Contacts of the strand formed by residues 58 - 63 (chain V) 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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S GLU* 4.3 0.9 + - - +
14V THR* 4.2 17.6 + - - +
22V ASP* 4.3 9.6 - - + +
23V VAL 3.4 14.1 - - - +
24V HIS* 3.1 20.6 - - - +
30V LEU* 4.2 0.2 - - - +
53V HIS* 3.8 0.7 - - - +
54V LEU* 2.9 37.0 + - + +
55V GLY 3.4 12.7 + - - -
56V GLU* 3.1 6.8 + - - +
57V ASN* 1.3 78.9 - - - +
59V VAL* 1.3 72.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V ASP* 3.4 5.6 - - - +
23V VAL* 3.1 54.0 + - + +
25V PHE* 4.0 14.6 - - + -
30V LEU* 3.8 18.6 - - + -
31V PRO* 4.6 4.3 - - + +
37V LEU* 5.1 1.8 - - + -
50V VAL* 4.2 17.9 - - + -
52V GLN 3.5 6.3 - - - +
53V HIS* 3.8 33.7 - - + +
54V LEU* 4.2 2.9 - - - +
58V THR* 1.3 78.9 - - - +
60V ARG* 1.3 60.3 + - - +
61V THR* 4.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V ILE* 3.6 26.1 - - + +
22V ASP* 3.1 34.1 + - - +
50V VAL* 4.0 0.7 - - - +
51V ALA* 2.8 28.6 + - - +
52V GLN* 3.0 36.8 + - + +
54V LEU* 3.6 24.9 - - + +
59V VAL* 1.3 72.6 - - - +
61V THR* 1.3 64.1 + - - +
271V LEU 5.4 0.6 + - - -
272V LEU* 3.2 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V ILE* 3.6 7.9 - - - +
21V VAL* 2.8 48.7 + - - +
23V VAL* 4.3 10.3 - - + +
37V LEU* 3.7 24.7 - - + -
48V LEU* 3.3 29.7 - - - +
49V GLU 3.1 26.2 - - - +
50V VAL* 3.7 7.9 - - + -
51V ALA 4.4 0.2 - - - +
59V VAL* 4.6 2.9 - - + -
60V ARG* 1.3 80.9 - - - +
62V ILE* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V ALA* 3.8 12.3 - - + +
20V ILE* 3.8 14.1 - - + -
48V LEU* 3.8 2.4 - - - -
49V GLU* 3.1 28.9 + - + +
51V ALA* 4.3 10.8 - - + -
61V THR* 1.3 75.9 - - - +
63V ALA* 1.3 66.4 + - - +
64V MET* 4.0 6.5 - - - +
226V PRO* 5.8 0.2 - - + -
227V GLY* 3.7 27.8 - - - +
231V ARG* 5.7 6.7 - - - +
268V VAL* 3.8 26.9 - - + -
271V LEU* 5.7 1.8 - - + -
272V LEU* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V ALA* 3.2 26.1 + - + +
46V LEU* 5.4 0.9 - - + -
47V VAL 3.8 5.8 - - - +
48V LEU* 3.9 8.8 - - + +
61V THR 4.1 0.6 + - - -
62V ILE* 1.3 75.8 - - - +
64V MET* 1.3 61.9 + - - +
65V ASP 3.3 20.2 - - - +
67V THR* 3.6 22.7 - - + -
225V PRO* 4.9 4.1 - - + +
227V GLY* 3.2 27.0 + - - -
----------------------------------------------------------
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