Contacts of the helix formed by residues 28 - 49 (chain B) in PDB entry 1FRP
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 GLY 28 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 3.0 7.3 + - - -
27B THR* 1.3 77.7 - - - +
29B GLU* 1.3 62.0 + - - +
30B MET 3.4 1.8 - - - -
31B THR* 3.8 17.9 - - - -
32B GLN* 3.1 28.1 + - - +
338B AMP 3.2 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 3.5 11.2 - - - +
28B GLY* 1.3 76.5 - - - +
30B MET* 1.3 67.4 + - - +
32B GLN* 3.3 7.8 + - + +
33B LEU 3.1 17.2 + - - -
88B SER 5.7 0.2 - - - +
89B PHE 3.9 6.9 - - - +
90B ALA* 3.6 21.9 - - + +
110B ARG 4.9 0.5 - - - +
111B GLY* 3.8 15.2 - - - -
112B LYS* 3.0 45.8 + - - +
113B TYR* 3.6 4.3 - - - -
338B AMP 2.9 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 1.3 79.1 - - - +
31B THR* 1.3 60.2 + - - +
33B LEU* 3.2 9.5 + - + +
34B LEU* 3.0 45.3 + - + +
113B TYR* 3.6 27.8 - - + +
138B ILE* 4.3 11.9 - - + -
160B VAL* 3.8 28.5 - - + -
161B ALA* 3.7 29.4 - - + -
177B MET* 4.9 2.9 - - - -
338B AMP 2.8 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.9 23.8 + - + +
18B MET* 4.0 31.1 - - + -
21B GLY* 3.9 6.9 - - - -
28B GLY* 3.6 17.7 + - - -
29B GLU 3.3 0.6 - - - -
30B MET* 1.3 72.6 - - - +
32B GLN* 1.3 65.1 + - - +
34B LEU* 3.3 2.4 + - - +
35B ASN* 3.0 35.6 + - - +
338B AMP 3.1 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY 3.1 19.2 + - - +
29B GLU* 3.4 8.5 - - + +
30B MET 3.3 0.2 - - - -
31B THR* 1.3 75.8 - - - +
33B LEU* 1.3 63.1 + - - +
35B ASN* 3.2 14.9 + - - +
36B SER* 2.9 27.7 + - - +
88B SER* 3.5 27.4 - - - +
90B ALA* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU 3.1 9.3 + - - +
30B MET* 3.2 14.1 + - + +
32B GLN* 1.3 78.3 - - - +
34B LEU* 1.3 62.8 + - + +
36B SER* 3.1 4.7 + - - -
37B LEU* 3.0 23.2 + - + +
85B LEU* 4.0 17.0 - - + +
88B SER* 4.0 15.0 - - - +
90B ALA* 3.9 5.8 - - + +
91B THR* 3.5 28.3 - - + -
113B TYR* 3.8 24.7 - - + -
115B VAL* 4.1 8.1 - - + -
138B ILE* 3.8 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.5 1.7 - - - +
17B VAL* 3.9 37.6 - - + +
30B MET* 3.0 33.7 + - + +
31B THR 3.8 3.4 - - - +
33B LEU* 1.3 76.5 - - + +
35B ASN* 1.3 61.7 + - - +
37B LEU* 3.3 13.8 + - + +
38B CYS* 3.0 23.0 + - - +
136B PHE* 5.4 0.9 - - + -
138B ILE* 4.0 26.7 - - + -
161B ALA* 4.8 0.7 - - + -
175B LEU* 4.6 20.2 - - + -
177B MET* 4.3 16.2 - - - -
338B AMP 4.2 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 4.1 33.3 + - - +
17B VAL* 4.3 15.0 - - - +
18B MET* 6.2 0.2 - - - +
31B THR* 3.0 30.1 + - - +
32B GLN* 3.6 18.1 + - - +
34B LEU* 1.3 75.2 - - - +
36B SER* 1.3 62.0 + - - +
38B CYS* 3.3 10.4 + - - +
39B THR* 3.1 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 2.9 15.2 + - - +
33B LEU 3.1 8.0 + - - -
35B ASN* 1.3 72.0 - - - +
37B LEU* 1.3 59.5 + - - +
39B THR* 3.4 5.0 + - - -
40B ALA* 3.0 24.4 + - - +
84B VAL* 3.1 38.5 + - - +
85B LEU* 4.4 6.1 - - - -
87B SER* 5.0 0.5 + - - -
88B SER* 3.2 22.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.0 12.4 + - + +
34B LEU* 3.3 20.4 - - + +
35B ASN 3.2 0.2 - - - -
36B SER* 1.3 73.9 - - - +
38B CYS* 1.3 65.7 + - - +
40B ALA* 3.2 6.8 + - + +
41B VAL* 3.0 38.2 + - + +
81B VAL* 5.1 7.9 - - + -
85B LEU* 3.7 28.5 - - + -
115B VAL* 5.4 2.9 - - + -
136B PHE* 3.6 55.2 - - + -
138B ILE* 5.6 3.8 - - + -
173B LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 26.5 - - + -
14B THR* 4.9 11.9 - - - -
34B LEU 3.0 11.8 + - - +
35B ASN* 3.5 12.3 - - - +
37B LEU* 1.3 76.5 - - - +
39B THR* 1.3 63.6 + - - +
41B VAL* 3.4 6.3 + - - +
42B LYS* 3.2 37.4 + - - +
173B LEU* 4.8 3.6 - - - -
191B GLY 5.9 0.4 - - - -
192B GLU* 6.2 0.2 - - - -
