Contacts of the strand formed by residues 221 - 226 (chain A) in PDB entry 3NY5
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 GLU 221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 2.9 53.5 + - - +
160A PHE* 3.5 31.7 - - + -
199A ARG* 3.6 4.3 - - - +
200A ILE* 3.4 37.7 + - + +
220A GLU* 1.3 76.1 + - - +
222A LEU* 1.3 62.7 + - - +
223A HIS* 3.9 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.6 26.9 - - + -
158A ARG 2.9 8.8 + - - +
159A VAL* 4.4 15.3 - - + -
160A PHE* 2.9 25.1 + - - -
177A VAL* 4.5 13.7 - - + -
181A LEU* 5.2 1.3 - - + -
197A VAL* 4.0 17.0 - - + -
198A TYR 3.1 13.7 - - - +
199A ARG* 3.7 17.3 - - + -
208A ILE* 4.3 5.2 - - + -
214A ILE* 4.5 7.4 - - + -
217A LEU* 4.0 30.5 - - + -
220A GLU* 4.9 3.1 - - + -
221A GLU* 1.3 78.2 - - - +
223A HIS* 1.3 70.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.5 39.0 - + + +
197A VAL* 3.3 3.7 - - - +
198A TYR* 2.7 48.1 + - + +
200A ILE* 3.8 31.7 - - + +
221A GLU* 3.9 19.5 + - - +
222A LEU* 1.3 84.1 - - - +
224A VAL* 1.3 64.1 + - - +
225A GLU* 5.7 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 4.0 10.3 - - + -
160A PHE 2.9 13.3 + - - +
161A LEU* 4.1 10.5 - - + -
162A PRO* 3.4 27.2 - - + +
181A LEU* 3.7 28.9 - - + -
185A LEU* 4.3 14.1 - - + -
195A CYS* 3.7 32.5 - - + -
196A ALA 3.3 4.0 - - - +
197A VAL* 4.2 5.6 - - + -
210A TRP* 4.2 12.1 - - + -
223A HIS* 1.3 77.1 - - - +
225A GLU* 1.3 66.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 4.8 2.0 - - - -
195A CYS* 3.1 5.9 - - - +
196A ALA 2.7 35.6 + - - -
198A TYR* 3.8 25.0 + - + -
223A HIS* 4.1 5.3 - - + +
224A VAL* 1.3 77.7 - - - +
226A VAL* 1.3 68.7 + - - +
205B LYS 4.8 3.8 - - - +
206B LYS* 5.4 3.1 - - - +
207B PRO* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 3.7 27.7 - - + +
190A LEU* 3.8 21.5 - - + -
194A CYS* 3.7 18.6 - - + +
195A CYS* 4.1 4.7 - - - +
225A GLU* 1.3 80.0 - - - +
227A LEU* 1.3 75.3 + - - +
228A GLU* 3.7 3.8 + - - +
207B PRO* 4.1 7.8 - - - +
----------------------------------------------------------
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