Contacts of the helix formed by residues 91 - 111 (chain F) in PDB entry 3PJA
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 TRP 91 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 4.0 20.0 - - + -
28F VAL* 3.7 21.1 - - + -
31F LEU* 6.3 1.1 - - + -
75F LEU* 4.3 13.5 - - + -
79F PHE* 3.5 37.7 - + - -
84F TYR* 3.3 65.4 + + - -
87F PHE* 3.6 27.6 - - + -
88F HIS* 3.0 16.3 + - - -
89F GLU 3.2 0.2 - - - -
90F HIS* 1.3 77.7 - - - +
92F ARG* 1.3 76.7 + - - +
93F PHE 3.2 3.1 - - - -
94F VAL* 3.1 9.4 + - + +
95F LEU* 2.8 35.6 + - + +
133F PHE* 3.7 14.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F HIS* 3.1 59.4 + - + +
89F GLU* 3.0 41.7 + - - +
91F TRP* 1.3 84.5 - - - +
93F PHE* 1.3 68.2 + - + +
95F LEU* 3.7 4.2 - - - +
96F GLN* 2.9 44.0 + - - +
136F ASP* 5.0 0.4 + - - -
138F GLU* 4.2 20.8 + - - +
139F ASP* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F GLU* 4.4 15.0 - - + -
89F GLU 5.0 2.1 + - - +
91F TRP* 3.1 0.6 + - - -
92F ARG* 1.3 84.8 - - + +
94F VAL* 1.3 75.8 + - + +
96F GLN* 3.2 15.8 + - - +
97F ARG* 3.0 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 3.4 33.9 - - + -
31F LEU* 3.9 31.9 - - + +
32F GLU* 3.6 35.4 - - + +
35F ALA* 5.2 3.1 - - + -
91F TRP* 3.1 11.2 + - + +
93F PHE* 1.3 82.1 - - + +
95F LEU* 1.3 65.2 + - - +
97F ARG* 3.1 7.8 + - + +
98F LEU* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LEU* 5.0 7.4 - - + -
84F TYR* 3.8 22.2 - - - +
91F TRP* 2.8 30.8 + - + +
92F ARG* 3.7 5.4 - - - +
94F VAL* 1.3 76.6 - - - +
96F GLN* 1.3 57.0 + - - +
98F LEU* 3.3 11.5 + - + +
99F VAL* 3.0 32.1 + - - +
123F LEU* 4.2 22.0 - - + -
125F ILE* 4.3 14.4 - - + -
133F PHE* 4.4 9.4 - - + -
134F HIS 4.7 1.1 - - - +
135F LEU* 3.7 27.8 - - + -
139F ASP* 4.0 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ARG* 2.9 34.8 + - - +
93F PHE* 3.4 14.2 - - - +
95F LEU* 1.3 74.2 - - - +
97F ARG* 1.3 64.7 - - + +
99F VAL* 3.2 4.3 + - - +
100F PHE* 3.0 22.5 + - - +
139F ASP* 3.0 48.8 + - + +
142F SER* 3.3 30.6 + - - -
143F GLY* 3.6 4.0 - - - +
146F ILE* 4.3 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ARG* 5.5 1.9 - - - +
32F GLU* 6.3 0.8 - - - +
35F ALA* 3.9 19.6 + - + +
36F ARG* 3.6 41.8 - - - +
39F LEU* 4.0 24.4 - - - +
93F PHE* 3.0 48.5 + - + +
94F VAL* 3.1 10.3 + - + +
96F GLN* 1.3 76.7 - - + +
98F LEU* 1.3 57.3 + - - +
100F PHE* 3.3 31.1 - - - +
101F LEU* 3.0 34.0 + - - +
146F ILE* 4.6 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 4.3 20.6 - - + +
35F ALA* 3.8 28.5 - - + -
38F ILE* 5.3 0.7 - - + -
65F PHE* 4.3 10.1 - - + -
68F VAL* 4.1 38.4 - - + -
72F LEU* 4.8 7.9 - - + -
94F VAL* 2.9 27.8 + - + +
95F LEU* 3.6 13.5 - - + +
97F ARG* 1.3 72.3 - - - +
99F VAL* 1.3 66.2 + - - +
100F PHE 3.0 1.6 - - - -
101F LEU* 3.0 9.7 + - + +
102F ALA* 3.0 24.3 + - - +
123F LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU* 3.0 22.2 + - + +
96F GLN* 3.2 6.7 + - - +
98F LEU* 1.3 74.3 - - - +
100F PHE* 1.3 57.9 + - - +
102F ALA* 3.5 1.6 + - - +
103F ALA* 3.0 30.0 + - + +
119F VAL* 4.0 20.2 - - + +
123F LEU* 4.6 3.8 - - + -
135F LEU* 3.8 33.7 - - + -
139F ASP 4.4 6.3 - - - +
140F TYR* 3.7 41.7 - - + +
143F GLY* 4.0 8.5 - - - -
144F VAL* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 3.9 22.0 - - + -
96F GLN 3.0 11.6 + - - +
97F ARG* 3.3 34.5 - - - +
99F VAL* 1.3 78.0 - - - +
101F LEU* 1.3 83.8 + - + +
103F ALA* 3.4 3.5 + - - +
104F PHE* 3.0 29.1 + + + +
143F GLY* 3.5 19.2 - - - +
146F ILE* 3.3 31.2 - - + -
147F LEU* 3.5 17.0 - - - -
