Contacts of the strand formed by residues 111 - 114 (chain F) in PDB entry 2NYM
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 ILE 111 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F PHE* 6.2 0.7 - - + -
75F SER* 3.4 23.8 - - - +
80F TYR* 3.4 26.2 - - + +
82F PHE* 4.6 9.4 - - + -
100F LEU* 3.5 11.9 - - + +
103F LEU* 3.1 29.2 - - + +
104F LYS* 3.1 61.4 + - + +
107F TYR* 4.0 3.8 - - + +
108F ARG 4.0 3.1 - - - +
109F GLU 3.7 1.2 - - - -
110F ARG* 1.3 83.4 - - + +
112F THR* 1.3 65.1 + - - +
113F ILE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F GLU* 5.2 1.3 - - - +
46F GLN* 4.5 20.0 - - + -
48F VAL* 3.3 27.7 - - + +
80F TYR 3.0 14.5 + - - -
81F LEU* 3.3 19.3 - - + +
82F PHE* 2.8 31.4 + - - +
104F LYS* 4.1 9.8 + - - +
109F GLU 6.1 0.5 - - - -
111F ILE* 1.3 75.3 + - - +
113F ILE* 1.3 65.5 + - - +
114F LEU* 4.0 22.2 - - + -
154F PRO* 5.4 0.4 - - + -
157F ALA* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 4.7 10.3 - - + -
42F GLU* 4.9 0.7 - - - +
82F PHE* 4.4 11.9 - - + -
86F TYR* 3.0 32.1 - - + +
100F LEU* 4.6 17.9 - - + +
101F VAL* 4.8 20.0 - - + -
104F LYS* 4.3 31.1 - - + +
111F ILE* 5.2 6.3 - - + -
112F THR* 1.3 77.4 - - - +
114F LEU* 1.3 68.3 + - - +
149F LEU* 5.9 0.2 - - + -
153F LEU* 3.5 24.6 - - + +
154F PRO* 3.6 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F GLN* 5.0 0.9 - - + -
81F LEU* 4.9 2.9 - - + -
82F PHE 3.2 16.2 + - - +
83F MET* 4.2 20.9 - - + -
84F GLY* 3.0 21.2 + - - +
86F TYR* 2.8 15.4 + - - -
112F THR* 4.0 17.0 - - + -
113F ILE* 1.3 84.3 - - - +
115F ARG* 1.3 62.7 + - - +
153F LEU* 4.2 5.6 - - - -
154F PRO* 3.6 24.7 - - + +
155F LEU 4.3 4.7 - - - +
156F THR* 3.9 20.4 - - - +
157F ALA* 3.8 27.4 - - + +
165F CYS* 4.1 11.4 - - + +
166F LEU* 4.6 1.8 - - - -
167F HIS 5.8 0.9 - - - +
----------------------------------------------------------
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