Contacts of the strand formed by residues 266 - 272 (chain A) in PDB entry 4MYF
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 VAL 266 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.3 14.2 - - + -
216A PHE* 3.7 38.1 - - + -
223A THR* 3.5 10.3 - - + +
225A PHE* 3.8 15.3 - - + -
260A ALA* 3.6 22.4 - - + +
263A THR* 2.9 21.4 + - + +
265A THR* 1.3 75.2 - - - +
267A MET* 1.3 59.8 + - - +
268A MET 3.7 18.8 - - - +
294A PHE* 4.6 2.0 - - + -
301A ARG* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.4 8.3 - - + +
104A GLY* 5.9 7.2 - - - +
105A ALA 4.5 0.5 - - - +
106A PHE* 3.4 14.5 - - - -
107A PRO* 3.4 15.6 - - - +
124A MET* 4.1 15.9 - - + -
128A PHE* 3.9 30.1 - - + -
222A ASN* 3.6 24.0 - - - +
223A THR 3.0 5.9 + - - -
264A PRO 3.6 23.8 - - - +
265A THR* 3.5 12.8 - - - +
266A VAL* 1.3 73.4 - - - +
268A MET* 1.3 64.6 + - - +
301A ARG* 4.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 3.6 27.4 - - + -
101A LEU* 4.2 2.7 - - + -
106A PHE* 3.3 11.8 - - - -
107A PRO* 3.4 18.8 - - + +
109A VAL* 4.0 9.4 - - + -
120A ASN* 3.7 36.3 - - + +
124A MET* 3.7 29.8 - - - +
223A THR 3.7 1.8 + - - +
224A PHE* 3.6 22.4 - - + -
225A PHE 3.1 22.7 + - - -
266A VAL* 3.7 7.3 - - - +
267A MET* 1.3 80.3 - - - +
269A MET* 1.3 78.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.5 16.5 - - + -
107A PRO 3.3 5.7 + - - +
108A PHE* 3.3 24.0 - - + -
109A VAL 3.1 20.6 + - - -
225A PHE* 3.1 47.1 - - + +
227A PHE* 4.0 17.3 - - + -
257A CYS* 3.8 19.1 - - - -
268A MET* 1.3 84.5 - - - +
270A ASP* 1.3 67.3 + - - +
271A MET* 4.0 19.5 - - + -
290A MET 5.4 1.1 - - - +
294A PHE* 4.3 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.9 0.4 - - - -
109A VAL* 3.3 14.8 - - + +
116A GLN* 3.6 10.5 - - - +
117A SER* 2.9 21.8 + - - -
120A ASN* 2.9 31.4 + - - +
224A PHE* 3.3 16.1 - - + -
225A PHE 3.2 3.6 + - - -
226A SER* 2.7 24.1 + - - -
227A PHE* 3.0 19.8 + - - +
268A MET* 4.6 0.2 - - + -
269A MET* 1.3 85.9 - - - +
271A MET* 1.3 63.1 + - - +
272A SER* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 4.3 0.9 - - - -
108A PHE* 4.0 27.4 - - + -
109A VAL 3.0 7.3 + - - +
110A ILE* 3.9 18.6 - - + +
111A GLY* 2.9 27.0 + - - -
116A GLN* 3.2 2.0 + - - -
227A PHE 3.2 5.8 - - - +
229A VAL* 3.7 19.7 - - + -
269A MET* 4.0 17.3 - - + -
270A ASP* 1.3 78.2 - - - +
272A SER* 1.3 60.6 + - - +
274A LEU* 5.5 2.6 + - + +
287A ALA* 3.6 45.3 - - - +
290A MET* 3.8 24.9 - - + -
291A PHE 4.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY 5.5 0.2 - - - -
112A GLY 3.5 5.6 - - - -
113A GLY 3.8 0.7 + - - -
114A ASN* 3.7 33.5 - - - -
116A GLN* 2.8 30.0 + - - +
117A SER* 3.9 7.8 + - - -
226A SER* 5.3 0.3 + - - -
227A PHE 3.0 8.2 + - - -
228A ASP* 4.4 5.8 - - - -
229A VAL* 3.0 28.1 + - - +
270A ASP* 4.2 2.8 + - - -
271A MET* 1.3 73.9 - - - +
273A GLU* 1.3 66.8 + - - +
274A LEU 3.4 3.1 - - - -
----------------------------------------------------------
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