Contacts of the strand formed by residues 272 - 278 (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 GLN 272 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D LYS* 6.1 2.0 - - - +
244F VAL 4.3 0.5 - - - +
245F MET 3.0 13.6 + - - +
246F GLU* 3.9 23.1 - - - +
247F GLY* 3.4 14.4 + - - -
260F PHE* 4.8 0.3 - - - +
263F PRO* 5.0 0.4 - - - -
270F GLY 4.4 0.4 + - - -
271F ASN* 1.3 89.2 + - - +
273F ALA* 1.3 60.7 + - - +
288F GLN* 3.0 32.0 + - + +
289F PHE 4.0 10.8 - - - +
290F ASP* 3.8 25.4 + - - +
291F PRO* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F GLY* 3.8 3.1 - - - -
260F PHE 3.3 15.0 - - - +
261F SER* 3.5 13.2 - - - +
262F ALA 3.9 1.3 - - - -
263F PRO* 3.5 34.8 - - + -
271F ASN* 4.5 0.2 - - - +
272F GLN* 1.3 73.5 - - - +
274F ALA* 1.3 58.6 + - - +
288F GLN* 3.3 1.1 - - - -
289F PHE* 2.6 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F GLY 3.6 15.5 + - - +
248F TYR* 4.3 9.2 - - + -
259F ILE* 3.4 11.5 - - - +
260F PHE 3.1 7.8 + - - +
261F SER* 3.3 13.6 + - - +
273F ALA* 1.3 76.3 - - - +
275F ILE* 1.3 73.8 + - - +
286F PHE* 5.5 0.4 - - + -
287F LEU 2.9 17.9 - - - +
288F GLN* 3.4 21.3 - - + -
289F PHE* 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F THR* 3.6 23.1 - - + -
54F VAL 3.5 13.9 - - - +
55F CYS* 4.2 4.0 - - - -
68F LEU* 4.0 32.5 - - + +
71F ILE* 4.2 8.7 - - + -
72F GLY* 4.0 26.2 - - - +
259F ILE* 4.1 3.6 - - - -
261F SER* 3.8 13.7 - - - +
274F ALA* 1.3 81.5 - - - +
276F MET* 1.3 60.8 + - - +
277F GLU* 4.1 0.4 + - + -
285F SER 4.1 0.5 - - - +
286F PHE* 3.7 6.1 - - - -
287F LEU* 2.8 46.1 + - + +
289F PHE* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F THR* 4.5 1.1 - - - -
54F VAL* 2.7 68.4 + - + +
163F ILE* 4.7 6.5 - - + -
236F LEU* 4.9 8.3 - - + -
238F SER* 4.6 14.8 - - - +
250F TRP* 5.8 0.2 - - - -
257F VAL* 4.7 7.0 - - - -
259F ILE* 3.6 15.5 - - + +
275F ILE* 1.3 71.9 - - - +
277F GLU* 1.3 68.1 + - - +
278F LEU* 3.2 32.3 - - + -
284F TYR* 5.1 4.3 - - - -
285F SER 3.5 8.1 - - - +
286F PHE* 3.1 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D HIS* 4.8 5.1 - - - +
494D ASN* 5.4 4.6 + - - +
496D LEU* 3.0 34.0 - - + +
52F VAL 3.7 4.9 - - - +
53F THR* 3.7 22.9 + - + +
71F ILE 5.0 0.5 - - - +
72F GLY* 4.2 11.6 - - - +
275F ILE* 5.2 1.3 - - + +
276F MET* 1.3 76.1 - - - +
278F LEU* 1.3 65.9 + - - +
279F ASP* 5.2 0.4 - - - +
283F LYS 3.0 15.8 - - - +
285F SER* 2.9 35.6 + - - +
287F LEU* 3.4 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D TYR* 5.2 0.9 - - - -
50F CYS* 5.0 1.1 - - + -
51F PRO* 3.1 1.4 - - - +
52F VAL* 2.8 43.1 + - + +
54F VAL* 4.2 8.1 - - + -
159F VAL* 3.6 22.2 - - + -
163F ILE* 3.7 20.4 - - + -
276F MET* 3.2 37.0 - - + -
277F GLU* 1.3 77.5 - - - +
279F ASP* 1.3 68.3 + - - +
282F LEU* 3.6 31.9 - - + -
283F LYS 3.7 14.6 - - - +
284F TYR* 4.7 6.1 - - + -
----------------------------------------------------------
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