Contacts of the strand formed by residues 253 - 258 (chain B) in PDB entry 3NMV
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 ARG 253 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 4.1 8.0 - - - +
251B ASP 5.0 0.2 - - - +
252B SER* 1.3 80.7 - - - +
254B ALA* 1.4 68.8 + - - +
255B VAL* 3.7 18.2 - - + -
264B ALA* 4.9 3.4 - - + -
266B SER* 3.4 22.4 + - - +
268B ASP* 2.9 36.2 + - - +
334B LEU* 3.5 1.4 - - - +
335B ALA 3.0 31.4 + - - +
340B TRP* 3.3 51.7 + - + +
343B MET 4.9 2.6 + - - -
344B THR* 5.7 0.6 - - - +
345B ASN* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 3.8 4.0 - - + +
246B VAL* 3.7 37.2 - - + -
253B ARG* 1.4 72.3 - - - +
255B VAL* 1.3 66.1 + - - +
264B ALA 3.7 0.3 - - - -
265B LEU* 2.8 27.4 + - + -
266B SER* 3.1 9.6 + - - +
332B LEU* 4.7 1.3 - - + -
333B ILE 3.4 5.8 - - - -
334B LEU* 3.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ARG* 3.7 11.2 - - - -
254B ALA* 1.3 79.4 - - - +
256B LEU* 1.3 63.1 + - - +
262B PRO* 3.9 15.3 - - + -
263B LEU 3.7 12.1 - - - +
264B ALA* 4.3 3.4 - - - -
332B LEU* 3.6 5.6 - - - +
333B ILE* 2.8 46.4 + - + +
340B TRP* 3.4 30.5 - - + -
345B ASN* 3.5 25.4 - - + +
349B CYS* 3.8 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 4.4 10.8 - - + -
255B VAL* 1.3 72.8 - - - +
257B CYS* 1.3 60.6 + - - +
258B ARG* 3.2 37.7 + - + +
262B PRO* 3.5 2.8 - - - +
263B LEU* 2.7 56.3 + - + +
265B LEU* 4.1 13.4 - - + +
323B VAL* 4.1 20.6 - - + -
325B ARG* 5.9 0.2 - - - -
329B ASP* 3.7 18.2 - - + +
331B CYS 3.6 8.3 - - - +
332B LEU* 4.2 5.3 - - + +
411B LEU* 3.3 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL 4.1 1.4 + - - -
256B LEU* 1.3 72.7 - - - +
258B ARG* 1.3 58.4 + - - +
259B GLY 3.1 9.7 + - - -
260B LYS* 4.5 2.5 - - - -
261B THR 4.1 1.6 - - - -
329B ASP* 3.7 0.7 - - - -
330B ASP* 2.9 27.9 + - - -
331B CYS* 2.9 31.2 + - - +
333B ILE* 4.5 1.1 - - + -
349B CYS* 3.6 32.1 - - + -
353B ARG* 3.3 43.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 3.2 22.8 + - + +
257B CYS* 1.3 68.9 - - - +
259B GLY* 1.3 51.6 + - - +
260B LYS 2.8 15.9 + - - -
261B THR* 3.0 31.9 + - - +
263B LEU* 4.1 25.0 - - + +
323B VAL* 4.7 7.0 - - - +
324B ARG 3.0 25.1 + - - -
325B ARG* 3.8 1.2 - - - +
326B VAL* 3.7 17.6 - - - +
328B GLU* 4.5 12.9 - - + +
329B ASP* 2.6 45.2 + - - +
----------------------------------------------------------
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