Contacts of the strand formed by residues 262 - 267 (chain A) in PDB entry 5DO7
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 LYS 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.1 37.1 + - - +
76A VAL* 4.9 1.6 - - + -
80A GLN* 4.0 19.1 - - - +
81A ILE 2.8 14.6 + - - +
82A MET* 3.1 22.0 - - + +
83A CYS* 2.8 31.7 + - - -
260A PHE* 3.3 2.4 - - - -
261A ASP* 1.3 81.0 - - + +
263A ILE* 1.3 53.6 + - - +
274A CYS* 3.8 19.1 + - - -
275A GLY* 3.4 18.4 - - - +
276A THR* 4.8 0.7 - - - +
279A GLU* 5.5 2.0 - - - -
337A LYS* 5.8 7.0 - - - +
338A THR* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A CYS* 3.3 22.2 - - + +
85A LEU* 5.5 2.0 - - + -
257A PHE* 4.0 8.1 - - + +
260A PHE* 4.7 10.0 + - + +
261A ASP 4.3 0.4 - - - -
262A LYS* 1.3 70.8 - - - +
264A ALA* 1.3 63.7 + - - +
265A ILE* 4.9 11.7 - - + -
273A PHE* 4.0 3.2 - - + -
274A CYS* 3.3 1.4 - - - -
275A GLY 2.8 45.1 + - - +
276A THR 4.6 0.4 - - - -
277A PRO* 4.4 16.8 - - + -
280A MET* 4.0 38.1 - - + -
298A PHE* 3.6 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.0 19.7 - - + -
82A MET* 4.0 9.9 - - + -
83A CYS 2.8 9.7 + - - -
84A ILE* 3.5 13.0 - - + +
85A LEU 3.3 20.8 + - - -
263A ILE* 1.3 78.1 - - - +
265A ILE* 1.3 64.3 + - - +
266A LEU* 5.3 1.6 - - + -
271A LEU* 5.1 3.8 - - + -
273A PHE 3.1 14.1 - - - +
274A CYS* 3.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.6 36.6 - - + +
87A SER* 5.2 0.4 - - - +
263A ILE* 4.9 9.2 - - + -
264A ALA* 1.3 78.8 - - - +
266A LEU* 1.3 75.1 + - - +
271A LEU* 3.9 0.7 - - - +
272A ILE* 2.8 42.9 + - + +
273A PHE* 2.8 18.7 + - + +
280A MET* 4.7 23.1 - - + -
284A PHE* 6.3 0.7 - - + -
298A PHE 5.7 2.2 - - - +
301A TYR* 5.6 2.5 - - + -
302A MET* 5.4 4.3 - - + +
305A THR* 3.6 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.3 14.6 - - + -
72A VAL* 4.7 8.5 - - + -
74A LEU* 5.7 1.6 - - + -
84A ILE* 4.9 10.8 - - + -
85A LEU 3.4 6.2 + - - +
86A GLY* 3.9 0.9 - - - -
87A SER* 3.3 26.7 + - - -
90A SER 4.4 5.1 - - - +
91A GLY* 4.0 5.8 - - - +
92A LYS* 3.6 43.7 - - + +
95A LEU* 4.3 14.1 - - + -
264A ALA* 4.1 2.9 + - + +
265A ILE* 1.3 87.9 - - - +
267A SER* 1.3 59.1 + - - +
268A PHE 4.2 0.7 - - - -
269A GLY 4.8 4.3 - - - +
270A GLU 3.5 10.8 - - - +
271A LEU* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 4.0 8.2 + - - -
90A SER 4.2 0.4 - - - -
265A ILE 4.4 0.2 - - - -
266A LEU* 1.3 73.0 - - - +
268A PHE* 1.3 90.0 + - - +
269A GLY 3.2 0.4 - - - -
270A GLU* 2.8 31.3 + - - +
272A ILE* 3.9 13.9 - - - +
305A THR 3.5 25.0 + - - -
306A SER* 4.1 4.3 - - - -
307A VAL* 4.6 1.7 + - - +
322A VAL* 4.2 9.1 - - - +
----------------------------------------------------------
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