Contacts of the helix formed by residues 302 - 320 (chain B) in PDB entry 4OSI
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 GLY 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLY 5.5 0.6 + - - -
300B HIS* 3.0 2.5 + - - -
301B ASP* 1.3 73.4 - - - +
303B GLY* 1.3 58.7 + - - +
304B LYS 3.2 3.6 - - - -
305B GLN* 2.8 26.3 + - - +
306B ALA* 3.0 10.9 + - - +
334B HIS 6.2 0.2 - - - -
336B GLY 5.8 0.4 - - - -
337B GLY 5.6 1.8 + - - -
3G T 3.7 32.6 + - - +
4G C 3.8 15.8 + - - -
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLY 5.6 0.4 + - - -
271B ALA* 5.0 3.6 - - - +
297B ILE 3.7 13.0 - - - -
298B ALA* 3.5 21.5 - - - -
300B HIS* 3.2 10.3 + - - +
301B ASP 3.7 0.2 - - - -
302B GLY* 1.3 72.5 - - - +
304B LYS* 1.3 58.7 + - - +
306B ALA* 3.7 5.1 - - - +
307B LEU* 2.8 39.9 + - - +
3G T 4.9 0.6 + - - -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR* 3.8 27.2 - - + +
271B ALA* 4.5 5.1 - - - +
274B ALA* 3.5 35.0 - - + +
278B TRP* 3.6 23.3 - - + -
302B GLY 3.2 1.0 + - - -
303B GLY* 1.3 76.8 - - - +
305B GLN* 1.3 61.5 + - - +
307B LEU* 3.5 1.0 + - - -
308B GLU* 2.9 41.7 + - - +
3G T 4.3 16.5 + - - +
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Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLY 2.8 12.6 + - - +
304B LYS* 1.3 80.6 - - - +
306B ALA* 1.3 55.5 + - - +
308B GLU* 3.5 19.8 - - - +
309B THR* 2.5 38.6 + - - -
338B LYS* 4.0 34.8 - - + +
3G T 3.6 48.9 + - - +
4G C 4.2 4.0 - - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 3.6 26.7 - - + +
300B HIS* 6.4 0.2 - - + -
302B GLY 3.0 12.2 + - - +
303B GLY* 3.9 5.6 - - - +
305B GLN* 1.3 77.2 - - - +
307B LEU* 1.3 56.0 - - - +
309B THR* 3.3 2.4 + - - -
310B VAL* 2.9 34.9 + - - +
332B ALA* 3.9 17.0 - - + +
334B HIS 5.3 1.6 - - - +
337B GLY* 4.1 14.8 - - - +
338B LYS 4.0 10.2 - - - +
341B LEU* 5.8 0.2 - - - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA 4.8 0.2 - - - +
274B ALA* 4.1 15.5 - - + -
275B VAL* 4.2 10.3 - - + +
278B TRP* 4.1 13.5 - - + -
282B LEU* 3.8 33.0 - - + -
294B VAL* 4.1 11.7 - - + +
297B ILE* 3.9 25.4 - - + -
298B ALA* 3.8 18.2 - - + -
303B GLY 2.8 32.2 + - - +
304B LYS* 3.7 9.0 - - - +
306B ALA* 1.3 71.7 - - - +
308B GLU* 1.3 61.3 + - - +
309B THR 2.9 6.0 + - - -
310B VAL* 3.2 17.8 - - - +
311B GLN* 3.4 17.5 + - - +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TRP* 3.9 30.6 - - + -
304B LYS* 2.9 28.4 + - - +
305B GLN* 3.3 23.5 + - - +
307B LEU* 1.3 76.7 - - - +
309B THR* 1.3 60.6 + - - +
311B GLN* 4.3 10.9 + - - +
312B ARG* 3.6 23.1 + - - +
338B LYS* 6.2 3.1 - - - -
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLN 2.5 21.7 + - - -
306B ALA 3.8 2.7 - - - -
307B LEU 2.9 0.6 - - - -
308B GLU* 1.3 79.2 - - - +
310B VAL* 1.3 60.7 + - - +
311B GLN 3.1 2.0 - - - -
312B ARG* 3.0 29.2 + - - +
313B LEU* 2.9 33.2 + - + +
338B LYS* 2.8 35.1 - - + +
341B LEU* 3.8 28.0 - - + -
342B GLU* 4.6 0.2 - - + -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 4.6 17.3 - - + -
287B LEU* 3.9 3.7 - - + +
289B LEU* 5.1 5.2 - - + -
297B ILE* 4.5 14.8 - - + -
306B ALA 2.9 20.9 + - - +
307B LEU* 3.2 22.2 - - - +
