Contacts of the helix formed by residues 35 - 47 (chain A) in PDB entry 1FPQ
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 LEU 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR 2.9 5.3 + - - +
34A ASN* 1.3 80.3 - - - +
36A VAL* 1.3 66.8 + - + +
38A PRO* 3.0 27.2 - - + +
39A ALA* 3.5 11.2 + - + +
145A LEU* 6.1 4.9 - - + -
149A MSE 5.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR 3.2 7.0 + - - +
35A LEU* 1.3 78.6 - - + +
37A TYR* 1.3 63.4 + - - +
39A ALA* 3.3 8.5 + - + +
40A VAL* 3.0 27.5 + - + +
91A LEU* 4.4 4.3 - - + -
324A THR* 3.4 42.0 - - + +
327A ASN* 3.9 20.0 - - + -
328A LEU* 4.1 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR 4.7 0.4 + - - -
34A ASN* 3.6 9.9 + - - +
35A LEU 3.2 0.2 - - - -
36A VAL* 1.3 79.5 - - - +
38A PRO* 1.3 66.6 - - + +
40A VAL* 3.3 1.4 + - + +
41A LEU* 2.9 36.4 + - + +
91A LEU* 4.4 14.8 - - + +
92A LEU* 4.5 19.1 - - + -
95A TYR* 3.2 74.3 + + + +
97A VAL* 3.8 12.6 - - + +
324A THR* 5.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN 3.1 15.9 - - - +
35A LEU* 3.0 34.5 - - + +
37A TYR* 1.3 89.4 - - + +
39A ALA* 1.3 54.3 + - - +
41A LEU* 3.8 10.0 - - + +
42A ASN* 2.8 33.1 + - - +
136A THR* 5.0 3.5 - - + +
140A CYS* 4.4 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.9 9.6 - - + +
36A VAL* 3.3 13.4 + - + +
37A TYR 3.2 0.6 - - - -
38A PRO* 1.3 79.8 - - - +
40A VAL* 1.3 63.9 + - + +
42A ASN* 3.5 7.7 + - - +
43A ALA* 3.1 23.0 + - - +
140A CYS* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.0 26.4 + - + +
37A TYR 3.7 3.4 - - - +
39A ALA* 1.3 75.7 - - + +
41A LEU* 1.3 67.3 + - - +
43A ALA* 3.2 6.9 + - - +
44A ALA* 2.9 21.5 + - - +
88A MSE 4.1 36.6 - - + +
91A LEU* 3.7 26.7 - - + -
92A LEU* 4.4 13.5 - - + -
327A ASN* 3.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 2.9 28.5 + - + +
38A PRO* 3.8 7.4 - - + +
40A VAL* 1.3 76.7 - - - +
42A ASN* 1.3 63.8 + - - +
44A ALA* 3.1 6.1 + - - +
45A ILE* 3.0 37.5 + - + +
50A PHE* 3.9 24.5 - - + -
92A LEU* 4.5 14.1 - - + +
97A VAL* 5.5 2.7 - - + -
123A LEU* 4.1 16.2 - - + -
136A THR* 3.8 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO 2.8 22.4 + - - +
39A ALA* 3.6 7.5 + - - +
41A LEU* 1.3 74.4 - - - +
43A ALA* 1.3 58.4 + - - +
45A ILE* 3.5 9.9 + - - +
46A ASP* 2.7 49.8 + - - +
136A THR* 4.4 3.5 - - + +
137A THR* 4.3 14.0 + - - +
140A CYS* 3.5 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA 3.1 17.5 + - - +
40A VAL* 3.5 7.4 - - - +
41A LEU 3.2 0.2 - - - -
42A ASN* 1.3 75.9 - - - +
44A ALA* 1.3 66.0 + - - +
46A ASP* 3.2 8.5 + - - +
47A LEU* 2.9 34.7 + - + +
88A MSE 4.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 2.9 13.2 + - + +
41A LEU* 3.4 9.9 - - - +
43A ALA* 1.3 78.4 - - - +
45A ILE* 1.3 59.4 + - - +
47A LEU* 3.4 1.0 + - - -
48A ASN 3.1 3.5 + - - -
49A LEU* 3.0 49.6 + - + +
50A PHE* 3.5 26.0 - - + -
88A MSE 5.2 2.2 - - - -
92A LEU* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.0 33.8 + - + +
42A ASN* 3.7 5.8 - - - +
44A ALA* 1.3 74.1 - - - +
46A ASP* 1.3 70.1 + - - +
48A ASN* 3.0 20.2 + - - +
50A PHE* 3.8 20.2 - - + -
123A LEU* 5.0 1.3 - - + -
131A TYR* 4.6 7.4 - - - +
133A ALA* 3.9 30.3 - - + +
136A THR* 3.7 33.4 - - + +
137A THR* 3.9 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 2.7 38.9 + - - +
43A ALA* 3.2 7.0 + - - +
45A ILE* 1.3 81.8 - - - +
47A LEU* 1.3 59.9 + - + +
48A ASN* 3.1 15.5 + - - +
137A THR* 4.6 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 2.9 26.0 + - + +
44A ALA 3.9 1.8 - - - +
46A ASP* 1.3 75.5 - - + +
48A ASN* 1.3 73.5 + - - +
49A LEU* 3.2 14.6 + - + +
52A ILE* 3.9 0.7 - - - +
72A LEU* 3.3 37.9 - - + +
73A PRO* 6.2 1.3 - - + -
76A THR* 6.0 6.1 - - + -
85A LEU* 4.5 9.6 - - + -
88A MSE 4.2 26.9 - - + -
----------------------------------------------------------
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