Contacts of the helix formed by residues 99 - 117 (chain F) in PDB entry 1HBS
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 99 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 5.0 3.4 - - + -
97F HIS 4.6 0.2 + - - -
98F VAL* 1.4 59.3 - - - +
100F PRO* 1.4 73.8 - - - +
101F GLU* 3.0 19.6 + - - +
102F ASN* 2.4 55.1 + - - +
103F PHE* 4.7 0.2 - - - -
145F TYR* 4.5 0.4 - - - -
38G THR* 3.3 18.0 + - - +
41G THR* 4.3 4.8 - - - +
42G TYR* 2.2 41.7 + - + +
94G ASP* 4.1 4.4 - - + +
96G VAL* 5.9 0.4 - - - +
97G ASN* 3.6 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL 3.5 0.4 - - - -
99F ASP* 1.4 83.9 - - - +
101F GLU* 1.3 69.1 + - - +
102F ASN 2.6 5.8 + - - -
103F PHE* 2.6 34.7 + - + +
104F ARG* 3.2 9.9 + - - +
142F ALA* 3.4 33.2 - - + -
145F TYR* 3.2 26.5 - - + -
38G THR* 3.1 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ASP* 3.8 22.7 - - - +
100F PRO* 1.3 80.3 - - + +
102F ASN* 1.4 50.8 + - - +
104F ARG* 2.6 54.0 + - - +
105F LEU* 2.6 35.3 + - + +
94G ASP* 3.8 20.4 - - - +
96G VAL* 3.5 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 4.0 1.9 - - - +
37F TRP* 5.0 2.6 - - - +
38F THR* 3.3 28.0 - - + +
41F PHE* 2.7 35.8 - - - -
98F VAL* 2.9 13.5 - - + +
99F ASP* 2.4 32.3 + - - +
101F GLU* 1.4 79.1 - - - +
103F PHE* 1.3 51.2 + - + +
105F LEU* 3.2 11.5 + - - +
106F LEU 2.8 26.7 + - - -
147F HEM 3.4 20.3 - - + +
94G ASP* 4.5 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F HIS* 3.7 22.9 - + - -
98F VAL* 4.2 11.0 - - + -
100F PRO* 2.6 36.1 + - + +
102F ASN* 1.3 66.4 - - + +
104F ARG* 1.3 64.7 + - + +
105F LEU 3.1 1.3 - - - -
106F LEU* 3.6 4.4 - - - +
107F GLY* 2.6 35.7 + - - +
138F ALA* 4.0 30.1 - - + +
141F LEU* 3.6 48.2 - - + -
145F TYR* 3.5 21.3 - - - -
147F HEM 3.7 41.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F PRO* 4.1 7.4 - - - +
101F GLU* 2.6 52.5 + - - +
103F PHE* 1.3 86.3 - - + +
105F LEU* 1.4 64.2 + - - +
107F GLY* 4.5 1.6 - - - -
108F ASN* 2.9 32.5 + - - +
134F VAL* 6.0 0.2 - - - -
135F ALA* 6.2 0.2 - - - -
138F ALA* 4.1 21.2 - - + +
139F ASN* 4.9 13.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
31F LEU* 3.5 9.6 - - + +
35F TYR* 3.4 50.4 - - + +
37F TRP* 3.4 17.5 - - + +
38F THR* 4.8 5.8 - - - +
101F GLU* 2.6 19.8 + - + +
102F ASN* 3.2 19.2 + - - +
103F PHE 3.1 0.2 - - - -
104F ARG* 1.4 79.2 - - - +
106F LEU* 1.3 56.1 + - - +
108F ASN* 3.4 7.5 + - - +
109F VAL* 3.8 14.4 + - - +
94G ASP* 3.1 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ALA* 3.5 46.0 - - + +
28F LEU* 3.6 11.0 - - + +
31F LEU* 3.3 14.1 - - + +
67F VAL* 3.7 23.8 - - + -
68F LEU* 5.8 0.4 - - - +
71F PHE* 6.1 0.7 - - + -
102F ASN 2.8 17.6 + - - +
103F PHE* 3.2 4.7 + - - +
105F LEU* 1.3 64.6 - - - +
107F GLY* 1.3 56.9 + - - +
108F ASN 3.3 0.2 - - - -
109F VAL* 4.0 3.4 - - + -
110F LEU* 2.7 45.1 + - + +
147F HEM 3.6 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F PHE 2.6 23.2 + - - -
104F ARG* 3.5 2.2 - - - -
106F LEU* 1.3 78.5 - - - +
108F ASN* 1.3 61.0 - - - +
110F LEU* 3.3 12.5 - - - +
111F VAL 3.7 3.8 + - - -
134F VAL* 2.9 40.0 - - - +
147F HEM 6.1 0.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
36E PHE* 5.5 2.1 - - - -
99E LYS* 4.0 23.0 - - - +
103E HIS* 3.6 35.8 + - + +
104F ARG* 2.9 24.9 + - - +
105F LEU* 4.0 2.7 - - - +
107F GLY* 1.3 73.8 - - - +
109F VAL* 1.3 65.0 + - + +
110F LEU 3.0 6.5 - - - -
111F VAL* 3.3 11.7 + - - +
112F CYS* 3.5 8.1 + - - +
