Contacts of the strand formed by residues 220 - 224 (chain B) in PDB entry 1E5E
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 220 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 3.5 2.6 - - - +
83B THR* 2.7 48.0 + - - +
85B SER 3.4 10.6 - - - -
86B GLY* 3.6 0.9 - - - -
89B ALA* 4.1 0.7 - - - -
205B HIS 3.2 11.4 - - - -
207B ALA* 3.9 1.1 - - - +
219B ALA* 1.3 76.1 - - - +
221B LEU* 1.3 68.3 + - - +
245B ILE* 5.2 0.2 - - - +
253B ILE* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 4.3 14.1 - - + -
71B ILE* 3.9 28.0 - - + -
80B CYS* 3.8 23.8 - - - -
81B VAL 3.5 3.1 - - - -
82B ALA* 4.0 16.8 - - + -
89B ALA* 3.7 3.7 - - - +
203B VAL 4.6 0.4 - - - -
204B VAL* 3.2 8.8 - - - +
205B HIS* 2.8 44.0 + - + +
207B ALA* 3.7 17.9 - - + -
211B ILE* 3.7 33.2 - - + -
220B GLY* 1.3 80.4 - - - +
222B ILE* 1.3 61.7 + - - +
223B CYS* 4.7 1.1 - - - -
253B ILE* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS* 3.0 5.7 - - - -
81B VAL* 2.8 46.2 + - + +
83B THR* 4.0 21.3 - - + -
89B ALA* 3.7 19.5 - - + +
92B ALA* 4.3 3.1 - - + -
93B THR* 3.5 27.6 - - - +
202B VAL* 3.8 19.1 - - + -
203B VAL 3.7 2.2 - - - -
204B VAL* 4.4 2.9 - - + -
221B LEU* 1.3 76.1 - - - +
223B CYS* 1.3 63.1 + - - +
229B LEU* 3.4 9.1 - - + +
232B ILE* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.5 31.9 - - - -
75B GLU* 4.1 15.5 - - + -
77B THR* 3.5 23.4 - - + +
79B ALA 3.4 4.0 - - - -
80B CYS* 4.0 7.0 - - - -
202B VAL* 3.5 5.7 - - - +
203B VAL* 2.8 49.8 + - + +
205B HIS* 4.4 9.6 - - - -
221B LEU* 4.7 0.4 - - - -
222B ILE* 1.3 82.3 - - - +
224B GLY* 1.3 58.7 - - - +
229B LEU* 4.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 3.5 14.1 - - - -
78B GLU 3.4 3.6 + - - -
79B ALA* 3.0 32.8 + - - +
201B ASP 3.9 13.5 - - - -
202B VAL* 4.8 0.9 - - - -
223B CYS* 1.3 75.9 - - - +
225B LYS* 1.3 65.3 + - - +
229B LEU* 3.5 11.5 - - - +
----------------------------------------------------------
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