Contacts of the strand formed by residues 145 - 149 (chain H) in PDB entry 3MQ6
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 VAL 145 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ALA* 4.0 22.1 - - + +
117H TRP* 4.3 7.4 - - + +
118H ASN* 3.0 31.0 + - - +
143H ARG 4.0 3.1 - - - +
144H GLN* 1.3 81.9 - - - +
146H ALA* 1.3 61.1 + - - +
191H VAL* 4.0 20.6 - - + -
192H VAL 3.2 13.9 - - - +
193H VAL* 4.3 2.7 - - - -
194H LEU* 3.7 8.5 - - - +
204H TRP* 4.9 1.0 - - - +
236H SER* 5.1 1.3 - - - +
326H PHE* 5.2 0.2 - - + -
330H LEU* 4.2 20.2 - - + -
334H MET* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ALA* 5.2 0.4 - - - -
145H VAL* 1.3 73.9 - - - +
147H VAL* 1.3 63.1 + - - +
148H LEU* 3.8 14.0 + - + -
190H ALA 3.7 1.2 - - - +
191H VAL* 3.3 5.6 - - - -
192H VAL* 2.7 41.4 + - + +
194H LEU* 4.3 5.8 - - + +
204H TRP* 3.5 33.4 - - + -
226H LEU* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H SER* 3.8 18.4 - - - +
110H MET* 3.5 16.6 - - + +
111H TRP* 3.3 39.7 - - + -
114H ALA* 3.5 27.5 - - + +
146H ALA* 1.3 73.2 - - - +
148H LEU* 1.3 64.0 + - - +
149H ASN 3.9 2.2 + - - +
189H LEU* 3.6 30.5 - - + -
190H ALA 3.9 2.2 - - - -
191H VAL* 4.2 5.8 - - + +
204H TRP* 5.1 0.4 - - - -
219H LEU 5.2 0.2 - - - +
222H ALA* 4.5 0.9 - - - +
326H PHE* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H ALA* 3.9 13.7 - - + +
147H VAL* 1.3 78.5 - - - +
149H ASN* 1.3 63.2 + - - +
150H LEU* 3.2 15.7 + - + +
159H LEU* 4.2 26.0 - - + -
189H LEU* 3.5 4.1 - - - -
190H ALA* 2.8 38.5 + - + +
192H VAL* 4.1 26.0 - - + -
222H ALA* 4.2 7.9 - - + +
223H TYR* 4.1 19.1 - - + +
226H LEU* 3.4 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU* 3.3 7.8 + - - +
104H ILE* 4.1 27.9 - - - +
107H SER* 4.1 27.1 + - - -
147H VAL* 3.9 4.0 + - - +
148H LEU* 1.3 70.2 - - - +
150H LEU* 1.3 60.6 + - - +
151H PRO* 3.9 2.9 - - - +
188H ASP 3.9 3.6 - - - -
189H LEU* 4.6 5.5 - - - +
219H LEU* 4.2 24.4 + - + +
220H SER* 3.9 26.9 - - - +
223H TYR* 4.1 6.1 + - - +
341H CA 2.5 30.2 - - - -
----------------------------------------------------------
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