Contacts of the strand formed by residues 40 - 45 (chain T) in PDB entry 3FKS
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 ILE 40 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T ALA 4.2 0.4 - - - +
36T VAL* 3.7 1.4 - - - +
37T GLY 3.1 35.0 + - - +
38T ASP* 4.2 12.1 - - + +
39T GLY* 1.3 85.2 - - - +
41T ALA* 1.3 62.7 + - - +
42T ARG* 5.3 11.4 - - + -
74T GLY* 5.8 2.2 - - - -
75T ILE 3.3 13.9 - - - +
76T VAL* 4.1 19.3 - - + -
77T LEU* 4.2 2.2 - - - -
283T LEU* 5.4 5.2 - - + -
286T LEU* 4.7 5.4 - - + +
287T LEU* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T VAL* 4.7 4.9 - - + -
35T ALA 3.5 5.6 - - - +
36T VAL* 4.3 12.3 - - + +
40T ILE* 1.3 75.4 - - - +
42T ARG* 1.3 62.7 + - - +
43T VAL* 3.8 2.4 + - + -
57T PHE* 4.4 15.7 - - + -
73T VAL 3.3 2.4 - - - +
74T GLY* 3.8 1.0 - - - -
75T ILE* 2.8 43.3 + - + +
77T LEU* 3.8 25.2 - - + +
84T VAL* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T VAL* 3.5 5.7 - - - +
34T LEU* 2.7 51.8 + - + +
35T ALA* 2.6 44.3 + - - +
40T ILE* 5.3 11.0 - - + -
41T ALA* 1.3 73.6 - - - +
43T VAL* 1.3 55.1 + - - +
72T GLN* 2.7 47.0 + - - +
73T VAL 3.6 5.2 - - - +
74T GLY* 5.3 5.2 - - - -
54W LEU 4.3 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T GLY 3.9 4.5 - - - -
32T ARG 3.1 15.3 - - - +
33T VAL* 3.9 14.8 - - + -
41T ALA* 4.5 4.3 - - + +
42T ARG* 1.3 76.9 - - - +
44T PHE* 1.3 68.2 + - - +
45T GLY 3.6 2.6 + - - +
46T LEU* 3.9 17.3 - - + -
57T PHE* 4.5 8.5 - - + -
72T GLN* 3.8 4.0 - - - +
73T VAL* 3.1 33.8 + - - +
75T ILE* 3.9 22.2 - - + -
90T VAL* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T LEU* 4.8 21.3 - - + -
31T GLY* 3.3 1.7 - - - -
32T ARG* 2.8 41.9 + - + +
34T LEU* 4.4 26.6 - - + +
42T ARG 4.3 0.8 + - - -
43T VAL* 1.3 71.3 - - - +
45T GLY* 1.3 61.7 - - - +
71T GLY* 3.0 33.0 - - - -
72T GLN* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T LEU* 3.7 26.7 - - - -
30T THR 4.0 4.0 - - - -
31T GLY* 4.2 0.7 - - - -
43T VAL 3.6 1.4 + - - +
44T PHE* 1.3 80.7 - - - +
46T LEU* 1.3 76.8 + - - +
47T ASN* 3.5 6.9 - - - +
71T GLY 4.8 2.2 + - - -
72T GLN* 5.6 0.2 - - - +
73T VAL* 4.1 12.5 - - - +
72X ARG* 4.1 2.8 + - - -
----------------------------------------------------------
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