Contacts of the strand formed by residues 12 - 17 (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 LYS 12 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V THR* 5.3 9.6 - - + +
11V GLY* 1.3 77.3 - - - +
13V VAL* 1.3 60.1 + - - +
14V THR* 3.0 11.0 + - + +
23V VAL* 4.1 1.1 - - - +
24V HIS* 2.7 54.0 + - + +
26V GLU* 5.1 9.2 + - - +
73V GLY* 5.0 11.7 - - - +
74V GLU 3.8 4.9 - - - +
75V LYS* 5.9 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V LYS* 1.3 66.5 - - - +
14V THR* 1.3 59.9 + - - +
15V ALA 3.6 3.8 - - - +
16V VAL* 3.6 23.3 - - + -
21V VAL* 3.6 24.9 - - + -
22V ASP 3.5 4.5 - - - -
23V VAL* 3.6 9.6 - - + -
39V ILE* 5.5 1.1 - - + -
48V LEU* 5.3 1.1 - - + -
70V LEU* 5.0 10.1 - - + -
71V VAL 4.8 2.7 - - - +
72V ARG* 3.4 10.0 - - - +
73V GLY* 2.8 37.1 + - - +
74V GLU* 3.6 18.3 + - + +
76V VAL* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68U LEU 3.8 3.1 - - - +
69U GLU 3.8 0.3 - - - -
70U PRO* 3.5 37.3 - - - +
12V LYS* 3.0 18.8 + - + +
13V VAL* 1.3 74.1 - - - +
15V ALA* 1.3 56.6 + - - +
22V ASP* 2.7 29.5 + - - +
23V VAL 4.4 0.2 + - - -
24V HIS* 3.5 22.7 - - + +
58V THR* 4.2 10.3 - - - +
72V ARG* 4.0 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68U LEU 3.2 8.7 - - - +
70U PRO* 3.9 17.3 - - + -
13V VAL* 3.5 0.6 - - - +
14V THR* 1.3 81.7 + - - +
16V VAL* 1.3 71.2 + - - +
17V ILE* 4.0 14.1 - - + -
21V VAL* 3.4 5.4 - - - +
22V ASP* 2.9 49.4 + - + +
72V ARG* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51U ALA* 4.0 27.1 - - + -
66U LEU 3.3 6.3 - - - +
68U LEU* 3.0 48.2 + - + +
13V VAL* 3.6 20.4 - - + -
15V ALA* 1.3 81.7 - - - +
17V ILE* 1.3 64.0 + - - +
18V GLY 4.8 4.7 - - - +
20V ILE 3.8 3.8 - - - -
21V VAL* 4.0 13.9 - - + +
67V THR* 4.5 15.5 - - - +
70V LEU* 4.6 14.6 - - + +
72V ARG* 5.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U LEU 3.9 2.7 - - - -
67U ASN* 3.9 27.1 - - + +
68U LEU 4.5 3.8 - - - +
69U GLU* 4.6 11.7 - - + -
289U ARG* 3.7 32.5 - - + +
290U PRO* 6.4 0.7 - - + -
15V ALA* 4.0 15.5 - - + -
16V VAL* 1.3 89.8 - - - +
18V GLY* 1.3 62.1 + - - +
19V ALA 3.0 0.9 + - - -
20V ILE* 2.9 45.5 + - + +
22V ASP* 5.9 0.9 - - - +
271V LEU* 5.4 2.3 - - - +
----------------------------------------------------------
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