Contacts of the helix formed by residues 152 - 159 (chain K) 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 LEU 152 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150K THR* 3.2 17.6 + - - +
151K GLY* 1.3 77.7 - - - +
153K LYS* 1.3 66.0 + - - +
154K ALA* 3.5 24.2 - - + +
155K VAL* 3.1 26.3 + - + +
156K ASP* 2.8 29.2 + - - +
180K VAL* 4.2 19.1 - - + +
183K ASP* 4.7 16.8 - - + +
365K PRO* 3.8 28.9 - - + -
432K GLN* 3.3 24.5 - - + +
443K GLN* 3.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K GLY 4.2 0.2 - - - -
152K LEU* 1.3 72.0 - - - +
154K ALA* 1.3 64.1 + - - +
155K VAL 3.2 0.2 + - - -
156K ASP* 4.1 0.5 - - - +
157K ALA* 3.2 26.0 + - - +
429K LEU* 2.9 21.2 + - + +
430K LEU* 3.8 14.8 - - + +
431K LYS 2.9 22.8 + - - -
432K GLN* 2.7 38.5 + - - +
438K LEU* 3.7 25.4 - - + -
443K GLN* 4.1 21.5 - - + +
446K LEU* 4.0 13.7 - - + -
447K ILE* 5.1 8.1 - - + +
467K GLU* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K LEU* 3.4 14.9 - - + +
153K LYS* 1.3 79.4 - - - +
155K VAL* 1.3 58.0 + - - +
158K LEU* 3.3 34.4 + - + +
159K VAL* 4.4 1.6 - - - +
365K PRO* 4.6 5.2 - - + +
367K ILE* 4.2 24.9 - - + +
430K LEU* 3.8 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150K THR* 3.8 25.8 - - + +
152K LEU* 3.1 35.7 + - + +
154K ALA* 1.3 74.8 - - - +
156K ASP* 1.3 55.2 + - - +
157K ALA 2.7 15.4 + - - -
159K VAL* 2.7 58.1 + - + +
161K ILE* 4.7 3.8 - - + -
180K VAL* 4.6 11.9 - - + -
352K ILE* 4.3 14.4 - - + -
367K ILE* 4.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148K VAL 3.7 7.0 - - - +
149K GLN* 3.7 10.8 - - - +
150K THR* 3.1 35.2 + - - +
151K GLY* 3.1 24.6 + - - -
152K LEU 2.8 17.9 + - - +
153K LYS 4.1 0.4 - - - -
155K VAL* 1.3 73.4 - - - +
157K ALA* 1.3 57.1 + - - +
160K PRO* 4.3 8.8 - - - +
161K ILE 4.8 4.2 + - - -
381K GLN* 3.0 18.0 + - - +
385K LEU* 3.1 21.3 - - + +
443K GLN* 3.7 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153K LYS 3.2 17.8 + - - +
154K ALA* 4.3 1.6 - - - +
155K VAL 2.7 3.4 + - - -
156K ASP* 1.3 78.8 - - - +
158K LEU* 1.3 66.3 + - + +
159K VAL 3.5 0.4 - - - -
160K PRO* 4.2 1.4 - - - +
381K GLN* 3.1 19.1 + - - +
385K LEU* 5.2 6.7 - - + -
389K ALA* 5.1 11.8 - - + +
392K LEU* 4.6 13.8 - - + +
430K LEU* 5.1 1.6 - - + -
443K GLN* 6.1 0.2 - - - +
447K ILE* 4.4 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K ALA* 3.3 19.2 + - + +
157K ALA* 1.3 81.4 - - + +
159K VAL* 1.3 72.5 + - + +
160K PRO* 3.8 4.3 - - - +
367K ILE* 4.9 11.7 - - + -
369K VAL* 3.8 31.4 - - + -
374K SER 4.9 1.6 + - - -
392K LEU* 3.8 26.9 - - + +
393K LYS* 3.6 54.3 - - + +
396K LEU* 3.9 13.0 - - + -
430K LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K ALA 4.4 2.9 - - - +
155K VAL* 2.7 46.2 + - + +
158K LEU* 1.3 87.9 - - + +
160K PRO* 1.3 66.0 - - - +
161K ILE* 3.7 4.0 + - - +
167K GLU* 4.5 6.3 - - - +
351K GLN 4.4 3.6 - - - +
352K ILE* 4.3 19.7 - - + -
367K ILE* 4.9 8.5 - - + -
372K SER* 4.1 10.5 - - - +
373K VAL* 3.7 18.8 - - - +
374K SER* 3.6 26.2 - - - +
----------------------------------------------------------
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