Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 2A0M
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 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP 3.1 15.1 + - - +
32A ILE* 3.4 13.3 - - + +
33A VAL 2.9 25.1 + - - -
108A VAL* 3.9 2.7 - - - -
113A ALA* 1.3 75.0 - - - +
115A PRO* 1.3 78.0 - - - +
116A PHE* 3.7 5.6 + - + -
274A VAL* 3.3 26.7 - - + -
275A MET* 3.4 20.0 - - - -
276A MET 3.4 18.6 - - - -
277A MET* 3.5 12.3 - - + -
302A PHE* 3.1 44.9 - + - -
306A PHE* 4.0 21.5 - + + -
309A ARG* 4.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL 3.5 5.6 - - - +
35A ILE* 4.3 17.3 - - + -
105A VAL* 3.9 18.8 - - + -
108A VAL* 3.8 21.5 - - + -
109A LEU* 3.7 15.5 - - + -
113A ALA 3.6 8.5 - - - +
114A PHE* 1.3 87.0 - - - +
116A PHE* 1.3 58.9 + - - +
117A VAL* 4.2 0.9 - - + -
275A MET 3.4 17.3 - - - +
276A MET* 3.4 15.1 - - + +
277A MET 3.2 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.4 8.1 - - + -
33A VAL 2.9 10.1 + - - +
34A ILE* 3.3 13.6 - - + -
35A ILE 2.9 24.1 + - - +
59A PHE* 3.6 27.4 - + - -
114A PHE* 3.7 6.2 + + + -
115A PRO* 1.3 74.2 - - - +
117A VAL* 1.3 62.5 + - - +
118A ILE* 4.0 15.9 - - + -
277A MET* 3.2 43.1 - - + -
279A MET* 3.9 39.7 - - + -
299A PHE* 3.8 37.5 - + + -
302A PHE* 5.8 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.2 18.4 - - + +
37A PHE* 4.2 8.1 - - + -
101A LEU* 3.9 19.3 - - + -
105A VAL* 3.8 18.2 - - + -
115A PRO 5.0 0.4 - - - -
116A PHE* 1.3 78.9 - - - +
118A ILE* 1.3 61.2 + - - +
124A GLN* 3.7 22.6 + - - +
128A ASN* 3.8 30.3 - - - +
276A MET* 4.0 9.2 - - + -
277A MET 3.0 6.1 + - - -
278A ASP* 3.2 4.6 - - + +
279A MET* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 4.3 16.2 - - + -
35A ILE 2.9 17.5 + - - +
36A GLY* 3.9 9.2 - - - -
37A PHE 2.9 24.7 + - - -
56A PRO* 3.5 19.2 - - + +
59A PHE* 3.7 45.8 - - + -
60A ARG* 5.1 3.8 - - - +
116A PHE* 4.0 11.3 + - + -
117A VAL* 1.3 71.1 - - - +
119A GLY* 1.3 73.7 + - - +
124A GLN* 3.9 2.5 - - - -
279A MET* 3.9 27.1 - - + +
282A LEU* 4.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE 3.7 2.5 - - - -
55A GLY* 3.6 9.2 - - - -
56A PRO* 3.3 20.0 - - - +
118A ILE* 1.3 82.0 - - - +
120A GLY* 1.3 67.0 + - - -
124A GLN* 3.1 17.7 + - - -
279A MET 2.8 18.1 + - - +
281A GLU 4.8 2.2 - - - -
282A LEU* 4.4 5.1 - - - +
----------------------------------------------------------
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