Contacts of the strand formed by residues 134 - 139 (chain B) in PDB entry 2EZT
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 ALA 134 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR 3.2 18.7 + - - +
131B ALA 3.7 11.4 - - - +
132B ASP 3.4 2.0 - - - +
133B VAL* 1.3 79.9 - - - +
135B ASP* 1.3 61.1 + - - +
136B TYR 3.3 23.3 - - - +
137B ASN* 3.8 9.7 - - + +
163B VAL* 3.4 8.5 - - - +
165B VAL* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL 3.9 1.8 + - - -
134B ALA* 1.3 73.8 - - - +
136B TYR* 1.3 59.5 + - + +
137B ASN* 5.6 0.2 - - - -
156B ARG* 4.0 19.7 + - - +
157B ALA* 5.9 0.7 - - - -
160B HIS* 2.8 50.4 + - + +
162B GLY* 4.8 5.2 - - - -
163B VAL 2.7 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 3.3 5.8 - - - +
135B ASP* 1.3 83.4 - - - +
137B ASN* 1.3 58.9 + - - +
138B VAL* 3.7 40.8 - - + +
149B VAL* 4.0 12.6 - - - +
152B GLU* 3.5 18.3 - - + +
153B ALA* 3.7 39.5 - - + -
156B ARG* 3.4 49.8 - - + -
163B VAL 3.4 1.6 + - - -
164B ALA* 4.1 11.7 - - + -
165B VAL 2.6 33.7 + - - -
166B VAL* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 2.8 45.6 + - - +
130B TYR* 3.4 15.7 - - - +
131B ALA* 3.4 20.6 - - - +
134B ALA* 3.8 14.6 - - + +
136B TYR* 1.3 80.3 - - - +
138B VAL* 1.3 65.5 + - - +
165B VAL* 3.3 4.9 - - - +
167B GLN* 2.7 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 3.7 2.5 - - - +
136B TYR* 3.7 38.1 - - + +
137B ASN* 1.3 81.5 + - - +
139B THR* 1.3 63.3 + - - +
140B ALA 3.9 0.5 + - - -
149B VAL* 3.7 30.5 - - + -
165B VAL 3.1 8.1 + - - +
166B VAL* 3.3 6.1 - - + -
167B GLN* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 5.2 4.6 + - + +
116B MET* 3.9 27.4 - - + -
125B ASN* 5.2 1.2 + - - -
126B GLU* 5.6 0.5 + - - +
127B ASN* 3.8 17.9 + - - +
138B VAL* 1.3 75.7 - - - +
140B ALA* 1.3 75.2 + - - +
141B VAL* 3.7 16.5 + - + +
167B GLN* 2.7 36.1 + - + +
169B PRO* 4.3 3.6 - - + -
----------------------------------------------------------
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