Contacts of the helix formed by residues 84 - 90 (chain B) in PDB entry 4IVR
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 PRO 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO 3.4 5.6 - - - +
83B GLU* 1.3 81.5 - - - +
85B MET* 1.3 62.6 + - - +
86B THR 3.3 2.9 - - - -
87B TYR* 3.2 11.3 + - + +
88B TRP* 3.2 48.9 + - + +
131B PRO* 3.9 23.6 - - + -
132B TYR* 3.9 17.5 - - + +
368B PHE* 3.9 17.7 - - + -
372B MET* 3.2 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 3.0 40.6 + - + +
84B PRO* 1.3 75.5 - - - +
86B THR* 1.3 52.5 + - - +
88B TRP* 3.1 21.5 + - + -
89B ARG* 2.8 70.9 + - - +
97B ILE* 4.7 7.6 - - + -
222B ARG* 4.0 19.3 - - + -
223B PRO* 4.1 17.7 - - + -
372B MET 3.2 0.8 + - - -
374B GLU* 3.5 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 1.3 74.9 - - - +
87B TYR* 1.3 60.9 + - - +
89B ARG* 4.5 3.8 - - - +
90B VAL* 3.0 32.1 + - + +
91B LEU* 3.1 24.4 + - + -
371B GLU 3.7 13.6 + - - +
372B MET* 3.2 17.8 + - - -
373B GLY 3.0 20.1 + - - -
374B GLU* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 4.0 10.2 + - - +
307A VAL* 3.6 21.3 - - + -
308A PHE* 3.5 30.3 - + - -
84B PRO 3.2 11.3 + - - +
86B THR* 1.3 78.9 - - - +
88B TRP* 1.3 66.6 + + - +
89B ARG 3.3 0.2 + - - -
90B VAL 3.6 0.7 + - - -
91B LEU* 3.5 17.8 + - + +
92B GLY* 3.0 44.6 + - - -
93B ALA 4.0 0.7 + - - -
96B THR* 4.7 0.2 + - - -
127B THR* 3.5 31.0 - - + +
130B MET* 3.3 36.2 - - + +
131B PRO* 3.7 15.0 - - + -
372B MET* 3.8 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 3.4 33.0 - - + -
84B PRO* 3.2 26.0 + - + +
85B MET* 3.1 31.0 + - + +
87B TYR* 1.3 83.1 - + - +
89B ARG* 1.3 59.0 + - - +
93B ALA 3.6 2.4 - - - +
96B THR* 2.5 38.0 + - - -
97B ILE* 4.3 7.4 - - + -
127B THR* 4.1 7.6 + - - -
128B MET* 2.9 69.0 + - + +
131B PRO* 4.5 1.4 - - - +
132B TYR* 3.1 35.2 - + - -
401B N50 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 2.8 51.7 + - - +
86B THR* 4.5 1.8 - - - +
88B TRP* 1.3 75.4 - - + +
90B VAL* 1.3 69.4 + - + +
93B ALA 3.2 5.4 - - - +
94B SER* 3.5 4.0 + - - -
95B GLU* 2.7 68.4 + - - +
96B THR 5.6 0.2 - - - +
97B ILE* 5.7 3.8 - - + -
223B PRO* 3.7 29.7 - - + +
374B GLU* 5.8 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 5.3 0.3 + - - -
86B THR* 3.0 20.5 + - + +
87B TYR 3.6 0.2 + - - -
89B ARG* 1.3 91.4 - - + +
91B LEU* 1.3 80.0 + - + +
93B ALA* 3.1 16.2 + - - +
94B SER* 5.0 0.8 - - - +
95B GLU* 6.0 0.7 - - - +
----------------------------------------------------------
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