Contacts of the strand formed by residues 255 - 265 (chain B) in PDB entry 3K3B
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 LEU 255 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B MET 3.5 1.7 - - - +
246B LYS* 3.2 4.5 - - - -
247B GLU* 2.8 72.0 + - + +
253B GLU* 3.8 17.9 - - + +
254B GLU* 1.3 80.3 - - - +
256B VAL* 1.3 63.1 + - - +
257B LYS* 3.8 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B HIS* 6.2 2.0 - - + -
245B MET 3.3 8.5 - - - +
246B LYS* 4.2 18.4 - - + -
254B GLU* 3.8 23.6 + - + +
255B LEU* 1.3 73.5 - - - +
257B LYS* 1.3 67.4 + - - +
258B ILE* 5.3 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.0 35.4 + - - +
95B MET* 3.5 22.9 - - - +
96B GLY* 3.9 4.7 - - - -
147B LEU* 5.6 0.2 - - - +
150B ASN* 6.2 0.6 - - - +
152B THR* 5.3 3.6 + - - -
244B HIS* 4.6 0.2 - - - +
245B MET* 2.8 58.0 + - + +
247B GLU* 3.7 23.6 + - - +
255B LEU* 3.8 25.8 + - + +
256B VAL* 1.3 77.6 - - - +
258B ILE* 1.3 71.5 + - - +
259B GLY 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY* 3.3 21.7 + - - +
97B TYR* 4.6 1.0 - - - +
98B ASN* 4.7 7.1 + - - +
242B THR* 4.1 16.8 - - + -
243B ILE 3.4 8.1 - - - +
244B HIS* 3.6 36.3 - - + +
256B VAL* 5.3 8.3 - - + +
257B LYS* 1.3 80.0 - - - +
259B GLY* 1.3 60.2 + - - +
260B LYS* 4.3 1.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.1 33.4 - - - -
97B TYR 3.7 3.1 - - - -
98B ASN* 4.9 0.2 - - - -
241B VAL 3.9 0.3 - - - +
242B THR* 3.4 4.9 - - - +
243B ILE* 2.7 40.5 + - - +
245B MET* 3.7 5.4 - - - +
258B ILE* 1.3 76.3 - - - +
260B LYS* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.5 5.1 - - - +
97B TYR 3.2 10.1 + - - +
98B ASN* 3.4 29.9 - - - +
99B CYS 2.9 26.2 + - - -
159B SER* 5.1 1.2 + - - -
199B LEU* 6.4 0.4 - - - +
201B GLU* 4.9 8.9 + - - -
240B SER* 3.9 17.2 + - - -
241B VAL 3.4 5.6 - - - +
242B THR* 3.5 24.2 + - + +
258B ILE* 6.0 0.9 - - + -
259B GLY* 1.3 74.6 - - - +
261B LEU* 1.3 63.8 + - - +
262B ASN* 3.2 28.7 - - - +
323B SER* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 5.1 2.7 - - + -
89B ILE* 3.6 30.7 - - + -
90B LEU* 4.8 6.5 - - + -
93B VAL* 3.8 15.0 - - + +
99B CYS* 3.3 20.2 - - + +
101B ILE* 4.3 8.7 - - + -
139B THR* 3.6 32.5 - - + +
239B PHE 3.7 1.6 - - - +
240B SER* 3.3 3.3 - - - -
241B VAL* 2.9 46.6 + - + +
243B ILE* 6.1 0.2 - - + -
260B LYS* 1.3 75.3 - - - +
262B ASN* 1.3 62.5 + - - +
263B LEU* 3.6 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B CYS 2.9 8.7 + - - -
100B THR* 3.1 11.6 + - + +
101B ILE 2.8 28.9 + - - +
238B VAL* 4.6 2.0 - - + -
239B PHE 3.7 3.6 - - - -
240B SER* 2.6 25.3 + - - +
260B LYS* 3.2 19.0 - - - +
261B LEU* 1.3 73.0 - - - +
263B LEU* 1.3 63.9 + - - +
264B VAL* 3.9 3.8 - - + -
319B ILE 5.7 0.6 + - - -
320B LEU* 3.5 30.7 - - + +
323B SER* 2.8 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.6 20.2 - - + -
115B MET* 4.0 9.6 - - - +
135B ILE* 3.7 22.2 - - + -
136B ILE* 3.5 45.7 - - + +
139B THR* 4.6 7.2 - - + -
140B LEU* 6.2 0.7 - - + -
237B SER 3.5 3.3 - - - +
239B PHE* 2.7 47.8 + - + +
241B VAL* 4.8 5.4 - - + -
261B LEU* 3.6 35.9 - - + +
262B ASN* 1.3 75.8 - - - +
264B VAL* 1.3 60.8 + - - +
265B ASP* 3.9 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 4.1 8.3 - - + -
101B ILE 2.8 13.3 + - - +
102B PHE* 3.4 30.3 - - + -
103B ALA 2.8 28.6 + - - -
115B MET* 3.5 7.7 - - - +
236B HIS* 4.9 1.6 - - + -
237B SER 3.5 7.6 - - - +
238B VAL* 4.2 18.4 - - + -
262B ASN 4.3 3.4 - - - +
263B LEU* 1.3 74.6 - - - +
265B ASP* 1.3 64.0 + - - +
266B LEU* 3.6 29.5 + - + -
316B LEU* 4.2 11.7 - - + -
320B LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA 4.4 1.1 - - - -
111B LYS* 3.2 29.4 - - - +
112B THR* 2.4 39.6 + - - +
115B MET* 4.4 11.2 - - + -
116B GLU* 4.5 10.3 - - + +
221B ARG* 5.5 0.7 + - - -
235B SER 3.8 2.3 - - - +
236B HIS* 3.3 0.7 - - - -
237B SER* 2.7 51.8 + - - +
263B LEU 3.9 1.4 + - - +
264B VAL* 1.3 71.0 - - - +
266B LEU* 1.3 65.4 + - - +
370B MG 4.5 1.3 - - - -
371B ADP 4.7 0.2 + - - -
----------------------------------------------------------
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