Contacts of the strand formed by residues 127 - 132 (chain E) in PDB entry 2ESV
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 GLU 127 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E PRO 3.8 2.4 + - - +
126E PRO* 1.3 76.0 - - - +
128E VAL* 1.3 60.3 + - - +
149E LEU 3.7 0.7 - - - +
150E ALA* 3.3 2.9 - - - -
151E THR* 2.8 49.7 + - - +
152E GLY* 6.1 0.8 - - - -
190E ARG* 5.1 8.1 + - - -
238E VAL* 4.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E PRO* 4.1 3.3 + - + -
127E GLU* 1.3 79.3 - - - +
129E ALA* 1.3 63.7 + - - +
148E CYS* 3.8 24.7 - - - -
149E LEU 3.4 2.7 - - - +
150E ALA* 4.4 4.9 - - + -
213E CYS* 4.0 8.7 - - - +
215E VAL* 3.6 22.0 - - + -
238E VAL* 3.5 39.7 - - + +
239E SER 4.1 5.3 - - - +
240E ALA* 3.3 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ASP* 4.2 14.6 - - - +
128E VAL* 1.3 75.9 - - - +
130E VAL* 1.3 62.8 - - - +
131E PHE* 3.7 24.9 - - + -
147E VAL 4.0 0.3 - - - +
148E CYS* 3.5 5.4 - - - -
149E LEU* 2.8 39.8 + - + +
240E ALA* 3.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ASP* 3.0 19.5 + - - +
130D SER* 3.1 27.0 + - - +
129E ALA* 1.3 73.0 - - - +
131E PHE* 1.3 67.5 + - - +
146E LEU* 4.2 25.4 - - + -
147E VAL 3.6 6.5 - - - +
148E CYS* 4.7 0.4 - - - -
162E TRP* 4.5 7.2 - - + -
211E PHE 5.3 0.9 - - - +
212E ARG 5.2 0.2 - - - -
213E CYS* 3.7 24.7 - - + +
240E ALA* 3.5 37.7 - - + +
241E GLU* 4.2 5.4 - - - +
242E ALA* 4.2 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LEU* 3.7 27.1 - - + +
128D ARG 3.5 3.6 - - - +
129D ASP* 3.6 21.1 - - + -
134D ASP* 5.4 4.0 - - + -
135D LYS* 3.3 35.7 - - - -
137D VAL* 3.7 24.0 - - + -
129E ALA* 3.7 30.1 - - + -
130E VAL* 1.3 76.7 - - - +
132E GLU* 1.3 64.4 + - - +
146E LEU* 3.5 7.3 - - - +
147E VAL* 2.8 46.6 + - + +
149E LEU* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LEU* 3.3 20.7 - - - +
128D ARG* 2.7 19.3 + - + +
129D ASP 5.0 1.1 - - - -
130D SER* 3.3 37.2 + - - +
130E VAL* 3.9 1.1 + - + -
131E PHE* 1.3 73.6 - - - +
133E PRO* 1.3 75.2 - - + +
146E LEU* 5.2 1.1 - - - -
204E TRP* 3.8 24.1 - - + -
242E ALA* 4.1 8.5 - - + +
243E TRP 4.9 2.9 + - - +
245E ARG* 2.6 40.8 + - - -
----------------------------------------------------------
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