Contacts of the helix formed by residues 105 - 127 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 3.6 26.2 - - - +
64F TRP* 3.5 19.5 + - - -
102F ARG* 3.4 11.0 + - - +
103F ALA 2.8 7.7 + - - -
104F SER* 1.3 85.9 + - - +
106F ILE* 1.3 63.7 + - - +
108F PRO* 3.2 18.7 - - - +
109F ILE* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ALA 4.6 5.4 - - - +
101F VAL* 4.2 17.1 + - - +
103F ALA 4.0 5.7 + - - +
104F SER* 3.2 24.9 - - - +
105F SER* 1.3 74.9 - - - +
107F PHE* 1.3 60.9 + - + +
108F PRO* 3.9 0.2 - - - +
109F ILE* 3.0 9.9 + - - +
110F LEU* 2.7 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TYR* 5.7 9.9 - + + -
101F VAL* 5.5 6.5 + - + -
106F ILE* 1.3 85.1 - - + +
108F PRO* 1.3 62.9 - - + +
110F LEU* 2.9 29.6 + - + +
111F SER* 2.9 25.6 + - - -
148F SER* 4.1 12.2 - - - +
151F ILE* 3.6 33.9 - - + -
152F GLY* 3.6 19.7 - - - +
155F VAL* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 5.7 8.7 - - + -
63F LEU* 5.1 5.4 - - + -
105F SER* 3.2 37.5 - - - +
107F PHE* 1.3 94.0 - - + +
109F ILE* 1.3 55.5 + - + +
111F SER* 2.1 32.0 + - - +
112F VAL* 2.9 15.4 + - - +
148F SER 5.2 1.8 - - - +
149F ASN* 5.4 3.4 - - - +
152F GLY* 4.4 13.4 - - - +
155F VAL* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 6.1 4.7 - - + -
64F TRP* 4.7 12.6 - - + -
104F SER 3.3 26.2 - - - +
105F SER* 3.1 15.1 + - - +
106F ILE* 3.0 10.8 + - - +
108F PRO* 1.3 72.2 - - + +
110F LEU* 1.3 67.1 + - + +
112F VAL* 2.9 24.3 + - + +
113F ILE* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F ILE* 2.7 31.0 + - + +
107F PHE* 2.9 43.0 + - + +
109F ILE* 1.3 75.5 - - + +
111F SER* 1.3 54.4 + - - +
113F ILE* 3.4 16.2 + - + +
114F LEU* 2.9 41.3 + - + +
148F SER* 4.6 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F MET* 5.3 4.9 - - - +
107F PHE 2.9 9.9 + - - -
108F PRO* 2.1 32.2 + - - +
110F LEU* 1.3 75.5 - - - +
112F VAL* 1.3 58.1 + - - +
114F LEU* 3.8 2.4 - - - +
115F LEU* 2.9 44.4 + - - +
145F ALA* 4.1 3.8 - - - +
148F SER* 3.4 21.6 + - - -
149F ASN* 4.0 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F PHE* 4.3 13.4 - - + -
24F MET* 5.2 10.5 - - + -
25F THR* 5.8 5.4 - - - +
28F VAL* 4.5 20.0 - - + -
108F PRO 2.9 20.6 + - - +
109F ILE* 2.9 20.9 + - + +
111F SER* 1.3 79.5 - - - +
113F ILE* 1.3 68.0 + - + +
115F LEU* 3.3 7.1 + - - +
116F PHE* 2.9 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE* 2.9 34.6 + - + +
110F LEU* 3.9 15.9 - - + +
112F VAL* 1.3 78.0 - - + +
114F LEU* 1.3 62.3 + - + +
116F PHE* 3.1 13.1 + - + +
117F MET* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 2.9 26.6 + - + +
111F SER 4.0 0.9 - - - +
113F ILE* 1.3 80.2 - - + +
115F LEU* 1.3 57.4 + - - +
117F MET* 3.2 14.0 + - + +
118F GLY* 2.9 22.3 + - - -
141F PHE* 4.1 25.4 - - + +
142F PHE* 5.3 0.3 - - - -
144F SER* 4.7 4.3 - - - +
145F ALA* 3.4 39.5 - - + +
148F SER* 3.8 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ALA* 4.0 25.4 - - + +
21F PHE* 4.0 22.9 - - + +
24F MET* 4.1 15.5 - - + -
111F SER* 2.9 32.8 + - - +
112F VAL* 3.7 4.9 - - - +
114F LEU* 1.3 72.1 - - - +
116F PHE* 1.3 59.0 + - - +
118F GLY* 2.6 21.4 + - - +
119F GLY* 2.9 13.2 + - - -
142F PHE* 3.6 33.8 - - + +
145F ALA* 4.5 10.5 - - + -
146F GLY 5.6 1.1 - - - +
190F ALA* 4.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F PHE* 4.0 26.6 - + + -
