Contacts of the helix formed by residues 96 - 110 (chain F) in PDB entry 1FQV
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 ASP 96 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F VAL* 1.3 74.9 - - - +
97F GLN* 1.3 65.4 + - - +
98F GLY 3.8 0.4 - - - +
99F THR* 2.7 31.5 + - - -
100F LEU* 3.1 9.6 + - - +
282O THR* 5.1 4.8 + - - -
283O GLU* 4.2 23.8 + - + +
284O LYS* 2.5 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 3.8 13.6 + - + +
95F VAL 3.9 0.6 + - - -
96F ASP* 1.3 72.3 - - - +
98F GLY* 1.3 57.7 + - - +
100F LEU* 3.4 10.1 + - - +
101F PHE* 2.9 31.4 + - - +
126F MET* 5.5 9.4 - - + +
138F THR* 2.7 48.9 + - - +
139F PHE* 3.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E VAL* 6.0 7.4 - - - -
96F ASP* 2.9 4.6 + - - +
97F GLN* 1.3 79.1 - - - +
99F THR* 1.3 55.2 + - - -
101F PHE* 3.1 8.6 + - - +
102F GLU* 2.9 37.1 + - - +
284O LYS* 3.0 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE* 3.9 18.2 - - + +
57F LYS* 5.2 8.1 - - + -
95F VAL* 3.4 30.6 - - + +
96F ASP* 2.7 29.9 + - - -
98F GLY* 1.3 72.0 - - - +
100F LEU* 1.3 57.5 + - - +
102F GLU* 3.2 9.3 + - - +
103F LEU* 2.8 37.3 + - + +
283O GLU* 5.4 0.7 + - - -
284O LYS* 3.9 6.3 - - - +
287O GLN* 5.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 4.3 5.4 - - + -
93F LEU* 4.5 16.2 - - + +
95F VAL* 3.7 10.2 - - + +
96F ASP 3.1 11.0 + - - +
97F GLN* 3.7 11.4 - - - +
99F THR* 1.3 76.9 - - - +
101F PHE* 1.3 57.4 + - - +
103F LEU* 3.2 5.6 + - + +
104F ILE* 3.0 33.8 + - - +
119F THR* 4.2 31.4 - - + +
122F THR* 4.1 14.1 - - + -
123F VAL* 3.6 26.2 - - + -
126F MET* 3.3 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E VAL* 4.7 16.4 - - + -
108E SER 3.7 18.6 - - - -
109E TRP* 3.4 56.7 - + + +
111E SER* 4.0 15.3 - - - -
112E LEU* 4.8 11.8 - - + +
97F GLN 2.9 19.1 + - - +
98F GLY* 3.1 6.9 + - - +
100F LEU* 1.3 73.1 - - - +
102F GLU* 1.3 75.5 + - - +
104F ILE* 3.6 2.8 + - - +
105F LEU* 3.2 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE* 3.5 25.3 - - + +
98F GLY* 2.9 23.1 + - - +
99F THR* 3.4 9.6 - - - +
101F PHE* 1.3 87.3 - - - +
103F LEU* 1.3 52.1 + - - +
105F LEU* 3.2 16.9 + - - +
106F ALA* 2.7 35.4 + - - +
284O LYS* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ILE* 3.5 27.8 - - + +
57F LYS* 4.0 25.6 - - + -
58F VAL* 4.2 11.0 - - + +
92F PHE* 4.4 11.2 - - + -
93F LEU* 3.6 29.6 - - + -
95F VAL* 5.1 2.5 - - + -
99F THR* 2.8 31.5 + - + +
100F LEU* 3.2 8.0 + - - +
102F GLU* 1.3 72.5 - - - +
104F ILE* 1.3 57.5 + - - +
105F LEU 3.0 1.8 - - - -
106F ALA* 3.5 2.1 - - - +
107F ALA* 2.6 38.3 + - - +
115F LEU* 4.1 8.5 - - + +
119F THR* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 3.6 20.0 - - + -
112E LEU* 5.1 11.0 - - + -
116E LEU* 5.0 15.5 - - + -
120E ILE* 4.9 6.7 - - + -
100F LEU* 3.0 18.4 + - + +
101F PHE* 4.0 4.5 - - - +
102F GLU 3.5 0.2 - - - -
103F LEU* 1.3 75.5 - - - +
105F LEU* 1.3 55.7 + - + +
107F ALA* 3.6 2.5 - - - +
108F ASN* 2.9 27.4 + - - +
116F LEU* 4.2 18.7 - - + +
119F THR* 3.5 32.1 - - - +
120F CYS* 4.4 8.3 - - - +
123F VAL* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E LEU* 4.1 25.8 - - + -
113E PRO* 5.1 5.2 - - + -
116E LEU* 4.7 8.5 - - + -
101F PHE* 3.2 44.4 + - + +
102F GLU* 3.2 18.1 + - - +
103F LEU 3.0 0.4 - - - -
104F ILE* 1.3 75.8 - - - +
106F ALA* 1.3 56.3 + - - +
108F ASN* 2.9 7.4 + - - +
109F TYR* 2.5 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ASN 5.3 2.9 - - - +
50F VAL* 4.4 17.5 - - + -
54F ILE* 3.4 26.0 - - + -
58F VAL* 4.2 12.3 - - + -
102F GLU 2.7 20.2 + - - +
103F LEU* 3.5 3.8 - - - +
105F LEU* 1.3 71.7 - - - +
107F ALA* 1.3 55.6 + - - +
109F TYR* 3.5 5.6 - - - +
110F LEU* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL* 5.3 1.1 - - - +
103F LEU 2.6 21.9 + - - +
104F ILE* 3.6 6.3 - - - +
106F ALA* 1.3 72.3 - - - +
108F ASN* 1.3 57.2 + - - +
110F LEU* 3.6 1.3 - - - -
111F ASP* 2.8 22.3 + - - -
112F ILE* 2.9 22.8 + - - +
115F LEU* 3.1 30.0 - - + +
116F LEU* 3.9 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E PRO* 5.5 3.2 - - - +
116E LEU* 3.3 41.5 - - + +
104F ILE 2.9 19.6 + - - +
105F LEU* 2.9 9.8 + - - +
107F ALA* 1.3 73.7 - - - +
109F TYR* 1.3 67.7 + - - +
111F ASP* 3.0 16.2 + - - +
116F LEU* 3.7 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F THR* 2.5 36.8 + - + -
30F MET* 4.3 14.5 - - + +
47F LEU* 4.2 8.2 - - + +
48F PRO* 3.6 22.7 - - - +
49F ASN* 3.0 51.3 + - + +
50F VAL* 3.4 26.5 - - + -
105F LEU 2.5 21.2 + - - +
106F ALA* 3.5 2.2 - - - +
108F ASN* 1.3 78.4 - - - +
110F LEU* 1.3 61.0 + - + +
111F ASP* 3.3 1.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
24F SER* 2.5 32.5 + - - +
25F VAL 3.2 0.3 + - - -
26F THR* 3.2 18.8 + - + -
27F ILE* 3.9 24.7 - - + -
47F LEU* 4.0 11.0 - - + -
50F VAL* 4.2 13.2 - - + -
55F LEU* 5.2 4.9 - - + -
58F VAL* 3.7 37.0 - - + -
106F ALA 2.7 21.4 + - - +
109F TYR* 1.3 94.1 - - + +
111F ASP* 1.3 69.3 + - - +
112F ILE* 3.9 11.2 - - + -
----------------------------------------------------------
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