 - + + -
112E VAL 2.9 8.3 + - - +
113E ILE* 3.2 18.4 - - + +
115E LEU* 1.3 75.7 - - - +
117E MET* 1.3 66.3 + - - +
119E GLY* 3.0 5.0 + - - +
120E LEU* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ILE* 2.9 11.7 + - + +
114E LEU* 3.0 13.0 + - - +
116E PHE* 1.3 78.4 - - - +
118E GLY* 1.3 57.7 + - - +
120E LEU* 3.3 9.6 + - - +
121E CYS* 2.9 27.5 + - - +
141E PHE* 5.9 10.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ALA* 6.0 0.2 - - - -
114E LEU 2.9 13.1 + - - -
115E LEU 3.0 6.8 + - - -
117E MET* 1.3 77.4 - - - +
119E GLY* 1.3 55.9 + - - +
121E CYS* 3.0 9.4 + - - +
122E ILE* 2.9 29.3 + - - +
138E ALA* 4.7 3.9 - - - +
141E PHE* 5.4 3.5 - - - +
142E PHE* 4.4 29.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ALA* 4.9 14.5 - - - +
18E PHE* 5.6 10.1 - - - -
115E LEU 2.9 12.2 + - - -
116E PHE* 3.0 5.1 + - - -
118E GLY* 1.3 75.7 - - - +
120E LEU* 1.3 57.8 + - - +
122E ILE* 4.1 5.1 - - - +
123E ALA* 2.9 34.5 + - - +
142E PHE* 5.3 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E PHE* 2.9 22.2 + - + +
117E MET* 3.5 12.8 - - - +
119E GLY* 1.3 75.7 - - - +
121E CYS* 1.3 58.3 + - - +
123E ALA* 4.4 3.1 - - - +
124E ALA* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E MET 2.9 13.3 + - - +
118E GLY* 3.0 10.3 + - - +
120E LEU* 1.3 75.8 - - - +
122E ILE* 1.3 59.8 + - - +
124E ALA* 3.6 4.1 - - - +
125E SER* 2.9 29.3 + - - -
134E ILE* 5.1 3.9 - - - +
137E SER* 4.9 6.3 - - - +
138E ALA* 3.6 29.7 - - + +
141E PHE* 5.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E THR* 4.4 22.4 - - + -
17E ALA* 5.5 6.1 - - + -
118E GLY 2.9 14.3 + - - +
119E GLY* 4.1 5.4 - - - +
121E CYS* 1.3 74.8 - - - +
123E ALA* 1.3 61.9 + - - +
125E SER* 2.9 21.4 + - - -
126E GLU* 2.9 15.6 + - - +
138E ALA* 4.3 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E PHE* 5.7 10.1 - - + -
119E GLY 2.9 17.5 + - - +
120E LEU* 4.4 3.8 - - - +
122E ILE* 1.3 77.7 - - - +
124E ALA* 1.3 60.4 + - - +
125E SER 3.4 0.3 + - - -
126E GLU* 3.6 12.0 + - - +
127E PHE* 3.7 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E LEU 2.8 22.6 + - - +
121E CYS* 3.6 5.4 - - - +
123E ALA* 1.3 75.5 - - - +
125E SER* 1.3 54.2 + - - +
127E PHE* 2.7 25.9 - - - +
128E TYR* 4.9 1.6 - - - +
134E ILE* 5.9 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E CYS 2.9 18.4 + - - -
122E ILE* 2.9 8.5 + - - -
124E ALA* 1.3 76.1 - - - +
126E GLU* 1.3 65.8 + - - +
127E PHE 3.2 6.7 + - - +
128E TYR 4.9 0.6 - - - -
129E LYS* 4.5 12.8 - - - +
134E ILE* 4.8 9.2 - - - -
135E ILE* 4.6 26.9 - - - -
138E ALA* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E MET* 6.4 2.7 - - + -
122E ILE 2.9 14.0 + - - +
123E ALA* 4.1 7.4 - - - +
124E ALA 3.6 0.2 - - - -
125E SER* 1.3 76.7 - - - +
127E PHE* 1.3 58.8 + - - +
129E LYS* 4.7 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E ALA 3.7 12.9 + - - +
124E ALA* 2.7 22.7 - - - +
125E SER* 3.2 4.2 - - - +
126E GLU* 1.3 78.0 - - + +
128E TYR* 1.3 73.0 + - + +
129E LYS 3.4 0.7 - - - -
----------------------------------------------------------
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