Contacts of the helix formed by residues 139 - 147 (chain R) in PDB entry 1MVW
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 139 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R VAL* 4.1 15.7 - - + +
91R LEU* 3.2 45.3 - - + -
92R ARG* 3.0 43.4 + - - -
95R ASP* 2.8 40.4 + - - -
99R ASN 4.2 0.2 + - - -
100R GLY* 2.9 34.5 + - - -
101R THR 3.5 0.2 - - - -
102R VAL* 3.2 23.1 - - + -
137R ILE* 3.2 4.4 + - + +
138R ASN* 1.3 69.0 - - - +
140R GLU* 1.3 64.6 + - + +
142R PHE* 3.5 16.8 - - + -
143R VAL* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R VAL* 5.3 11.9 - - + +
92R ARG* 3.8 23.7 + - - +
99R ASN* 4.5 5.5 + - - -
100R GLY* 3.3 18.6 + - - -
138R ASN* 3.0 27.4 + - - +
139R TYR* 1.3 83.8 - - + +
141R ALA* 1.3 62.7 + - - +
143R VAL* 4.2 1.0 - - - +
144R LYS* 3.3 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R GLN* 5.5 1.8 - - + -
138R ASN* 3.1 15.2 + - + +
140R GLU* 1.3 76.9 - - - +
142R PHE* 1.3 60.3 + - - +
144R LYS* 3.3 15.4 + - + +
145R HIS* 2.9 53.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R LEU* 4.5 8.7 - - + -
107R LEU* 3.9 24.5 - - + -
111R LEU* 5.9 2.2 - - + -
126R LEU* 3.2 25.6 - - + -
127R MET* 3.8 26.2 - - + -
130R GLN* 3.6 30.5 - - + +
137R ILE* 4.2 7.6 - - + -
138R ASN 2.9 18.5 + - - +
139R TYR* 3.5 15.7 - - + -
140R GLU 3.4 0.4 - - - -
141R ALA* 1.3 75.5 - - - +
143R VAL* 1.3 69.2 + - + +
145R HIS* 3.2 4.5 + - - +
146R ILE* 3.0 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R PHE* 5.4 0.2 - - + -
87R PHE* 4.2 16.8 - - + +
88R VAL* 4.0 27.1 - - + -
91R LEU* 3.8 28.3 - - + -
139R TYR* 2.9 22.2 + - + +
140R GLU 4.4 0.9 - - - +
142R PHE* 1.3 81.1 - - + +
144R LYS* 1.3 64.2 + - - +
146R ILE* 3.2 7.8 + - + +
147R MET* 3.0 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R GLU* 3.3 18.7 + - - +
141R ALA* 3.3 17.2 - - + +
143R VAL* 1.3 79.5 - - - +
145R HIS* 1.3 75.7 + - + +
147R MET* 3.2 7.0 + - - +
148R SER* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797P PHE* 3.5 9.6 - - - -
130R GLN* 4.0 27.0 - - + +
141R ALA* 2.9 37.2 + - + +
142R PHE 3.8 4.3 - - - +
144R LYS* 1.3 88.7 - - + +
146R ILE* 1.3 65.5 + - - +
148R SER* 3.1 25.0 + - - -
149R VAL* 3.9 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793P ARG* 5.1 10.8 - - + -
794P CYS* 5.2 9.6 - - - -
797P PHE* 2.4 97.4 - - + +
800P ARG* 4.9 1.0 + - - -
126R LEU* 4.1 7.9 - - + +
130R GLN* 4.3 10.1 - - - +
142R PHE* 3.0 51.8 + - + +
143R VAL* 3.2 10.5 + - + +
145R HIS* 1.3 75.6 - - - +
147R MET* 1.3 62.6 + - + +
149R VAL* 3.1 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793P ARG* 4.2 35.0 - - + +
800P ARG* 6.1 0.2 - - - +
82R GLY 4.8 4.3 - - - +
84R PHE* 3.6 39.3 - - + +
87R PHE* 4.0 15.0 - - + -
143R VAL* 3.0 30.7 + - + +
144R LYS* 3.2 6.7 + - - +
146R ILE* 1.3 82.1 - - + +
148R SER* 1.3 58.9 + - - +
149R VAL 3.3 8.0 - - - +
----------------------------------------------------------
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