112F VAL* 2.9 14.7 + - + +
113F ILE* 3.2 16.2 - - + +
115F LEU* 1.3 74.2 - - - +
117F MET* 1.3 70.2 + - - +
119F GLY 3.6 0.4 + - - +
120F LEU* 2.9 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ILE* 2.9 26.3 + - + +
114F LEU* 3.4 16.4 - - + +
115F LEU 3.2 0.2 - - - -
116F PHE* 1.3 87.8 - - + +
118F GLY* 1.3 57.4 + - - +
120F LEU* 4.3 5.4 - - + -
121F CYS* 2.9 58.9 + - - +
138F ALA* 4.8 1.1 - - - +
141F PHE* 5.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LEU 2.9 9.5 + - - -
115F LEU* 2.6 17.1 + - - -
117F MET* 1.3 72.7 - - - +
119F GLY* 1.3 61.7 + - - -
121F CYS* 4.0 1.6 - - - +
122F ILE* 2.9 35.8 + - - +
138F ALA* 5.0 5.2 - - - -
141F PHE* 6.3 0.9 - - - -
142F PHE* 4.5 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ALA* 4.4 22.8 - - - +
115F LEU 2.9 12.1 + - - -
116F PHE* 4.2 0.7 - - - -
118F GLY* 1.3 71.2 - - - -
120F LEU* 1.3 62.1 + - - +
122F ILE* 3.9 5.4 - - - +
123F ALA* 2.9 27.9 + - - +
142F PHE* 5.7 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F PHE* 2.9 37.3 + - + +
117F MET* 4.1 6.5 - - - +
119F GLY* 1.3 76.0 - - - +
121F CYS* 1.3 60.4 + - - +
123F ALA* 3.8 4.9 - - - +
124F ALA* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F MET* 2.9 53.1 + - - +
120F LEU* 1.3 75.6 - - - +
122F ILE* 1.3 61.0 + - - +
124F ALA* 3.3 11.5 - - + +
125F SER* 2.9 23.6 + - - -
134F ILE* 3.7 11.3 - - + +
137F SER* 5.6 2.5 - - - +
138F ALA* 3.7 21.7 - - + +
141F PHE* 6.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F MET* 6.1 5.2 - - + -
13F THR* 3.5 37.7 - - + +
14F THR* 5.8 4.7 - - + -
17F ALA* 5.5 4.9 - - + -
118F GLY* 2.9 28.7 + - - +
119F GLY* 3.9 6.5 - - - +
120F LEU 3.3 0.2 - - - -
121F CYS* 1.3 73.7 - - - +
123F ALA* 1.3 59.8 + - - +
124F ALA 3.0 1.6 - - - -
125F SER* 2.3 42.2 + - - +
126F GLU* 3.0 5.7 + - - +
135F ILE* 6.6 0.2 - - - -
138F ALA* 4.2 15.5 - - + +
142F PHE* 5.5 14.6 - - + -
197F ALA* 6.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F GLY 2.9 17.9 + - - +
120F LEU* 3.9 5.6 - - - +
122F ILE* 1.3 77.6 - - - +
124F ALA* 1.3 60.4 + - - +
126F GLU* 3.2 29.8 - - - +
127F PHE* 4.0 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F LEU 2.9 16.4 + - - +
121F CYS* 3.3 15.9 - - + +
122F ILE 3.0 0.2 - - - -
123F ALA* 1.3 77.0 - - - +
125F SER* 1.3 56.2 + - - +
126F GLU 3.1 2.4 + - - -
127F PHE* 2.9 34.6 + - - +
128F TYR* 4.7 4.9 - - - +
134F ILE* 5.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F MET* 6.2 0.2 - - - -
121F CYS 2.9 13.0 + - - -
122F ILE* 2.3 43.0 + - - +
124F ALA* 1.3 68.8 - - - +
126F GLU* 1.3 65.8 + - - +
127F PHE 3.7 5.2 - - - +
128F TYR 5.7 1.1 - - - -
129F LYS* 5.0 7.8 - - - +
130F THR* 6.0 0.2 - - - -
134F ILE* 3.8 21.3 - - - -
135F ILE* 4.9 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F MET* 6.3 3.4 - - - -
122F ILE 3.0 7.3 + - - +
123F ALA* 3.2 24.4 - - - +
124F ALA 3.1 0.6 - - - -
125F SER* 1.3 79.8 - - - +
127F PHE* 1.3 72.9 + - + +
129F LYS* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ALA 4.0 13.5 - - - -
124F ALA* 2.9 24.1 - - - +
125F SER 3.7 4.9 - - - +
126F GLU* 1.3 94.8 - - + +
128F TYR* 1.3 87.1 + - + +
129F LYS* 3.5 3.1 - - - +
----------------------------------------------------------
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