Contacts of the helix formed by residues 155 - 164 (chain E) in PDB entry 5FWP
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 TYR 155 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E PHE* 2.9 49.7 + + + +
152E VAL 3.4 3.4 - - - -
154E LYS* 1.3 121.3 + - + +
156E GLU* 1.3 52.9 + - - +
157E LYS* 3.3 2.9 - - - -
158E GLN* 3.0 19.4 + - + +
159E ILE* 2.8 34.3 + - + +
180E HIS* 3.3 34.8 + + + +
181E LEU* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E VAL* 2.7 20.1 + - - +
153E GLU* 3.2 23.2 + - - +
154E LYS 3.5 0.6 + - - -
155E TYR* 1.3 72.5 - - - +
157E LYS* 1.3 61.6 + - + +
159E ILE* 3.2 6.8 + - - +
160E LYS* 2.8 41.3 + - + +
189E TYR* 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E LYS 5.4 0.2 + - - -
155E TYR 3.3 0.4 - - - -
156E GLU* 1.3 81.0 - - + +
158E GLN* 1.3 67.4 + - + +
160E LYS* 3.7 13.9 - - + +
161E HIS* 2.8 27.7 + - - +
164E MET* 5.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E LYS 5.6 0.4 - - - +
155E TYR* 3.0 32.5 + - + +
157E LYS* 1.3 82.4 + - + +
159E ILE* 1.3 65.2 + - - +
161E HIS* 4.1 6.9 + - - +
162E PHE 3.1 11.8 + - - -
174E TYR* 2.5 42.9 + - - +
178E ASN* 3.2 24.6 + - - +
181E LEU* 3.4 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E PHE* 4.6 3.1 - - + -
152E VAL* 3.8 41.3 - - + +
155E TYR 2.8 18.8 + - - +
156E GLU* 3.5 6.5 - - - +
158E GLN* 1.3 77.0 - - - +
160E LYS* 1.3 60.3 + - - +
162E PHE* 3.2 7.9 + - - +
163E GLY 3.0 17.2 + - - -
181E LEU* 3.6 22.0 - - + -
186E THR* 3.8 35.9 - - + +
189E TYR* 3.4 27.8 - - + -
190E LEU* 3.7 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E GLU* 2.8 29.5 + - + +
157E LYS* 3.7 13.3 - - + +
159E ILE* 1.3 74.2 - - - +
161E HIS* 1.3 64.4 + - - +
163E GLY* 3.0 2.8 + - - -
164E MET* 2.9 37.4 + - + +
189E TYR* 3.5 32.1 - - + +
193E TRP* 3.5 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E LYS 2.8 18.5 + - - +
158E GLN* 3.5 14.9 + - - +
159E ILE 3.2 0.4 - - - -
160E LYS* 1.3 75.6 - - - +
162E PHE* 1.3 63.2 + - - +
164E MET* 3.1 26.8 + - + +
165E LEU* 3.3 26.2 + - + +
174E TYR* 3.4 37.2 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E GLN 3.1 8.8 + - - +
159E ILE* 3.4 9.2 - - - +
161E HIS* 1.3 76.9 - - - +
163E GLY* 1.3 63.1 + - - +
165E LEU* 3.0 21.0 + - + +
171E SER* 3.9 13.0 - - - -
174E TYR* 3.6 32.5 - + + -
175E LEU* 3.5 33.0 - - + -
181E LEU* 4.8 2.9 - - + -
186E THR* 5.0 2.2 - - + -
190E LEU* 4.0 15.0 - - + -
212E GLN* 3.1 59.2 - - + +
215E VAL* 3.9 19.5 - - + -
216E MET* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E ILE 3.0 7.7 + - - -
160E LYS 3.0 8.7 + - - -
162E PHE* 1.3 76.1 - - - +
164E MET* 1.3 59.8 + - - +
165E LEU 3.3 1.3 + - - -
190E LEU* 3.9 18.6 - - - -
193E TRP* 4.1 4.0 - - - -
208E GLN* 3.5 23.7 - - - +
209E VAL* 3.6 15.0 - - - +
212E GLN* 3.5 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E LYS 5.3 1.3 - - - +
160E LYS* 2.9 32.1 + - + +
161E HIS* 3.6 22.4 - - + +
162E PHE 3.1 1.0 - - - -
163E GLY* 1.3 73.6 - - - +
165E LEU* 1.3 63.4 + - - +
166E ARG* 5.4 0.5 - - - +
193E TRP* 3.9 16.8 - - + -
205E LEU* 4.2 21.1 - - + -
208E GLN* 4.6 5.8 - - - +
----------------------------------------------------------
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