Contacts of the helix formed by residues 163 - 168 (chain B) in PDB entry 5FL6
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 ARG 163 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 5.5 1.0 + - - -
63B LEU* 3.9 13.7 - - + -
159B GLN 3.4 20.1 + - - +
160B LEU 3.1 8.4 + - - +
161B LEU 3.1 1.4 - - - -
162B SER* 1.3 87.9 + - - +
164B LEU* 1.3 62.3 + - - +
165B GLU 3.3 2.5 - - - -
166B GLU* 2.7 64.1 + - - +
167B ILE* 3.7 8.4 - - - +
174B THR* 4.4 2.2 - - + +
175B GLN 3.7 15.8 + - - -
176B VAL* 3.8 15.5 - - + +
177B PRO* 3.2 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.7 2.0 - - + -
70B VAL* 3.9 35.2 - - + -
160B LEU* 3.7 13.2 - - + +
161B LEU* 3.1 41.8 + - + +
163B ARG* 1.3 76.5 - - - +
165B GLU* 1.3 61.8 + - - +
167B ILE* 2.9 29.2 + - + +
168B ALA 3.2 10.0 + - - -
226B THR 4.0 17.9 - - - +
227B LEU* 4.1 16.2 - - + +
230B THR* 3.6 16.6 - - + +
231B LEU* 3.6 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU 4.8 0.4 + - - -
162B SER 4.7 7.5 + - - +
163B ARG 3.3 0.4 - - - -
164B LEU* 1.3 78.0 - - - +
166B GLU* 1.3 61.6 + - + +
167B ILE 3.2 1.0 + - - -
168B ALA* 3.5 15.0 + - - +
230B THR* 3.5 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER 5.1 1.2 - - - +
163B ARG* 2.7 51.5 + - - +
164B LEU 3.2 0.6 - - - -
165B GLU* 1.3 78.1 - - + +
167B ILE* 1.3 61.0 + - - +
168B ALA 3.6 1.0 + - - -
172B SER* 4.4 5.2 + - - -
173B GLU 5.0 2.1 - - - +
174B THR* 2.5 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.9 17.9 - - + -
64B ARG 4.0 0.4 - - - -
65B ASN* 3.1 35.5 + - + +
70B VAL* 3.7 29.6 - - + -
163B ARG 3.7 7.9 - - - +
164B LEU* 2.9 20.6 + - + +
166B GLU* 1.3 82.1 - - - +
168B ALA* 1.3 65.0 + - - +
172B SER* 3.0 22.0 + - - +
173B GLU* 3.5 25.1 - - - +
174B THR* 3.4 25.6 - - + -
231B LEU* 3.5 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASN* 3.2 4.3 + - - -
164B LEU 3.2 6.8 + - - +
165B GLU* 3.5 17.1 + - - +
166B GLU 3.6 0.8 - - - -
167B ILE* 1.3 76.5 - - - +
169B GLU* 1.3 56.9 + - - +
230B THR* 3.6 22.4 - - + +
231B LEU* 4.0 2.9 - - - -
232B TRP* 2.8 39.3 + - + +
----------------------------------------------------------
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