Contacts of the strand formed by residues 133 - 138 (chain B) in PDB entry 5C16
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 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 5.7 1.1 - - - -
99B PRO* 2.8 31.8 + - - +
100B LEU* 4.3 0.2 - - - +
101B PHE* 4.8 3.4 - - - +
104B GLU* 2.9 34.0 + - - +
128B THR 3.8 0.5 - - - +
129B VAL* 3.7 2.4 - - - -
130B THR* 2.8 50.0 + - + +
132B PHE* 1.3 92.3 - - + +
134B LEU* 1.3 68.4 + - - +
135B TYR* 3.7 26.2 - - + -
148B ASP* 3.5 24.3 + - - +
149B VAL 3.4 15.7 - - - +
150B PRO* 4.1 0.9 - - + -
151B LEU* 3.7 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.8 21.1 - - + -
128B THR 3.7 2.0 - - - +
129B VAL* 3.5 20.2 - - + -
133B LYS* 1.3 77.4 - - - +
135B TYR* 1.3 60.0 + - - +
147B LEU 3.7 1.6 - - - +
148B ASP* 3.6 5.0 - - - -
149B VAL* 2.7 46.8 + - + +
151B LEU* 3.7 14.1 - - + +
154B ILE* 4.6 7.4 - - + -
174B ILE* 3.7 30.3 - - + -
182B LEU* 4.8 10.8 - - + -
184B LEU* 4.9 2.9 - - + -
200B LEU* 3.4 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 4.0 16.6 - - + -
99B PRO* 3.3 36.9 - - + +
126B THR 3.5 1.3 - - - +
127B LEU* 3.5 3.8 - - - +
128B THR* 2.6 56.6 + - + +
130B THR* 5.8 0.2 - - + -
133B LYS* 3.7 22.9 - - - -
134B LEU* 1.3 75.1 - - - +
136B PHE* 1.3 64.4 + - - +
137B LYS* 4.0 30.0 + - + +
146B ILE* 3.5 40.5 - - + +
147B LEU 3.6 3.8 - - - -
148B ASP* 3.7 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.3 38.4 - - + -
115B TYR* 3.8 20.4 - - + -
123B VAL* 3.5 28.7 - - + -
124B SER 3.7 0.7 - - - -
125B GLY* 3.5 22.9 - - - -
126B THR 3.2 13.5 - - - -
127B LEU* 4.3 11.4 - - + -
135B TYR* 1.3 76.9 - - - +
137B LYS* 1.3 65.7 + - - +
145B PHE* 3.8 35.7 - + - -
146B ILE* 3.5 6.1 - - - +
147B LEU* 3.0 47.1 + - + +
184B LEU* 5.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY* 3.1 4.9 - - - -
126B THR* 2.8 36.4 + - - +
135B TYR* 4.0 24.9 + - + -
136B PHE* 1.3 78.6 - - - +
138B ASN* 1.3 67.6 + - - +
139B VAL* 5.6 3.6 - - + -
144B HIS* 4.1 29.6 - - - -
145B PHE 3.3 10.8 - - - +
146B ILE* 3.7 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL* 3.5 21.8 - - + +
124B SER* 3.1 37.4 + - - +
125B GLY* 4.5 1.4 - - - -
136B PHE* 5.0 0.2 - - + -
137B LYS* 1.3 77.6 - - - +
139B VAL* 1.3 75.8 + - - +
144B HIS* 3.7 8.8 - - - -
145B PHE* 3.0 38.9 + - + +
----------------------------------------------------------
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