Contacts of the strand formed by residues 330 - 335 (chain B) in PDB entry 1OFD
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 ALA 330 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 4.1 7.2 - - - +
227B ASN 3.3 7.6 - - - -
230B ILE* 5.6 5.4 - - + -
274B LEU* 5.7 0.2 - - + -
296B VAL* 5.1 6.7 - - + -
326B TRP 6.2 0.2 - - - +
328B GLY 4.1 2.2 - - - +
329B PRO* 1.3 76.2 - - - +
331B LEU* 1.3 59.6 + - - +
332B LEU* 3.9 25.4 - - + -
344B LEU* 3.3 9.8 - - - +
345B ASP* 3.0 45.9 + - + +
350B ARG* 3.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.2 34.7 - - + +
225B GLY 3.7 2.1 - - - +
226B HIS* 3.7 3.6 - - - -
227B ASN* 2.8 37.1 + - + +
330B ALA* 1.3 70.8 - - - +
332B LEU* 1.3 71.8 + - - +
333B VAL* 4.0 5.2 - - + -
342B ALA* 4.0 14.8 - - + -
343B GLY 3.6 11.2 - - - +
344B LEU* 3.7 19.1 - - + -
350B ARG* 3.7 12.2 - - + +
351B PRO 3.5 20.9 - - - +
352B ALA* 4.0 15.3 - - + -
364B LEU* 4.7 3.6 - - + -
366B SER* 4.2 8.7 - - - +
384B LEU* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.5 18.8 - - + -
225B GLY 3.6 3.4 - - - -
226B HIS* 3.6 28.3 - - + -
274B LEU* 3.7 19.3 - - + -
278B LEU* 5.7 4.0 - - + -
292B ALA* 4.4 21.1 - - + -
296B VAL* 4.0 28.7 - - + -
330B ALA* 3.9 13.7 - - + -
331B LEU* 1.3 72.5 - - - +
333B VAL* 1.3 60.4 + - - +
334B PHE* 3.8 11.2 - - + -
342B ALA* 3.0 7.6 - - - +
343B GLY* 3.0 36.6 + - - +
344B LEU* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.6 38.8 - - + -
4B GLY* 3.8 14.6 - - - +
5B PHE* 3.7 23.8 - - + -
202B VAL* 3.7 24.2 - - + +
223B LEU 4.0 0.2 - - - +
224B LEU* 3.4 1.7 - - - -
225B GLY 2.7 36.9 + - - -
331B LEU* 4.0 8.5 - - + -
332B LEU* 1.3 79.0 - - - +
334B PHE* 1.3 63.5 + - - +
341B GLY 3.3 11.0 - - - +
342B ALA* 4.1 8.1 - - + -
364B LEU* 4.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.4 5.2 - - - -
223B LEU* 3.1 26.5 - - + +
224B LEU* 4.3 6.1 - - + -
278B LEU* 4.7 8.5 - - + -
288B PRO* 3.6 31.4 - - + -
289B LEU* 3.6 35.7 - - + -
292B ALA* 4.4 14.8 - - + -
332B LEU* 3.8 31.9 - - + -
333B VAL* 1.3 79.7 - - - +
335B SER* 1.3 64.3 + - - +
339B ILE* 4.8 3.4 - - + -
340B VAL* 3.3 3.1 - - - +
341B GLY* 2.9 47.7 + - - +
342B ALA* 3.9 7.4 - - - -
343B GLY* 4.1 3.6 - - - -
389B MET* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B MET* 3.8 18.3 - - - +
172B THR* 5.0 2.8 - - - +
200B PHE* 3.6 31.1 - - - -
202B VAL* 4.4 1.3 - - - +
222B ARG 4.3 1.9 - - - +
223B LEU* 3.0 29.2 + - - +
334B PHE* 1.3 77.8 - - - +
336B ASP* 1.3 58.7 + - - +
337B GLY* 2.8 21.6 + - - -
339B ILE 2.8 21.0 + - - -
340B VAL* 3.8 8.3 - - - +
394B LEU* 5.1 0.5 - - - +
----------------------------------------------------------
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