Contacts of the strand formed by residues 219 - 224 (chain A) in PDB entry 4NTY
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 LEU 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.1 10.7 - - + -
91A VAL* 4.5 20.4 - - + -
173A CYS* 3.6 30.7 - - - -
174A PHE 3.4 9.6 - - - +
175A PHE* 3.8 9.5 - - + -
180A CYS* 4.3 0.7 - - - -
198A PHE* 3.8 41.7 - - + -
215A THR 5.2 2.0 - - - +
218A GLY* 1.3 73.5 - - - -
220A GLU* 1.3 63.7 + - - +
221A ILE* 3.8 26.2 - - + +
407A LEU* 4.3 0.9 - - + +
408A ASP* 3.4 5.9 - - - +
409A ILE* 3.0 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 3.9 5.4 + - - +
173A CYS* 3.3 1.9 - - - -
174A PHE* 2.7 53.7 + - + +
215A THR 6.0 0.9 - - - +
219A LEU* 1.3 76.2 - - - +
221A ILE* 1.3 65.1 + - - +
222A MET* 5.7 1.6 + - - +
271A GLN* 3.9 6.1 + - - -
406A VAL* 3.6 27.0 - - + +
407A LEU 3.3 3.4 - - - +
408A ASP* 2.9 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 5.7 3.6 - - + -
93A PHE* 4.7 16.8 - - + -
170A LEU* 4.2 7.2 - - + -
172A SER 3.3 4.7 - - - +
173A CYS* 3.6 33.0 - - + -
185A PHE* 4.1 13.2 - - + -
219A LEU* 3.8 23.3 - - + -
220A GLU* 1.3 75.8 - - - +
222A MET* 1.3 59.1 + - - +
223A LEU* 4.1 21.0 + - + -
246A ILE* 5.9 0.2 - - + -
405A LEU* 3.9 1.2 - - - +
406A VAL* 3.3 6.4 - - - +
407A LEU* 2.9 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.7 3.5 - - - -
171A LEU* 2.9 43.3 + - + -
172A SER* 2.7 33.5 + - - +
220A GLU* 5.7 2.2 + - - +
221A ILE* 1.3 73.0 - - - +
223A LEU* 1.3 62.8 + - - +
380A ILE* 4.0 17.5 - - + -
389A LEU* 4.6 13.0 - - + -
393A TYR* 3.9 26.5 - - - -
404A ILE* 4.0 11.4 - - + -
405A LEU 3.4 10.3 - - - +
406A VAL* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.6 44.2 - - + -
169A MET* 3.1 20.9 - - + +
170A LEU* 4.0 24.5 - - + +
171A LEU* 4.4 4.0 - - - -
221A ILE* 4.6 15.0 - - + -
222A MET* 1.3 76.4 - - - +
224A ASP* 1.3 63.5 + - - +
225A ILE* 5.1 1.8 - - + +
246A ILE* 3.8 32.8 - - + -
403A ASN 3.4 2.6 - - - +
404A ILE* 3.5 4.7 - - - +
405A LEU* 3.0 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLU 4.3 6.8 - - - +
169A MET* 2.7 37.1 + - - +
171A LEU* 4.1 15.8 - - + +
223A LEU* 1.3 74.9 - - - +
225A ILE* 1.3 65.8 + - - +
226A GLN* 3.1 15.2 + - - +
395A LYS* 4.0 12.4 + - - -
399A TYR* 2.6 37.4 + - - -
403A ASN* 3.1 17.6 - - - +
404A ILE* 4.0 11.7 - - + -
----------------------------------------------------------
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