193B PHE* 3.8 28.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN 3.1 14.4 + - - -
36B SER* 3.7 10.2 - - - -
37B LEU 3.3 0.2 - - - -
38B CYS* 1.3 77.7 - - - +
40B ALA* 1.3 60.4 + - - +
42B LYS* 3.5 16.3 + - - +
43B ALA* 3.2 23.4 + - + +
84B VAL* 4.4 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER 3.0 17.2 + - - +
37B LEU* 3.2 10.7 + - + +
39B THR* 1.3 73.5 - - - +
41B VAL* 1.3 64.1 + - + +
43B ALA* 3.3 7.6 + - - +
44B ILE* 3.1 28.9 + - - +
80B LEU* 4.6 3.7 - - - +
81B VAL* 4.4 26.9 - - + +
84B VAL* 4.0 22.0 - - + +
85B LEU* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.0 30.9 + - + +
38B CYS 3.8 4.7 - - - +
40B ALA* 1.3 75.1 - - + +
42B LYS* 1.3 58.1 + - - +
44B ILE* 3.4 1.9 + - + +
45B SER* 2.9 28.4 + - - -
81B VAL* 6.5 0.2 - - + -
134B THR* 5.0 11.2 - - + -
136B PHE* 5.6 2.5 - - + -
165B ALA* 3.5 30.3 - - + -
167B TYR* 3.8 20.3 - - + +
171B THR* 4.7 2.0 - - + -
173B LEU* 4.2 7.9 - - + -
193B PHE* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 3.2 29.1 + - - +
39B THR* 3.8 18.8 + - - +
41B VAL* 1.3 74.4 - - - +
43B ALA* 1.3 63.8 + - - +
45B SER* 3.4 6.0 + - - -
46B THR* 3.1 27.8 + - - -
186B LEU* 3.8 29.6 - - + +
191B GLY* 3.0 34.9 + - - +
193B PHE* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.2 13.2 + - + +
40B ALA* 3.6 9.0 - - - +
41B VAL 3.3 0.2 - - - -
42B LYS* 1.3 80.6 - - - +
44B ILE* 1.3 59.5 + - - +
46B THR* 3.5 6.9 + - - -
47B ALA* 3.2 21.3 + - - +
80B LEU* 3.9 29.7 - - + +
84B VAL* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA* 3.1 20.4 + - + +
41B VAL* 3.8 2.2 - - + +
42B LYS 3.3 0.2 - - - -
43B ALA* 1.3 72.8 - - - +
45B SER* 1.3 66.0 + - - +
47B ALA* 3.2 5.6 + - - +
48B VAL* 2.9 28.4 + - + +
77B SER* 3.4 33.0 - - - +
80B LEU* 3.9 20.4 - - + -
81B VAL* 3.7 29.8 - - + -
119B PRO 4.7 0.4 - - - +
120B LEU* 4.7 1.6 - - + -
134B THR* 4.1 10.1 - - + +
167B TYR* 3.5 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL 2.9 19.3 + - - -
42B LYS* 3.6 8.1 - - - -
44B ILE* 1.3 75.3 - - - +
46B THR* 1.3 56.6 + - - +
48B VAL* 3.1 4.0 + - - +
49B ARG* 2.9 41.3 + - - -
167B TYR* 3.8 18.9 - - - -
171B THR* 2.7 26.9 + - - -
186B LEU* 4.0 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS 3.1 15.2 + - - -
43B ALA* 3.7 7.4 - - - -
45B SER* 1.3 79.3 - - - +
47B ALA* 1.3 61.6 + - - +
49B ARG* 3.5 8.8 + - - +
50B LYS 3.5 0.2 + - - -
51B ALA* 3.5 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA 3.2 10.9 + - - +
44B ILE* 3.2 10.5 + - + +
46B THR* 1.3 78.6 - - - +
48B VAL* 1.3 60.1 + - - +
50B LYS* 3.2 19.1 + - - +
51B ALA 5.2 4.0 - - - +
73B LEU* 3.6 18.9 - - + +
76B LEU* 3.9 27.4 - - + -
77B SER* 6.0 0.7 - - - +
80B LEU* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.2 37.5 + - - +
170A ALA* 3.6 4.0 - - - +
44B ILE* 2.9 34.4 + - + +
45B SER* 3.5 6.3 - - - +
47B ALA* 1.3 69.5 - - - +
49B ARG* 1.3 59.4 + - - +
50B LYS* 3.0 22.8 + - - +
73B LEU* 4.0 27.3 - - + +
120B LEU* 4.3 3.8 - - + -
132B ILE* 4.1 12.6 - - + -
167B TYR* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 3.8 28.7 - - + +
168A GLY 3.4 6.5 + - - -
169A SER* 2.9 30.0 + - - +
170A ALA* 4.1 7.6 - - - +
171A THR 5.0 0.9 + - - -
186A LEU 4.1 2.6 - - - +
188A PRO* 3.5 23.6 - - + +
45B SER* 2.9 32.2 + - - +
46B THR* 3.9 7.0 - - - +
47B ALA 3.4 0.4 - - - -
48B VAL* 1.3 75.7 - - - +
50B LYS* 1.3 67.9 + - - +
51B ALA* 3.5 1.6 - - + -
167B TYR* 3.8 9.9 - - - +
168B GLY 2.9 30.5 + - - +
169B SER 3.9 2.6 + - - -
170B ALA* 3.4 18.8 + - - +
171B THR* 3.2 20.1 + - - +
----------------------------------------------------------
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