Contacts of the strand formed by residues 268 - 273 (chain A) in PDB entry 5EAA
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 GLY 268 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.9 6.5 - - - -
104A GLN* 3.7 3.3 - - - +
105A THR* 2.7 39.7 + - - +
107A GLY 3.9 8.5 - - - -
254A SER 3.2 15.3 - - - -
255A SER* 4.0 2.7 - - - -
256A TYR* 4.3 5.2 - - - -
267A VAL* 1.3 78.1 - - - +
269A ALA* 1.3 56.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.9 15.7 - - + -
83A THR* 4.2 10.1 - - + -
102A THR* 3.9 19.1 - - + -
103A ALA 3.2 11.7 - - - +
105A THR* 4.2 0.7 - - - -
111A ALA* 3.3 10.9 - - - +
252A VAL 4.0 0.2 - - - +
253A ALA* 3.5 0.2 - - - -
254A SER* 3.0 41.0 + - - +
256A TYR* 5.1 1.5 - - + -
268A GLY* 1.3 76.3 - - - +
270A CYS* 1.3 60.8 + - - +
271A THR* 3.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG 4.3 0.3 - - - +
102A THR* 3.7 0.7 - - - -
103A ALA* 2.8 37.4 + - + +
105A THR* 4.0 10.7 + - - +
111A ALA* 3.6 30.7 - - + -
114A VAL* 4.8 4.5 - - + -
115A ALA* 4.2 10.5 - - - -
251A ILE* 4.6 7.9 - - - -
252A VAL 3.6 7.2 - - - -
253A ALA* 5.3 0.9 - - - -
269A ALA* 1.3 74.6 - - - +
271A THR* 1.3 62.4 + - - +
272A LEU 4.0 0.5 + - - -
284A PHE* 5.0 0.2 - - - -
287A MET* 3.9 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.2 5.4 - - - +
84A GLN* 4.8 1.9 - - + +
87A LEU* 4.2 11.9 - - + +
88A PHE* 4.0 21.1 - - + -
100A ALA* 4.5 4.5 - - + -
101A ARG 3.7 5.2 - - - +
102A THR* 2.8 31.6 + - - +
251A ILE* 3.5 6.9 - - - +
252A VAL* 2.7 61.2 + - + +
254A SER* 5.2 0.4 + - - -
269A ALA* 3.9 1.8 - - - +
270A CYS* 1.3 73.0 - - - +
272A LEU* 1.3 62.1 + - - +
273A VAL* 4.2 7.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA* 3.4 1.9 - - - -
101A ARG 2.9 34.3 + - - +
118A PHE* 4.0 23.8 - - + -
250A LEU 4.2 0.9 - - - -
251A ILE* 3.9 23.8 - - + -
270A CYS 4.0 0.4 + - - -
271A THR* 1.3 72.3 - - - +
273A VAL* 1.3 70.3 + - - +
274A ALA* 5.9 0.7 - - + -
280A VAL* 3.3 15.6 - - + +
283A ALA* 3.9 17.3 - - + +
284A PHE* 3.8 37.0 - - + +
287A MET* 4.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.9 28.0 - - + -
94A LEU* 4.1 18.2 - - + -
99A ARG* 3.3 11.9 - - - +
100A ALA* 4.2 9.6 - - + -
247A HIS 5.7 0.2 - - - +
248A LYS 4.1 5.2 - - - +
249A GLU* 3.7 9.9 - - - +
250A LEU* 3.0 57.7 + - + +
252A VAL* 5.1 0.2 - - + -
271A THR* 4.2 5.8 - - + -
272A LEU* 1.3 85.8 - - - +
274A ALA* 1.3 61.5 + - - +
280A VAL* 4.6 0.4 - - - -
----------------------------------------------------------
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