Contacts of the helix formed by residues 319 - 331 (chain B) in PDB entry 1OGS
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 PRO 319 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.8 16.6 - - + -
317B LEU 4.8 0.4 - - - -
318B ALA* 1.3 79.3 - - - +
320B ALA* 1.3 57.4 + - - +
321B LYS* 3.5 1.6 - - + +
322B ALA* 4.1 23.3 - - + +
323B THR* 2.7 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 4.1 10.1 - - - +
318B ALA 3.0 6.0 + - - -
319B PRO* 1.3 71.6 - - - +
321B LYS* 1.3 60.4 + - - +
323B THR* 3.1 4.4 + - - -
324B LEU* 2.9 37.1 + - + +
325B GLY 3.2 4.2 + - - -
369B THR* 3.7 29.6 - - + -
373B TYR* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PRO* 3.5 1.0 - - + +
320B ALA* 1.3 78.9 - - - +
322B ALA* 1.3 60.0 + - - +
325B GLY* 3.0 7.9 + - - +
326B GLU* 3.0 27.1 + - - +
329B ARG* 5.1 12.7 - - - +
373B TYR* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU 4.3 0.2 - - - +
289B PRO* 3.6 19.4 - - - +
319B PRO* 3.8 25.5 + - + +
320B ALA 3.5 0.2 - - - -
321B LYS* 1.3 79.4 - - - +
323B THR* 1.3 59.3 + - + +
326B GLU* 3.7 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 3.3 52.1 - - + +
286B LEU* 4.2 16.2 - - + -
288B LEU* 3.7 16.8 - - - +
289B PRO 4.6 0.5 - - - -
319B PRO* 2.7 27.9 + - + +
320B ALA* 3.1 2.8 + - - -
321B LYS 3.1 0.6 - - - -
322B ALA* 1.3 82.0 - - + +
324B LEU* 1.3 68.0 + - - +
325B GLY 3.3 0.7 - - - -
326B GLU 3.7 0.5 + - - -
327B THR* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 4.5 9.6 - - + +
288B LEU* 4.2 12.1 - - + -
310B VAL* 4.3 3.4 - - + -
312B TRP* 3.6 40.2 - - + -
320B ALA* 2.9 12.7 + - + +
323B THR* 1.3 88.0 + - - +
325B GLY* 1.3 64.0 + - - +
327B THR* 3.5 1.9 + - - -
328B HIS* 3.1 21.0 + - - +
336B LEU* 3.5 33.2 - - + +
369B THR* 5.1 0.7 - - + +
370B ASN* 4.4 6.5 - - - +
373B TYR* 3.9 27.1 - - + +
374B HIS* 4.3 0.3 - - - -
375B VAL* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ALA 3.2 3.6 + - - -
321B LYS* 3.0 22.0 + - - -
324B LEU* 1.3 80.9 - - - +
326B GLU* 1.3 61.7 + - - +
328B HIS* 3.2 4.2 + - - +
329B ARG* 3.1 21.6 + - - +
373B TYR* 4.2 11.8 - - - -
374B HIS* 4.5 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PRO* 4.2 11.7 - - + -
293B LYS* 5.5 2.2 - - - +
321B LYS* 3.0 9.1 + - - +
322B ALA* 3.7 20.4 - - - +
323B THR 3.7 1.0 + - - +
325B GLY* 1.3 74.5 - - - +
327B THR* 1.3 58.1 + - - +
329B ARG* 3.2 42.5 + - - -
330B LEU* 2.9 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 3.5 15.2 - - + +
289B PRO* 3.3 20.8 - - - +
292B ALA* 3.9 13.9 - - + -
308B ILE* 3.7 29.8 - - + -
323B THR 2.7 22.7 + - - -
324B LEU* 3.7 6.5 - - - -
326B GLU* 1.3 78.0 - - - +
328B HIS* 1.3 57.0 + - - +
330B LEU* 3.3 3.0 + - - -
331B PHE* 2.8 32.9 + - + +
334B THR 6.0 0.2 - - - +
336B LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN* 6.3 1.8 - - + -
324B LEU 3.1 9.1 + - - +
325B GLY 3.6 4.3 - - - +
327B THR* 1.3 75.6 - - - +
329B ARG* 1.3 62.1 + - - +
331B PHE 4.2 5.1 + - - -
332B PRO* 2.8 67.8 + - + +
334B THR 5.8 1.9 + - - -
336B LEU* 4.3 7.5 - - + +
374B HIS* 3.3 63.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LYS* 5.1 13.9 - - - +
325B GLY 3.1 13.4 + - - +
326B GLU* 3.2 37.9 + - - +
328B HIS* 1.3 84.3 - - + +
330B LEU* 1.3 62.7 + - + +
332B PRO* 3.6 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PRO* 4.0 15.3 - - + -
293B LYS* 3.3 41.5 - - + +
326B GLU* 2.9 38.1 + - + +
327B THR* 4.7 0.2 - - - -
329B ARG* 1.3 78.5 - - + +
331B PHE* 1.3 87.1 + - + +
332B PRO* 3.5 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.8 37.7 - - + -
293B LYS* 3.9 14.8 - - + -
296B LEU* 3.4 50.0 - - + -
297B THR* 4.2 11.9 - - + -
308B ILE* 5.4 1.3 - - + -
327B THR* 2.8 20.9 + - + +
328B HIS* 3.2 6.9 + - - +
330B LEU* 1.3 106.3 - - + +
332B PRO* 1.3 64.3 - - - +
333B ASN 3.2 4.1 + - - -
334B THR* 3.3 25.0 + - - +
----------------------------------------------------------
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