Contacts of the strand formed by residues 45 - 52 (chain I) in PDB entry 1FSK
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 45 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H PHE* 4.4 9.0 - - + -
38H GLN* 4.7 0.4 - - - +
44H PRO* 4.0 25.8 - - + -
87H HIS* 4.1 27.3 - - + +
98H PHE* 3.6 49.2 + - + +
99H GLY 5.2 0.8 + - - -
37I VAL* 3.8 12.6 - - + -
38I LYS 3.9 2.9 - - - -
39I GLN* 3.4 42.0 - - + +
44I GLY* 1.3 77.8 - - - -
46I GLU* 1.3 65.7 + - - +
95I TYR* 5.2 1.6 - - + -
108I TRP* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H PHE* 3.9 0.9 - - - -
37I VAL* 3.3 6.0 - - - +
38I LYS* 3.0 51.1 + - - +
40I ARG* 5.5 4.4 + - - -
44I GLY 4.5 5.2 - - - +
45I LEU* 1.3 82.6 - - - +
47I TRP* 1.3 64.8 + - - +
48I VAL* 3.2 1.7 + - - +
61I ASN* 5.8 1.6 - - - +
63I LYS* 5.6 3.1 - - - +
64I PHE* 3.2 31.0 - - + -
89I GLU* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H TYR* 3.8 17.0 - + + -
95H PRO* 3.8 23.6 - - + -
96H TYR* 3.1 59.8 + + + +
97H THR* 5.7 0.2 - - - +
98H PHE* 3.4 17.2 - + + -
35I ASN* 2.7 24.8 + - + -
36I TRP 4.0 7.4 - - - -
37I VAL* 4.5 1.8 - - + +
46I GLU* 1.3 70.7 - - - +
48I VAL* 1.3 60.6 + - - +
49I GLY* 3.3 32.2 + - - -
50I ASN* 3.3 18.4 - - + -
59I ASN* 3.5 13.5 - - + -
60I TYR 4.2 2.5 - - - -
61I ASN* 2.9 58.5 + - + +
64I PHE* 3.9 3.5 - - - -
105I PHE* 4.1 15.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I TRP* 2.6 31.9 + - + +
37I VAL 4.0 0.4 - - - -
38I LYS* 3.6 34.5 - - + +
46I GLU 3.8 2.0 - - - +
47I TRP* 1.3 73.8 - - - +
49I GLY* 1.3 57.3 + - - +
60I TYR* 3.8 4.6 - - + +
61I ASN* 2.8 27.3 + - - +
64I PHE* 4.1 27.5 - - + +
68I ALA* 4.5 6.7 - - + -
70I LEU* 4.7 5.8 - - + -
81I MET* 3.4 36.8 - - + -
94I TYR* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I TRP* 3.0 23.8 + - - -
47I TRP* 3.3 21.3 + - - -
48I VAL* 1.3 82.1 - - - +
50I ASN* 1.3 60.2 + - - +
59I ASN 3.0 15.3 - - - -
60I TYR* 4.1 2.2 - - - -
70I LEU* 3.7 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H TYR* 2.9 26.9 + - - -
96H TYR* 4.5 2.4 + - - -
33I TRP* 2.9 26.2 - - + -
34I ILE 3.3 9.0 - - - +
35I ASN* 3.3 25.3 + - - +
47I TRP* 3.6 8.0 - - - -
49I GLY* 1.3 73.2 - - - -
51I ILE* 1.3 65.6 + - - +
58I THR* 3.3 4.5 - - - -
59I ASN* 2.8 47.7 + - - +
70I LEU* 3.4 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I TRP* 3.1 4.6 - - - -
34I ILE* 3.1 38.2 + - + +
36I TRP* 4.5 6.3 - - - +
50I ASN* 1.3 82.6 - - - +
52I PHE* 1.3 69.5 + - - +
53I PRO* 3.6 4.3 - - - +
56I SER* 4.2 10.8 - - - +
57I TYR 3.1 13.5 - - - +
58I THR* 3.6 18.8 - - + -
70I LEU* 3.8 18.2 - - + +
71I THR* 3.7 24.9 - - - +
72I VAL* 3.6 30.5 - - + -
79I ALA* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ILE* 4.0 11.9 - - + -
70G ARG* 3.8 18.8 - - - +
86G ILE* 4.1 25.8 - - + -
30I THR 3.1 23.8 - - - -
31I SER* 3.4 29.2 - - - -
32I TYR 3.7 9.6 - - - -
33I TRP* 3.2 51.1 - + + -
51I ILE* 1.3 73.3 - - - +
53I PRO* 1.3 87.7 - - - +
54I SER* 3.5 11.2 - - - -
55I ASP* 4.1 6.1 - - - +
56I SER* 3.0 22.0 + - - -
57I TYR* 2.9 9.2 + - + +
----------------------------------------------------------
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