Contacts of the strand formed by residues 256 - 262 (chain C) in PDB entry 4NY0
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 256 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TRP* 4.5 5.5 + - - -
127C ARG* 2.7 57.0 + - - +
255C LYS* 1.3 79.4 - - - +
257C CYS* 1.3 63.4 + - - +
258C PHE* 3.5 16.5 - - + -
272C LEU 3.8 0.5 - - - +
273C ALA* 3.6 0.9 - - - -
274C ILE* 2.9 32.7 + - - +
343C LEU* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C LYS* 2.6 45.5 - - - +
256C GLU* 1.3 75.6 - - - +
258C PHE* 1.3 72.0 + - - +
271C GLU* 3.7 18.4 - - + +
272C LEU 3.1 10.8 - - - +
273C ALA* 4.0 3.1 - - - -
283C LEU* 3.9 21.1 - - - -
288C CYS* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ARG* 3.9 12.6 - - - -
256C GLU* 3.5 35.7 - - + -
257C CYS* 1.3 81.5 - - - +
259C LYS* 1.3 65.7 + - - +
260C CYS* 3.3 6.5 + - - -
271C GLU* 3.6 3.1 - - - -
272C LEU* 3.0 35.4 + - + +
274C ILE* 4.1 13.2 - - + -
336C ILE* 4.2 14.6 - - + -
339C ASN* 4.9 5.4 - - + -
340C MET* 3.3 53.8 - - + -
343C LEU* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C PHE* 1.3 72.6 - - - +
260C CYS* 1.3 61.9 + - - +
270C VAL 3.6 7.8 + - - +
271C GLU* 3.5 32.0 + - + +
332C PRO* 3.5 22.8 - - + +
336C ILE* 5.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C PHE 3.5 14.4 - - - -
259C LYS* 1.3 76.0 - - - +
261C ALA* 1.3 59.1 + - - +
262C LEU* 5.6 0.2 - - - -
269C SER* 3.3 7.5 - - - -
270C VAL* 2.7 39.5 + - - +
272C LEU* 3.8 21.5 - - - -
329C VAL* 3.8 21.5 - - + -
330C THR 3.3 19.1 - - - +
331C ALA* 4.1 8.5 - - + -
332C PRO* 4.6 2.9 - - - -
340C MET* 4.0 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C CYS* 1.3 82.4 - - - +
262C LEU* 1.3 64.4 + - - +
267C ILE* 3.3 31.2 - - + -
268C ILE 3.3 8.3 - - - +
269C SER* 3.9 9.0 - - - -
270C VAL* 4.3 0.7 - - - +
328C THR 3.6 0.5 - - - +
329C VAL* 3.5 5.1 - - - -
330C THR* 2.8 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C CYS* 5.6 0.2 - - - -
261C ALA* 1.3 74.8 - - - +
263C GLY* 1.3 61.7 + - - +
266C TRP 4.3 0.7 - - - +
267C ILE* 3.4 4.6 - - - -
268C ILE* 2.8 38.9 + - + +
270C VAL* 3.8 27.6 - - + -
272C LEU* 4.5 13.0 - - + -
282C TYR* 4.9 7.6 - - + -
293C LEU* 3.6 28.7 - - + -
327C LEU* 4.1 17.9 - - + -
328C THR 3.4 12.3 - - - +
329C VAL* 3.8 21.8 - - + -
----------------------------------------------------------
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