131F GLN* 3.6 22.2 + - - -
134F VAL* 5.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E HIS* 6.2 1.1 - - + -
122E HIS* 3.2 30.3 - - + +
27F ALA* 3.7 21.3 - - - +
30F ARG* 4.8 0.9 - - + +
31F LEU* 3.0 37.2 - - + +
34F VAL* 5.2 1.8 - - + -
35F TYR* 4.1 24.5 - - + +
105F LEU 3.8 5.8 + - - +
106F LEU* 3.6 4.4 + - - -
108F ASN* 1.3 73.4 - - + +
110F LEU* 1.5 46.9 + - - +
111F VAL 3.3 0.4 - - - -
112F CYS* 3.4 11.7 - - + -
113F VAL* 2.7 38.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
15F TRP* 5.2 10.8 - - + -
23F VAL* 5.5 9.4 - - + +
27F ALA* 4.5 17.4 - - + +
68F LEU* 5.8 5.8 - - + -
71F PHE* 3.8 33.7 - - + -
106F LEU* 2.7 34.9 + - + +
107F GLY* 3.3 11.7 - - - +
109F VAL* 1.5 67.2 - - - +
111F VAL* 1.5 47.2 - - - +
112F CYS 3.2 0.7 - - - -
113F VAL* 4.2 4.0 - - + +
114F LEU* 3.6 32.2 + - + +
130F TYR* 6.4 1.6 - - + -
134F VAL* 4.3 18.4 - - + -
147F HEM 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E HIS* 4.6 2.2 - - + -
107E VAL* 3.9 18.1 - - + +
107F GLY 3.7 2.5 + - - +
108F ASN* 3.3 11.7 + - - +
110F LEU* 1.5 58.0 - - + +
112F CYS* 1.3 68.8 + - - +
114F LEU* 3.9 8.4 - - + +
115F ALA* 3.4 16.8 + - - +
122F PHE* 3.6 28.5 - - + -
127F GLN* 4.1 12.8 - - + -
130F TYR* 4.3 8.5 - - + +
131F GLN* 4.0 22.0 - - + +
134F VAL* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E HIS* 4.4 8.1 - - - -
106E LEU* 4.3 15.0 - - - -
107E VAL* 3.3 39.3 - - - -
110E ALA* 4.7 5.2 - - - +
117E PHE* 4.6 8.0 - - + -
122E HIS* 3.6 24.9 - - + +
108F ASN 3.5 6.1 + - - +
109F VAL* 3.2 19.0 - - - +
111F VAL* 1.3 86.7 - - - +
113F VAL* 1.1 51.7 + - - +
115F ALA* 3.4 5.2 - - - +
116F HIS* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 5.5 0.2 - - + -
122E HIS* 3.8 3.4 - - + -
23F VAL* 3.9 21.3 - - + +
26F GLU* 3.7 35.0 - - + +
27F ALA* 4.5 10.5 - - + +
30F ARG* 3.1 43.1 - - + +
109F VAL 2.7 24.7 + - - +
110F LEU* 4.2 6.7 - - + +
112F CYS* 1.1 72.6 - - - +
114F LEU* 1.3 53.4 + - - +
115F ALA 3.1 1.6 - - - -
116F HIS* 2.7 18.8 + - + -
117F HIS* 2.6 27.8 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
14F LEU* 3.7 9.6 - - + -
15F TRP* 4.0 26.9 - - + -
18F VAL* 5.0 7.2 - - + -
23F VAL* 5.2 6.9 - - + +
110F LEU* 3.6 23.9 + - + +
111F VAL* 3.9 5.6 - - + +
113F VAL* 1.3 74.0 - - - +
115F ALA* 1.4 55.5 - - - +
117F HIS* 3.1 5.2 - - + +
118F PHE* 3.0 57.2 + - + +
122F PHE* 3.5 31.0 - - + -
130F TYR* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E VAL* 3.7 24.9 - - + +
111E ALA* 3.6 18.8 - - + +
111F VAL 3.4 16.2 - - - +
112F CYS 3.4 4.5 + - - +
114F LEU* 1.4 76.7 - - - +
116F HIS* 1.2 69.2 + - - +
117F HIS 2.9 2.1 + - - -
118F PHE 4.4 1.3 - - - +
119F GLY 3.4 13.5 + - - -
122F PHE* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ALA 3.4 17.5 + - - +
111E ALA* 5.3 0.2 - - - -
113E LEU 4.1 0.6 + - - -
114E PRO* 2.2 36.5 + - - +
115E ALA* 4.3 10.3 - - + -
117E PHE* 3.6 38.5 - + + -
26F GLU* 5.1 3.6 + - - +
30F ARG* 4.1 10.7 + - - +
112F CYS 2.9 9.3 + - - +
113F VAL* 2.7 25.6 + - + +
115F ALA* 1.2 73.6 - - - +
117F HIS* 1.2 74.3 + + + +
119F GLY* 4.1 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F GLU* 2.8 35.4 + - - -
23F VAL* 4.2 6.7 - - + -
26F GLU* 2.9 28.6 + - - -
113F VAL* 2.6 31.9 + - + +
114F LEU* 3.1 16.2 - - + +
116F HIS* 1.2 86.4 - + + +
118F PHE* 1.4 73.1 + + + +
119F GLY 3.2 7.0 + - - -
----------------------------------------------------------
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