Contacts of the helix formed by residues 173 - 186 (chain E) in PDB entry 3VBI
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 173 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E ASP* 4.9 3.0 + - - +
157E TRP* 3.3 63.8 - - + +
158E TYR* 5.9 3.0 - - - -
171E ARG 3.9 5.8 + - - +
172E LYS* 1.3 77.4 - - - +
174E LYS* 1.3 53.3 + - - +
175E ILE 2.9 5.4 - - - +
176E VAL* 2.7 42.3 + - + +
177E GLU* 4.2 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY 3.4 9.3 + - - +
99A ASN* 3.4 41.2 + - - +
172E LYS* 4.4 1.1 - - + +
173E ARG* 1.3 76.4 - - - +
175E ILE* 1.3 62.5 + - - +
176E VAL 3.1 1.4 + - - -
177E GLU* 3.2 24.5 + - + +
178E LEU* 3.1 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY* 3.0 22.1 + - - +
100A ALA 3.1 31.4 - - - +
101A LEU* 3.9 14.7 - - + +
102A MET* 5.1 2.5 - - + -
123E HIS* 3.5 44.0 - - + +
157E TRP* 4.0 14.1 - - + -
171E ARG* 3.9 23.3 - - - +
173E ARG 4.2 1.8 - - - +
174E LYS* 1.3 75.9 - - - +
176E VAL* 1.3 57.0 + - - +
178E LEU* 3.4 9.1 + - - +
179E GLU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E HIS* 5.1 3.6 - - + -
140E GLU* 5.5 1.8 - - - +
157E TRP* 3.7 31.4 - - + -
173E ARG* 2.7 30.1 + - + +
175E ILE* 1.3 69.4 - - + +
177E GLU* 1.3 70.2 + - - +
179E GLU* 3.4 14.0 + - - +
180E ASN* 3.3 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E ARG 4.6 4.0 - - - +
174E LYS* 3.2 29.3 + - + +
176E VAL* 1.3 79.6 - - - +
178E LEU* 1.3 58.9 + - + +
180E ASN* 2.9 15.0 + - - +
181E GLU* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN 3.5 26.7 - - - +
100A ALA* 3.6 17.7 - - - -
101A LEU* 3.9 18.3 - - + +
109A GLN 5.4 1.6 - - - +
110A TYR* 4.2 26.3 - - + +
174E LYS* 3.1 34.5 + - + +
175E ILE* 3.4 5.8 + - - +
177E GLU* 1.3 79.0 - - + +
179E GLU* 1.3 56.6 + - - +
181E GLU* 3.7 20.0 - - - +
182E PHE* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.2 10.7 - - + +
80E PHE* 3.6 28.7 - - + -
122E LYS* 3.0 30.3 + - - -
123E HIS* 2.8 29.7 + - + +
175E ILE 3.0 14.0 + - - +
176E VAL* 3.4 15.6 - - - +
178E LEU* 1.3 74.2 - - - +
180E ASN* 1.3 64.2 + - - +
182E PHE* 3.8 2.3 - - - +
183E LEU* 2.8 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E VAL* 3.3 23.1 + - - +
177E GLU* 2.9 14.4 + - - +
179E GLU* 1.3 84.3 - - - +
181E GLU* 1.3 63.2 + - - +
183E LEU* 3.2 10.5 + - - +
184E LYS* 3.0 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLN* 5.4 1.7 + - - -
110A TYR* 3.5 23.8 + - + +
177E GLU* 2.7 19.1 + - + +
178E LEU* 3.7 19.6 - - - +
180E ASN* 1.3 74.9 - - - +
182E PHE* 1.3 60.8 + - - +
184E LYS* 3.5 17.2 + - + +
185E SER* 3.5 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.3 5.4 - - + -
105A THR 4.9 0.4 - - - -
106A ILE* 3.9 17.5 - - + -
107A PRO* 3.7 25.6 - - + -
110A TYR* 3.5 41.6 - + + -
59E TYR* 3.6 42.0 - + - -
80E PHE* 3.9 21.5 - + - -
178E LEU 2.9 20.3 + - - +
179E GLU 3.8 2.2 - - - +
181E GLU* 1.3 70.6 - - - +
183E LEU* 1.3 70.2 + - + +
185E SER* 3.3 6.5 - - - -
186E MET* 3.3 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E TYR* 4.6 13.7 - - + +
80E PHE* 4.4 17.5 - - + -
179E GLU* 2.8 48.9 + - + +
180E ASN* 3.2 9.2 + - - +
182E PHE* 1.3 74.7 - - + +
184E LYS* 1.3 57.9 + - - +
186E MET* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ASN* 3.0 23.2 + - + +
181E GLU* 3.5 11.9 - - - +
182E PHE 3.2 0.2 - - - -
183E LEU* 1.3 74.4 - - - +
185E SER* 1.3 64.4 + - - +
186E MET 2.9 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.0 23.3 + - - -
181E GLU 3.5 4.4 + - - -
182E PHE* 3.3 14.8 + - - -
184E LYS* 1.3 75.1 - - - +
186E MET* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ASN* 5.4 5.6 - - - +
59E TYR* 2.8 42.6 - - + +
182E PHE* 3.3 35.0 + - + +
183E LEU* 2.8 33.7 + - + +
184E LYS 3.0 11.7 - - - +
185E SER* 1.3 77.8 - - - +
----------------------------------------------------------
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