150F GLU* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ALA* 3.2 45.1 - - + +
38F ILE* 3.8 16.6 - - + -
39F LEU* 3.8 29.2 - - + +
42F LEU* 4.0 8.2 - - + +
65F PHE* 3.8 12.8 - - + -
97F ARG* 3.0 22.1 + - - +
98F LEU* 3.0 12.7 + - + +
100F PHE* 1.3 95.6 - - + +
102F ALA* 1.3 66.5 + - - +
104F PHE* 3.1 5.7 + - + +
105F VAL* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F PHE* 3.6 19.4 - - + -
98F LEU 3.0 14.1 + - - +
99F VAL 3.7 4.0 - - - +
101F LEU* 1.3 76.2 - - - +
103F ALA* 1.3 65.5 + - - +
105F VAL* 3.0 16.0 + - - +
106F VAL* 3.0 15.8 + - - +
114F VAL* 4.3 2.2 - - + -
119F VAL* 4.3 17.0 - - + -
122F ILE* 4.2 27.4 - - + -
123F LEU* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F VAL* 3.0 22.0 + - + +
100F PHE* 3.6 6.3 - - - +
102F ALA* 1.3 75.7 - - - +
104F PHE* 1.3 57.4 + - - +
106F VAL 3.4 0.5 + - - -
107F TYR* 3.0 28.6 + - - +
112F THR 4.8 0.7 - - - +
113F LEU* 5.1 6.7 - - + -
114F VAL* 3.0 28.6 - - + +
119F VAL* 5.4 1.1 - - + +
140F TYR* 6.4 0.9 - - + -
143F GLY 5.3 1.6 - - - +
144F VAL* 5.4 4.7 - - + -
147F LEU* 3.8 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 4.9 3.4 - - + -
42F LEU* 3.7 37.7 - - + -
43F GLN* 4.8 4.5 - - + -
45F VAL* 6.1 1.6 - - + -
46F HIS* 5.1 4.7 - + - -
100F PHE* 3.0 26.3 + + + +
101F LEU* 3.3 11.2 - - + +
102F ALA 3.1 0.2 - - - -
103F ALA* 1.3 74.1 - - - +
105F VAL* 1.3 64.9 + - - +
107F TYR* 3.2 2.3 + - + +
108F LEU* 3.0 51.0 + - + +
147F LEU* 3.7 21.5 - - + +
150F GLU* 3.7 32.8 - - + -
151F LEU* 4.1 18.8 - - + -
154F LEU* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 3.7 33.6 - - + +
58F CYS* 3.8 11.3 - - - +
61F ALA* 3.9 16.2 - - + -
62F ARG* 3.8 23.6 - - + +
65F PHE* 4.4 10.3 - - + -
101F LEU 3.0 10.0 + - - +
102F ALA* 3.4 11.0 - - - +
104F PHE* 1.3 76.3 - - - +
106F VAL* 1.3 66.3 + - + +
108F LEU* 3.2 5.0 + - - +
109F GLU* 3.0 45.2 + - + +
122F ILE* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ARG* 4.6 7.4 - - - +
102F ALA 3.0 12.6 + - - +
105F VAL* 1.3 82.6 - - + +
107F TYR* 1.3 55.1 + - - +
109F GLU* 4.5 5.8 - - - -
110F THR* 2.6 55.0 + - + +
112F THR* 4.4 8.7 - - - +
114F VAL* 3.3 42.4 - - + -
122F ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ALA 3.0 18.1 + - - +
104F PHE* 3.6 7.6 - + - +
105F VAL 3.1 0.4 - - - -
106F VAL* 1.3 76.1 - - - +
108F LEU* 1.3 73.9 + - + +
109F GLU 3.1 0.2 - - - -
111F GLU* 2.6 79.9 + - + +
112F THR 3.8 13.7 + - - +
147F LEU* 4.6 9.0 - - + -
151F LEU* 3.6 45.7 - - + +
154F LEU* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 4.2 31.2 - - + +
54F ILE* 3.9 31.1 - - + +
57F ARG* 5.4 2.7 - - - -
58F CYS* 3.7 12.6 - - - -
104F PHE* 3.0 52.3 + - + +
105F VAL 3.7 4.0 - - - +
107F TYR* 1.3 84.0 - - + +
109F GLU* 1.3 62.4 + - - +
111F GLU* 5.3 3.0 - - - +
154F LEU* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F PRO* 6.5 0.4 - - + -
58F CYS* 3.8 19.7 - - + +
62F ARG* 2.7 41.3 + - - -
105F VAL* 3.0 29.3 + - - +
106F VAL* 3.9 2.5 - - - +
108F LEU* 1.3 81.2 - - - +
110F THR* 1.3 75.3 + - + +
111F GLU* 3.5 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL* 2.6 33.1 + - + +
109F GLU* 1.3 88.4 - - + +
111F GLU* 1.3 69.2 + - - +
112F THR* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F TYR* 2.6 64.6 + - + +
108F LEU* 5.3 2.2 - - - +
109F GLU 5.1 2.2 - - - +
110F THR* 1.3 73.8 + - - +
112F THR* 1.3 61.2 + - - +
----------------------------------------------------------
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