Contacts of the strand formed by residues 111 - 114 (chain M) in PDB entry 2X86
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 PHE 111 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M ILE* 3.7 8.3 - - + -
74M HIS* 3.7 37.2 - + + -
97M SER 4.1 13.0 - - - -
100M LEU* 3.7 20.9 - - + -
101M LEU* 3.8 27.1 - - + -
104M CYS* 3.8 24.9 - - + -
105M LEU* 6.3 0.2 - - + -
109M ILE 4.0 7.0 - - - +
110M PRO* 1.3 74.2 - - - +
112M LEU* 1.3 62.9 + - - +
113M TYR* 3.5 29.8 - + + -
147M PHE* 4.0 15.3 - + - -
161M GLN 3.0 12.7 + - - +
162M ILE* 3.3 8.4 - - + -
163M VAL 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M ALA* 4.3 12.1 - - + -
72M ILE 2.9 14.4 + - - +
73M PHE* 3.2 25.7 - - + -
74M HIS* 2.7 31.2 + - - -
75M GLU* 3.7 4.5 - - - +
110M PRO* 4.0 17.3 - - + +
111M PHE* 1.3 80.8 - - - +
113M TYR* 1.3 56.5 + - - +
161M GLN* 4.0 16.4 - - - +
163M VAL* 3.3 13.7 - - + +
165M PHE* 4.2 12.8 - - + -
221M ASN* 4.1 8.1 - - - +
224M PHE* 4.0 15.3 - - + -
225M LEU* 3.9 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M HIS* 3.5 16.8 - + + +
75M GLU* 4.5 4.5 - - - -
97M SER* 5.9 0.2 - - - -
111M PHE* 3.5 37.0 - + + -
112M LEU* 1.3 75.6 - - - +
114M ALA* 1.3 77.4 + - - +
115M SER* 4.1 1.8 - - - -
147M PHE* 3.7 17.0 - + - -
148M ASP* 2.7 29.8 + - - -
151M VAL* 3.5 33.6 - - + +
162M ILE* 4.2 7.0 - - + -
163M VAL 2.7 26.7 + - - -
164M GLY* 3.4 22.5 - - - -
165M PHE* 2.9 31.5 + - - -
232M ILE* 3.7 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M HIS* 3.2 11.3 + - - +
75M GLU* 3.7 9.2 + - - +
113M TYR* 1.3 84.3 - - - +
115M SER* 1.3 58.8 + - - +
144M LYS* 3.0 22.1 + - - +
165M PHE 3.9 4.3 - - - -
167M TYR* 3.5 16.8 - - + -
400M NAP 3.5 37.9 - - - +
----------------------------------------------------------
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