Contacts of the strand formed by residues 58 - 63 (chain M) 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 THR 58 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J GLU* 3.9 2.8 + - - +
14M THR* 4.5 8.6 - - + +
22M ASP* 4.5 7.0 - - + -
23M VAL 3.3 21.8 - - - +
24M HIS* 3.3 16.2 - - - -
25M PHE* 4.7 0.4 - - - +
53M HIS* 3.6 1.9 - - - +
54M LEU* 2.9 41.8 + - + -
55M GLY 3.3 15.6 + - - -
56M GLU* 3.3 6.1 + - - +
57M ASN* 1.3 81.7 + - - +
59M VAL* 1.3 74.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M VAL 4.0 0.5 - - - +
22M ASP* 3.6 0.9 - - - -
23M VAL* 2.9 32.6 + - + +
25M PHE* 3.3 35.0 - - + -
30M LEU* 4.9 5.6 - - + -
31M PRO* 4.4 3.6 - - + +
50M VAL* 3.9 20.4 - - + -
52M GLN 3.3 8.7 - - - +
53M HIS* 3.4 38.1 - - + +
54M LEU* 4.2 4.9 - - - +
58M THR* 1.3 82.8 - - - +
60M ARG* 1.3 61.1 + - - +
61M THR* 3.9 10.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M ILE* 3.7 20.6 - - + +
21M VAL 4.2 0.2 - - - -
22M ASP* 3.0 36.8 + - - +
50M VAL* 3.9 0.2 - - - -
51M ALA* 2.7 31.6 + - - +
52M GLN* 2.9 24.6 + - + +
54M LEU* 3.7 35.0 - - + +
59M VAL* 1.3 71.5 - - - +
61M THR* 1.3 56.1 + - - +
271M LEU 3.1 20.0 + - - -
272M LEU* 3.7 41.5 + - + -
273M GLY* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M ILE* 3.5 10.2 - - - +
21M VAL* 2.7 47.7 + - - +
23M VAL* 4.9 2.7 - - + -
37M LEU* 3.8 24.7 - - + -
48M LEU* 3.7 19.2 - - - +
49M GLU 3.1 12.6 - - - -
50M VAL* 3.6 21.3 - - + +
51M ALA 4.0 0.4 - - - +
59M VAL* 4.2 9.6 - - + +
60M ARG* 1.3 78.7 - - - +
62M ILE* 1.3 68.7 + - - +
63M ALA 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA* 3.6 4.7 - - + +
20M ILE* 4.2 12.6 - - + -
48M LEU* 3.6 2.9 - - - -
49M GLU* 2.9 40.7 + - + +
51M ALA* 4.0 13.5 - - + -
61M THR* 1.3 80.6 - - - +
63M ALA* 1.3 63.5 + - - +
64M MET* 3.6 7.8 + - + +
227M GLY* 3.6 30.3 - - - +
231M ARG* 5.9 6.1 - - + +
268M VAL* 4.4 17.0 - - + -
272M LEU* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA* 2.8 21.7 + - + +
21M VAL* 4.6 1.8 - - + +
46M LEU* 4.3 4.3 - - + -
48M LEU* 3.8 21.2 - - + +
61M THR 4.2 0.4 - - - -
62M ILE* 1.3 73.2 - - - +
64M MET* 1.3 62.8 + - - +
65M ASP 3.4 10.0 - - - +
67M THR* 3.4 33.7 - - + -
225M PRO* 5.0 1.9 - - - +
227M GLY* 3.5 21.5 + - - -
----------------------------------------------------------
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