Contacts of the helix formed by residues 152 - 159 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L THR* 2.9 22.4 + - - +
151L GLY* 1.3 76.4 - - - +
153L LYS* 1.3 67.1 + - - +
154L ALA 3.4 1.1 - - - +
155L VAL* 3.1 18.9 + - + +
156L ASP* 3.0 23.6 + - - +
180L VAL* 3.7 47.1 - - + +
183L ASP* 3.7 25.8 - - + +
365L PRO* 5.0 13.9 - - + -
432L GLN* 3.5 24.5 - - + +
433L ASN 5.0 3.4 - - - +
436L SER 5.5 0.7 - - - +
437L PRO* 5.7 2.2 - - + -
443L GLN* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151L GLY 3.3 2.7 + - - +
152L LEU* 1.3 72.4 - - - +
154L ALA* 1.3 64.1 + - - +
156L ASP 4.1 0.2 - - - -
157L ALA* 3.1 26.3 + - - +
428L GLN 5.6 0.2 + - - -
429L LEU* 3.2 21.7 + - + +
430L LEU* 3.6 14.4 - - + +
431L LYS 2.8 29.4 + - - -
432L GLN* 2.8 26.6 + - - +
438L LEU* 3.8 25.6 - - + -
443L GLN* 4.1 23.6 - - + +
446L LEU* 4.5 10.5 - - + -
447L ILE* 5.8 5.8 - - + -
467L GLU* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152L LEU* 3.4 1.0 - - - +
153L LYS* 1.3 78.3 - - - +
155L VAL* 1.3 57.4 + - - +
158L LEU* 3.1 37.2 + - + +
159L VAL* 3.9 1.9 + - - +
365L PRO* 4.3 17.2 - - + +
367L ILE* 4.1 19.3 - - + +
430L LEU* 3.8 40.4 + - + +
432L GLN* 4.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L THR* 3.2 35.2 - - + +
152L LEU* 3.1 30.5 + - + +
154L ALA* 1.3 73.6 - - - +
156L ASP* 1.3 60.7 + - - +
157L ALA 3.1 1.8 - - - -
159L VAL* 2.8 53.5 + - - +
161L ILE* 4.4 4.3 - - + -
180L VAL* 4.6 6.5 - - + -
352L ILE* 4.3 19.1 - - + -
365L PRO* 5.2 2.9 - - + -
367L ILE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L VAL 3.8 5.9 - - - +
149L GLN* 3.7 10.9 - - - +
150L THR* 2.9 33.7 + - - +
151L GLY* 2.9 26.2 + - - -
152L LEU 3.0 8.3 + - - +
155L VAL* 1.3 80.3 - - - +
157L ALA* 1.3 50.9 + - - +
160L PRO* 3.6 14.7 - - - +
161L ILE 4.8 4.0 + - - -
381L GLN* 2.7 29.1 + - - +
385L LEU* 3.3 10.5 - - + +
443L GLN* 3.6 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L LYS 3.1 18.5 + - - +
154L ALA* 4.3 2.2 - - - +
155L VAL 3.1 0.6 - - - -
156L ASP* 1.3 78.9 - - - +
158L LEU* 1.3 72.1 + - + +
160L PRO* 4.2 1.4 - - - +
381L GLN* 3.3 18.1 + - - +
385L LEU* 4.1 9.8 - - + +
389L ALA* 4.4 14.0 - - + +
392L LEU* 5.1 1.6 - - + -
393L LYS* 5.8 0.3 - - - +
430L LEU* 5.2 1.6 - - + -
443L GLN* 5.2 1.6 - - - +
447L ILE* 4.3 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154L ALA* 3.1 19.6 + - + +
157L ALA* 1.3 84.9 - - + +
159L VAL* 1.3 71.4 + - + +
160L PRO* 3.4 6.7 - - - +
367L ILE* 5.9 4.7 - - + -
369L VAL* 3.9 22.4 - - + -
374L SER* 4.8 0.9 - - - -
392L LEU* 3.7 37.5 - - + -
393L LYS* 3.4 40.8 + - + +
396L LEU* 3.5 23.3 - - + -
430L LEU* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154L ALA 4.3 2.9 - - - +
155L VAL* 2.8 28.3 + - - +
158L LEU* 1.3 87.8 - - + +
160L PRO* 1.3 65.9 - - - +
161L ILE* 3.3 15.1 - - - +
167L GLU* 4.6 6.5 - - - +
351L GLN 4.6 0.9 - - - +
352L ILE* 4.0 20.4 - - + -
367L ILE* 4.4 12.8 - - + -
372L SER* 3.8 15.3 - - - +
373L VAL* 3.6 37.0 - - - +
374L SER* 3.7 8.9 - - - -
393L LYS* 4.6 1.3 - - - +
----------------------------------------------------------
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