Contacts of the strand formed by residues 2202 - 2205 (chain B) in PDB entry 4YNM
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 MET2202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2080B VAL* 3.7 37.9 - - + -
2081B LYS 4.2 2.0 - - - +
2082B PRO* 3.5 41.7 - - + -
2083B LEU 6.0 0.7 - - - +
2173B VAL* 4.8 0.9 - - + -
2174B VAL 3.5 7.2 - - - +
2176B GLU* 4.3 1.2 + - - +
2197B ASN* 3.9 4.9 + - - +
2198B LEU* 2.9 33.9 + - + +
2199B ASP* 3.0 23.0 + - + +
2200B SER* 3.6 18.4 - - - +
2201B GLY* 1.3 81.1 - - - +
2203B VAL* 1.3 69.1 + - - +
2235B TYR* 6.1 2.2 - - + -
2260B PHE* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172B GLU 3.4 1.7 - - - +
2173B VAL* 3.3 5.0 - - - +
2174B VAL* 2.9 41.1 + - + +
2176B GLU* 4.3 7.9 - - + -
2179B PHE* 4.0 24.7 - - + -
2195B CYS* 3.8 16.4 - - + -
2196B LEU 3.3 13.5 - - - +
2198B LEU* 4.1 2.5 - - - +
2202B MET* 1.3 81.7 - - - +
2204B ILE* 1.3 77.8 + - - +
2205B ASP 4.0 1.6 - - - +
2260B PHE* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2075B ASN* 4.2 13.2 - - - +
2169B TYR* 3.7 33.1 - - + +
2170B LEU 3.7 5.8 - - - -
2171B GLY* 3.5 37.2 - - - +
2172B GLU 3.5 3.1 - - - +
2173B VAL* 4.2 7.0 - - + -
2195B CYS* 3.0 6.9 - - - +
2196B LEU* 2.7 42.2 + - + +
2198B LEU* 3.5 25.3 - - + +
2203B VAL* 1.3 71.3 - - - +
2205B ASP* 1.3 57.2 + - - +
2206B SER 3.9 0.3 + - - -
2236B ARG* 5.9 0.4 - - - -
2237B ILE* 3.9 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171B GLY* 3.6 0.6 - - - -
2172B GLU* 2.7 42.8 + - - +
2174B VAL* 4.3 7.9 - - + -
2179B PHE* 4.0 17.7 - - + -
2182B ARG* 2.8 26.0 + - - +
2187B TYR* 2.6 32.9 + - - -
2194B TYR 3.9 3.4 - - - -
2195B CYS* 4.3 3.4 - - - -
2203B VAL 3.7 0.6 + - - -
2204B ILE* 1.3 70.6 - - - +
2206B SER* 1.3 57.9 + - - +
2207B TYR* 2.8 30.3 + - - +
2208B ARG 5.2 0.4 - - - -
2209B MET 3.8 2.6 + - - +
----------------------------------------------------------
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