Contacts of the strand formed by residues 36 - 41 (chain A) in PDB entry 1F0K
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 GLN 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS 2.7 15.0 + - - +
8A ARG* 2.9 48.3 + - + +
9A LEU* 2.7 32.7 + - - +
34A GLY 3.7 4.9 + - - +
35A TRP* 1.3 74.7 - - - +
37A VAL* 1.3 56.3 + - - +
95A TYR* 3.0 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.2 20.6 - - + +
11A VAL* 4.1 14.8 - - + -
27A ALA* 3.9 31.4 - - + +
30A LEU* 4.9 0.7 - - + -
31A MET* 3.4 36.6 - - + +
35A TRP* 3.9 9.3 + - + +
36A GLN* 1.3 79.2 - - - +
38A ARG* 1.3 72.1 + - - +
39A TRP* 5.3 1.3 - - + -
56A ILE* 3.8 18.1 - - + +
57A GLU* 4.7 4.3 + - - +
95A TYR* 3.3 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 2.9 4.9 + - - -
10A MET* 3.2 14.7 - - + -
11A VAL* 2.9 24.4 + - - +
37A VAL* 1.3 79.1 - - - +
39A TRP* 1.3 64.3 + - - +
56A ILE* 4.3 1.1 - - - -
57A GLU* 3.7 42.1 + - - +
58A ILE 5.3 1.6 + - - +
59A ASP* 2.8 43.3 + - - +
95A TYR* 3.3 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 3.8 8.6 - - - +
11A VAL* 3.5 35.4 - - + -
13A ALA* 3.4 42.5 + - + +
20A VAL* 3.6 34.5 - - + -
23A GLY* 3.7 15.0 - - - -
24A LEU* 3.7 22.9 - - + -
27A ALA* 4.6 2.9 - - + -
37A VAL* 5.3 0.7 - - + -
38A ARG* 1.3 75.6 - - - +
40A LEU* 1.3 86.0 + - - +
41A GLY* 4.1 1.1 - - - -
47A GLU* 4.1 4.4 - - - +
51A VAL* 3.7 29.3 - - + +
56A ILE* 4.4 8.5 - - + -
57A GLU 3.0 18.7 + - - +
58A ILE* 3.6 20.0 - - + -
59A ASP* 2.9 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 4.0 10.5 - - + -
11A VAL 2.8 14.7 + - - +
12A MET* 3.6 17.4 - - + -
13A ALA 3.6 17.0 + - - -
39A TRP* 1.3 83.2 - - - +
41A GLY* 1.3 60.0 + - - +
59A ASP 3.4 7.2 - - - +
61A ILE* 3.7 34.3 - - + -
88A ALA* 4.8 2.5 - - + -
91A ILE* 3.8 33.4 - - + -
92A MET* 4.4 8.5 - - + -
107A VAL* 4.1 9.6 - - + +
111A GLY* 3.7 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 4.7 0.4 - - - -
39A TRP* 4.1 2.3 - - - -
40A LEU* 1.3 76.4 - - - +
42A THR* 1.3 64.6 + - - -
47A GLU* 3.6 18.6 - - - -
58A ILE* 4.3 2.1 - - - +
59A ASP 3.1 7.9 + - - -
60A PHE* 3.2 8.1 - - - -
61A ILE 3.0 25.5 + - - -
107A VAL* 3.9 14.7 - - - +
----------------------------------------------------------
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