Contacts of the strand formed by residues 251 - 258 (chain B) in PDB entry 6UPR
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 251 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL 3.5 0.3 - - - +
247B LYS* 3.3 6.3 - - - +
248B VAL* 2.9 33.4 + - - +
249B GLY 3.7 0.4 - - - -
250B ASN* 1.3 98.3 - - - +
252B LEU* 1.3 63.1 + - - +
253B VAL* 3.6 16.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLU* 4.0 39.7 - - + +
246B VAL 3.7 2.7 - - - -
247B LYS* 3.7 33.4 - - + +
251B LYS* 1.3 73.0 - - - +
253B VAL* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLU* 4.1 3.4 - - - -
246B VAL 2.9 34.6 + - - +
248B VAL* 4.8 8.7 - - + -
251B LYS* 4.3 21.1 - - + +
252B LEU* 1.3 78.6 - - - +
254B ARG* 1.3 77.6 + - - +
255B ALA* 3.3 3.2 + - + +
264B GLN* 4.2 34.1 - - + +
265B VAL 4.8 1.3 - - - +
266B GLU* 4.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN 4.1 0.4 + - - -
63B THR* 2.3 52.2 + - - +
66B ASN* 3.7 36.6 + - - +
242B SER 3.4 21.7 + - - +
243B THR* 4.5 12.8 - - - +
244B GLU 3.2 10.3 - - - +
245B GLU* 4.6 10.1 - - + +
253B VAL* 1.3 79.6 - - + +
255B ALA* 1.3 58.8 + - - +
265B VAL* 3.0 32.3 + - + +
266B GLU* 2.9 37.8 + - + +
273B PHE* 4.5 2.0 - - - -
277B ARG* 4.2 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 2.5 27.1 + - - -
244B GLU* 3.0 20.1 + - - +
246B VAL* 4.0 10.6 - - + +
248B VAL* 5.4 0.2 - - + -
253B VAL* 3.3 10.3 + - + +
254B ARG* 1.3 75.7 - - - +
256B ARG* 1.3 59.0 + - - +
257B GLN 4.2 0.4 + - - -
262B VAL* 3.6 25.4 - - + -
263B VAL 3.0 18.8 - - - +
264B GLN* 3.9 5.4 - - + -
265B VAL* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A THR 3.2 10.9 + - - -
188A THR* 3.5 16.2 - - + +
191A GLU* 2.8 42.4 + - - -
189B ASP* 3.0 23.6 + - - -
240B VAL* 3.9 11.7 - - + -
241B GLY 4.0 3.5 + - - -
242B SER* 3.8 14.8 - - - +
244B GLU* 6.5 0.2 - - + -
246B VAL* 4.8 0.2 - - - -
255B ALA* 1.3 77.3 - - - +
257B GLN* 1.3 62.2 + - - +
258B TYR* 2.9 28.3 + - + -
261B GLY 3.9 0.2 - - - +
262B VAL* 3.5 6.5 - - - -
263B VAL* 3.1 33.9 + - + +
401B GTP 3.2 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A THR* 3.4 26.8 - - - +
189A LEU 5.1 0.3 + - - -
246B VAL* 3.6 35.2 - - + +
255B ALA 4.2 1.0 + - - -
256B ARG* 1.3 70.3 - - - +
258B TYR* 1.3 80.1 + - - +
259B PRO* 4.8 0.3 - - - +
261B GLY 3.6 1.2 - - - +
262B VAL* 3.3 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASP 3.2 20.7 + - - -
186A THR* 3.4 4.5 + - - -
187A LEU 3.4 28.3 - - - -
188A THR* 3.8 6.7 - - + -
260A TRP* 4.7 3.1 - - - -
189B ASP* 2.7 26.1 + - + -
256B ARG* 2.9 30.0 + - + -
257B GLN* 1.3 87.2 - - - +
259B PRO* 1.3 71.5 - - + +
260B TRP* 3.4 40.4 - + + +
261B GLY 2.9 23.5 + - - +
263B VAL* 3.6 32.5 - - + -
401B GTP 3.2 6.4 + - - -
----------------------------------------------------------
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