Contacts of the helix formed by residues 156 - 162 (chain F) in PDB entry 1F1H
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 GLY 156 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ASP 2.9 16.7 + - - -
155F GLU* 1.3 75.0 - - - +
157F ALA* 1.3 61.5 + - - -
158F TRP* 3.0 21.8 - - - -
159F ASN* 2.9 22.9 + - - +
172F ARG* 3.2 11.4 - - - -
215F THR* 3.7 4.9 - - - -
216F ALA* 3.7 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F GLU 4.0 2.2 - - - -
156F GLY* 1.3 71.2 - - - -
158F TRP* 1.3 64.3 + - + +
159F ASN 3.1 0.9 + - - -
160F SER* 3.2 24.5 + - - -
172F ARG* 4.3 6.7 - - - +
173F PRO 3.8 10.3 - - - +
174F GLY* 4.1 13.5 - - - -
175F VAL* 4.3 17.3 - - + +
215F THR* 3.1 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 158 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ILE* 3.7 23.7 + - + -
152F ASP* 2.9 31.2 + - - -
153F ASP 4.2 3.1 - - - -
156F GLY* 3.9 12.8 - - - -
157F ALA* 1.3 82.4 - - + +
159F ASN* 1.3 70.8 + - - +
160F SER* 3.2 3.3 + - - -
161F SER* 3.4 19.6 + - - -
162F THR* 4.2 2.8 + - - -
215F THR* 4.3 7.9 - - + -
216F ALA* 3.4 26.5 - - + -
260F MET* 3.8 24.7 - - - -
144L ILE* 3.7 30.1 - - + -
145L SER* 3.7 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F ASP* 2.9 28.1 + - - +
153F ASP 2.8 27.9 + - - -
156F GLY 2.9 10.9 + - - +
158F TRP* 1.3 87.7 - - - +
160F SER* 1.3 50.1 + - - +
161F SER 2.9 7.3 + - - -
162F THR* 2.6 32.0 + - - +
164F TYR* 3.3 23.4 + - - +
168F ASN* 2.7 30.8 + - - -
172F ARG* 3.6 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE 4.1 1.6 - - - +
139A ARG* 3.3 9.0 - - - -
140A PHE* 2.8 72.5 + - - -
141A GLY* 4.3 4.7 - - - -
157F ALA 3.2 18.1 + - - -
158F TRP* 4.5 1.6 - - - -
159F ASN* 1.3 78.6 - - - +
161F SER* 1.3 52.7 + - - +
168F ASN* 3.6 5.0 + - - -
170F GLY* 6.0 0.2 - - - -
172F ARG* 3.7 18.9 - - - +
463G GLU* 4.6 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.8 14.5 + - - +
140A PHE 3.1 18.6 + - - +
141A GLY* 4.5 3.1 - - - -
148A HIS* 3.4 25.6 + - - -
158F TRP 3.4 15.2 + - - -
160F SER* 1.3 81.1 + - - +
162F THR* 1.3 63.2 + - - +
163F LYS* 3.7 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.3 7.2 - - - +
158F TRP 4.2 3.1 + - - -
159F ASN* 2.6 40.4 + - - +
161F SER* 1.3 79.1 + - - +
163F LYS* 1.3 76.2 + - - +
164F TYR* 3.4 22.2 - - + -
168F ASN* 2.8 24.8 + - - +
----------------------------------------------------------
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