Contacts of the strand formed by residues 135 - 139 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A DIO 4.5 24.0 - - - +
130A LEU 3.7 0.2 - - - +
131A ALA* 3.4 3.5 - - - -
132A MET 2.8 34.6 + - - +
133A GLU 3.8 13.6 + - - +
134A GLY* 1.3 84.2 - - - +
136A VAL* 1.3 64.5 + - - +
137A MET* 4.0 10.0 - - + +
166A PHE* 3.9 32.3 - - + -
167A ALA 3.2 14.4 - - - +
168A GLN* 4.7 2.2 - - + -
169A LEU* 3.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 4.3 9.6 - - + -
130A LEU 3.2 11.7 - - - +
135A LYS* 1.3 74.7 - - - +
137A MET* 1.3 60.8 + - - +
146A ILE* 4.2 18.6 - - + -
151A LEU* 3.8 24.5 - - + -
154A LEU* 4.0 15.5 - - + -
156A PHE* 3.9 12.5 - - + -
166A PHE* 3.1 8.3 - - - +
167A ALA* 2.9 56.4 + - + +
168A GLN 5.0 0.7 - - - +
169A LEU* 4.1 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A DIO 4.3 7.6 - - - +
128A HIS 4.3 0.2 - - - +
129A ALA* 3.2 4.5 - - - -
130A LEU* 2.8 48.5 + - + +
132A MET* 3.7 33.0 - - + +
135A LYS* 4.2 17.3 - - + +
136A VAL* 1.3 81.4 - - - +
138A LYS* 1.3 61.2 + - - +
164A MET* 3.4 16.4 - - + -
165A GLU 3.5 6.3 - - - +
166A PHE* 4.4 6.5 - - + -
216A GLY* 5.5 0.7 - - - +
229A ILE* 3.1 32.8 - - + -
247A TRP* 3.2 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 4.0 22.7 - - + -
128A HIS 3.7 9.4 - - - +
129A ALA* 3.9 5.4 - - + -
137A MET* 1.3 76.9 - - - +
139A PRO* 1.3 93.1 + - + +
140A LEU 4.2 0.6 + - - -
142A VAL* 2.7 31.2 + - - -
144A GLY 4.8 6.2 + - - +
146A ILE* 3.9 26.0 - - + -
156A PHE* 4.4 9.6 - - + -
164A MET* 3.1 7.8 - - - +
165A GLU* 2.7 61.8 + - + +
216A GLY* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A HIS 3.5 17.5 - - - +
138A LYS* 1.3 101.8 + - + +
140A LEU* 1.3 66.6 + - - +
141A HIS* 3.8 17.3 - - + +
142A VAL* 3.3 23.4 + - + +
163A ASP 3.3 9.2 - - - +
164A MET* 3.4 6.7 - - + -
215A SER* 3.9 9.4 - - - +
216A GLY* 3.4 27.8 - - - +
229A ILE* 5.1 0.2 - - + -
231A LEU* 4.0 15.5 - - + -
----------------------------------------------------------
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