Contacts of the strand formed by residues 135 - 139 (chain B) in PDB entry 1WYK
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 135 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B DIO 4.8 13.2 - - - -
22B DIO 5.2 6.1 - - - +
130B LEU 3.7 0.2 - - - +
131B ALA* 3.3 4.0 - - - -
132B MET 2.7 38.1 + - - +
133B GLU 3.7 14.1 + - - +
134B GLY* 1.3 81.8 - - - +
136B VAL* 1.3 60.2 + - - +
137B MET* 3.8 27.7 + - + +
166B PHE* 4.5 22.0 - - + -
167B ALA 3.3 15.0 - - - +
168B GLN* 4.6 11.0 - - + +
169B LEU* 3.5 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 4.7 1.8 - - + -
129B ALA* 4.4 7.4 - - + -
130B LEU 3.2 14.8 - - - +
131B ALA* 4.8 0.2 - - - -
135B LYS* 1.3 73.7 - - - +
137B MET* 1.3 64.2 + - - +
146B ILE* 3.9 24.2 - - + -
151B LEU* 4.2 18.4 - - + -
154B LEU* 4.1 16.4 - - + -
156B PHE* 4.0 9.7 - - + -
166B PHE* 3.2 4.5 - - - +
167B ALA* 2.9 49.3 + - + +
169B LEU* 3.7 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B DIO 4.3 11.2 - - - +
22B DIO 4.2 15.7 - - - +
128B HIS 4.4 0.2 - - - +
129B ALA* 3.1 5.7 - - - -
130B LEU* 2.9 47.4 + - + +
132B MET* 3.8 29.8 - - + +
135B LYS* 3.8 36.1 - - + +
136B VAL* 1.3 76.2 - - - +
138B LYS* 1.3 62.6 + - - +
146B ILE* 5.9 0.2 - - - -
164B MET* 3.3 29.6 - - + -
165B GLU 3.2 8.5 - - - +
166B PHE* 4.0 6.7 - - + -
216B GLY* 5.4 0.5 - - - +
229B ILE* 4.0 1.8 - - + -
247B TRP* 4.0 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 4.1 20.6 - - + -
128B HIS 3.9 2.9 - - - +
129B ALA* 3.9 13.7 - - + -
137B MET* 1.3 76.0 - - - +
139B PRO* 1.3 83.4 + - + +
140B LEU 4.0 0.8 + - - -
142B VAL* 2.6 32.3 + - - -
144B GLY 4.7 7.5 + - - +
146B ILE* 4.2 23.6 - - + -
156B PHE* 5.1 5.2 - - + -
164B MET* 3.1 10.4 - - - +
165B GLU* 2.9 72.1 + - + +
216B GLY* 5.4 0.4 - - - -
229B ILE* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS 3.3 17.3 - - - +
138B LYS* 1.3 100.4 + - + +
140B LEU* 1.3 66.5 + - - +
141B HIS* 3.2 27.0 + - + +
142B VAL* 3.2 16.7 + - + +
163B ASP 3.3 10.1 - - - +
164B MET* 3.9 3.1 - - + -
215B SER* 3.7 9.9 - - - +
216B GLY* 3.3 28.5 - - - +
229B ILE* 5.1 2.7 - - + -
230B VAL 4.3 3.8 - - - +
231B LEU* 4.2 6.7 - - + -
----------------------------------------------------------
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