Contacts of the strand formed by residues 152 - 156 (chain W) 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 152 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211T LYS* 4.1 13.9 - - - +
150W GLY 5.1 0.2 - - - -
151W GLY* 1.3 78.9 - - - +
153W ILE* 1.3 63.4 + - - +
293W GLN* 2.9 57.1 + - - +
294W GLU* 5.0 1.8 + - - +
296W ILE* 3.1 29.6 - - + -
306W SER 3.6 4.3 - - - -
308W GLN* 3.8 13.7 - - - +
328W HIS* 3.5 34.8 + - - +
329W LEU* 3.4 12.9 - - + +
330W ASP* 2.8 40.9 + - - +
331W ALA 3.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147W TYR* 3.6 60.3 - - + +
148W ALA* 4.4 8.1 - - + +
151W GLY 4.4 0.4 - - - -
152W LYS* 1.3 79.5 - - - +
154W GLY* 1.3 69.0 + - - +
155W LEU* 4.6 1.3 - - + +
305W THR* 3.6 31.0 - - + -
306W SER 2.8 14.3 + - - +
307W VAL* 3.6 9.4 - - + -
308W GLN* 2.8 30.3 + - - +
329W LEU* 3.6 4.7 - - - +
330W ASP* 6.2 0.4 - - + -
331W ALA* 3.3 21.3 - - + +
333W THR* 3.7 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153W ILE* 1.3 73.2 - - - +
155W LEU* 1.3 61.8 + - - -
156W PHE* 3.7 7.0 - - - -
308W GLN 3.3 7.6 - - - -
310W VAL* 4.5 2.2 - - - -
329W LEU* 3.5 22.6 - - - +
331W ALA 2.8 15.1 + - - -
332W THR* 3.1 9.0 - - - -
333W THR 2.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147W TYR* 5.0 1.8 - - - +
153W ILE* 3.9 1.0 + - + -
154W GLY* 1.3 73.0 - - - -
156W PHE* 1.3 65.7 + - - +
163W LYS* 4.1 17.5 - - + -
166W PHE* 4.5 10.8 - - + -
167W ILE* 3.5 31.6 - - + -
307W VAL* 4.2 22.7 - - + -
308W GLN 3.1 7.7 + - - -
309W ALA* 3.2 18.7 - - + +
310W VAL 3.1 24.3 + - - -
333W THR* 3.1 41.7 - - + +
335W LEU* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154W GLY* 3.7 21.3 - - - -
155W LEU* 1.3 76.2 - - - +
157W GLY* 1.3 59.4 + - - +
163W LYS* 5.8 0.2 - - - -
310W VAL* 3.6 42.6 - - + -
312W VAL* 4.4 13.2 - - + -
317W LEU* 5.9 1.1 - - + -
326W PHE* 3.6 28.0 - + - -
329W LEU* 5.2 1.3 - - + -
332W THR* 3.9 20.0 - - + -
333W THR 3.1 8.3 + - - +
334W VAL* 4.1 33.0 - - + -
335W LEU* 2.9 33.6 + - - +
----------------------------------------------------------
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