Contacts of the helix formed by residues 139 - 150 (chain Y) 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 139 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 ASN 4.3 15.7 - - - +
371 ARG* 4.0 25.7 + - - +
391 GLN* 5.2 5.7 + - + +
137Y ALA* 3.1 17.8 + - + +
138Y PRO* 1.3 74.6 - - - +
140Y PHE* 1.3 63.9 + - - +
141Y GLN* 4.3 0.8 - - - +
142Y GLU* 3.0 39.5 + - - +
143Y SER* 3.7 5.5 + - - -
219Y LEU* 3.2 14.1 - - - +
222Y MET* 3.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131 TYR 5.5 3.1 - - - -
141 LEU 5.4 7.6 - - - -
151 ASN* 6.3 0.4 - - - -
181 ALA* 6.2 4.7 - - + -
139Y THR* 1.3 70.9 - - - +
141Y GLN* 1.3 63.7 + - - +
142Y GLU 3.2 1.8 - - - -
143Y SER* 3.2 4.0 + - - +
144Y ALA* 2.9 39.2 + - + +
211Y GLU 5.6 1.8 - - - -
215Y ALA* 4.1 26.0 - - + -
216Y ASN* 3.4 28.3 - - + -
219Y LEU* 3.7 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ASN* 5.6 13.4 - - + +
191 GLN* 5.4 8.0 - - - +
371 ARG 3.7 12.9 - - - +
381 SER* 3.3 28.0 - - - +
391 GLN 3.5 6.1 - - - +
401 THR* 3.4 39.4 - - - +
139Y THR* 3.5 1.6 + - - +
140Y PHE* 1.3 80.3 - - - +
142Y GLU* 1.3 58.8 + - + +
144Y ALA* 3.8 6.2 - - - +
145Y LEU* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 GLN* 3.2 32.4 - - + +
411 ASP* 4.8 6.0 + - - +
133Y ILE* 3.7 37.4 - - + +
137Y ALA 5.4 2.0 - - - +
139Y THR* 3.0 30.6 + - - +
140Y PHE 3.2 0.4 - - - -
141Y GLN* 1.3 80.1 - - + +
143Y SER* 1.3 56.6 + - - +
145Y LEU* 3.9 5.4 - - - +
146Y ILE* 3.1 42.1 + - - +
222Y MET* 4.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Y THR 3.7 7.0 + - - -
140Y PHE 3.2 7.6 + - - -
142Y GLU* 1.3 78.2 - - - +
144Y ALA* 1.3 58.1 + - - +
146Y ILE* 4.5 0.7 - - - -
147Y ALA* 2.9 29.3 + - - +
215Y ALA 4.0 8.7 - - - +
218Y MET* 3.5 25.4 + - - +
219Y LEU* 3.3 39.6 + - - -
222Y MET* 4.1 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131 TYR* 4.3 19.5 - - + +
151 ASN* 5.0 16.5 - - + +
140Y PHE* 2.9 35.5 + - + +
141Y GLN* 3.9 7.4 - - - +
143Y SER* 1.3 76.2 - - - +
145Y LEU* 1.3 59.4 + - - +
147Y ALA* 3.7 6.2 - - - +
148Y ASP* 3.0 25.1 + - - +
215Y ALA* 4.7 9.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ASN* 4.9 15.0 - - + -
391 GLN 5.2 0.4 - - - +
401 THR* 3.8 36.1 - - - -
411 ASP 4.6 4.3 - - - +
421 ALA* 5.1 15.9 - - + -
141Y GLN* 2.9 36.1 + - + +
142Y GLU* 3.9 5.4 - - - +
144Y ALA* 1.3 77.1 - - - +
146Y ILE* 1.3 62.0 + - + +
148Y ASP* 3.1 16.5 + - + +
149Y LYS* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110Y ILE* 5.6 12.3 - - + +
131Y ASN 6.2 1.8 - - - +
142Y GLU* 3.1 26.7 + - - +
143Y SER* 3.9 4.3 - - - +
145Y LEU* 1.3 77.6 - - + +
147Y ALA* 1.3 64.1 + - - +
149Y LYS* 3.0 21.7 + - + +
150Y LEU* 3.1 20.2 + - + +
218Y MET* 3.7 22.0 - - + -
222Y MET* 6.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131 TYR* 6.0 2.2 - - + -
143Y SER 2.9 19.3 + - - +
144Y ALA* 3.7 7.9 - - - +
146Y ILE* 1.3 77.4 - - - +
148Y ASP* 1.3 62.1 + - - +
150Y LEU* 3.0 36.8 + - + +
151Y LEU* 4.1 4.3 + - - +
210Y PHE* 6.1 4.2 - - + -
214Y LEU* 4.7 7.7 - - + +
215Y ALA* 4.5 18.2 - - + -
218Y MET* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 ALA* 4.7 8.8 - - - +
131 TYR* 4.4 19.4 - - + +
144Y ALA 3.0 16.1 + - - +
145Y LEU* 3.1 22.9 + - + +
147Y ALA* 1.3 76.3 - - - +
149Y LYS* 1.3 60.6 + - - +
150Y LEU 3.1 1.1 + - - -
151Y LEU* 3.4 34.6 + - - +
152Y SER* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 ALA* 6.0 7.4 - - + +
431 PHE 5.8 6.1 - - - +
110Y ILE* 4.8 18.1 - - + +
145Y LEU 2.9 12.9 + - - +
146Y ILE* 3.0 19.2 + - + +
148Y ASP* 1.3 72.2 - - - +
150Y LEU* 1.3 61.4 + - - +
151Y LEU 3.0 6.6 + - - -
152Y SER* 3.1 28.3 + - - -
153Y VAL* 4.0 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108Y VAL* 4.7 7.6 - - + -
146Y ILE* 3.1 20.9 + - + +
147Y ALA* 3.0 24.1 + - - +
149Y LYS* 1.3 74.6 - - - +
151Y LEU* 1.3 49.9 + - + +
152Y SER 3.1 5.8 - - - -
153Y VAL* 4.0 12.6 - - + -
154Y MET* 3.2 34.3 + - + -
155Y LYS* 2.5 40.2 + - - +
214Y LEU* 3.6 33.2 - - + -
218Y MET* 3.7 16.4 - - + -
----------------------------------------------------------
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