309B THR* 1.3 74.4 - - - +
311B GLN* 1.3 58.5 + - + +
312B ARG 3.4 0.2 - - - -
314B LEU* 2.9 41.0 + - + +
328B VAL* 4.6 11.7 - - + -
329B VAL* 5.6 0.7 - - + -
332B ALA* 3.4 30.7 - - + -
341B LEU* 3.6 15.5 - - + -
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TRP* 3.9 23.1 - - - +
281B ALA* 3.7 26.1 - - - +
282B LEU* 3.7 21.0 + - + +
287B LEU* 3.5 28.1 - - + +
307B LEU 3.4 17.7 + - - +
308B GLU* 4.4 11.6 + - - +
309B THR 3.1 1.0 - - - -
310B VAL* 1.3 82.4 - - + +
312B ARG* 1.3 60.5 + - - +
315B PRO* 3.5 19.2 - - - +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 3.6 22.3 + - - +
309B THR* 3.0 23.3 + - - +
311B GLN* 1.3 78.7 - - - +
313B LEU* 1.3 78.3 + - + +
315B PRO* 4.4 3.6 - - - +
316B VAL* 4.7 9.9 - - - +
338B LYS* 4.4 6.5 - - - +
342B GLU* 3.0 40.4 + - - +
345B GLN* 5.7 0.6 - - - +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 2.9 19.6 + - + +
312B ARG* 1.3 115.0 - - + +
314B LEU* 1.3 66.5 + - - +
315B PRO* 3.4 3.1 - - - -
316B VAL* 3.5 7.3 + - + +
317B LEU* 2.9 42.4 + - + +
341B LEU* 3.9 17.5 - - + +
342B GLU* 3.9 34.3 - - + +
345B GLN* 4.0 29.6 - - + +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO 5.5 4.0 - - - +
287B LEU* 3.9 25.6 - - + +
289B LEU* 5.2 13.9 - - + -
310B VAL* 2.9 25.8 + - + +
313B LEU* 1.3 73.6 - - - +
315B PRO* 1.3 77.3 - - + +
317B LEU* 3.4 2.0 + - - -
318B CYS* 3.1 35.4 + - - -
325B PRO* 4.4 19.5 - - + +
328B VAL* 3.5 41.0 - - + +
329B VAL* 5.2 3.6 - - + -
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Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO* 5.4 15.7 - - + +
287B LEU* 4.7 7.4 - - + -
310B VAL 4.1 0.2 - - - +
311B GLN 3.5 21.3 - - - +
312B ARG 4.4 2.2 - - - +
313B LEU* 3.4 5.2 - - - +
314B LEU* 1.3 102.4 - - + +
316B VAL* 1.3 66.6 + - + +
318B CYS* 3.3 2.7 + - + +
319B GLN* 3.2 37.6 + - + +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG 4.7 11.7 - - - +
313B LEU* 3.5 11.4 + - + +
314B LEU 3.4 0.2 - - - -
315B PRO* 1.3 84.9 - - + +
317B LEU* 1.3 69.3 + - + +
318B CYS 3.1 0.3 + - - -
319B GLN* 4.8 9.2 - - - +
320B ALA* 3.0 35.7 + - + +
321B HIS* 6.4 0.9 - - + -
345B GLN* 5.9 5.8 - - + -
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 2.9 50.4 + - + +
314B LEU* 3.9 4.7 - - - +
316B VAL* 1.3 75.9 - - + +
318B CYS* 1.3 57.7 + - - +
321B HIS* 3.1 46.2 - - + +
323B LEU* 3.4 17.3 - - + +
328B VAL* 4.7 13.0 - - + -
331B ILE* 6.1 0.9 - - + -
341B LEU* 4.1 26.9 - - + +
344B VAL* 4.5 11.4 - - + -
345B GLN* 3.9 34.5 - - + +
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Residues in contact with CYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 3.1 35.6 + - + +
315B PRO* 3.7 6.7 - - + +
317B LEU* 1.3 73.9 - - - +
319B GLN* 1.3 69.0 + - + +
321B HIS 3.1 0.2 + - - -
322B GLY* 2.8 27.9 + - - -
323B LEU 2.9 28.0 - - - +
325B PRO* 4.0 19.7 - - - -
328B VAL* 4.1 7.4 - - - -
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Residues in contact with GLN 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PRO* 3.2 27.5 + - - +
316B VAL* 3.9 7.9 - - - +
318B CYS* 1.3 80.8 - - + +
320B ALA* 1.3 60.5 - - + +
321B HIS 3.3 2.3 + - - -
322B GLY* 3.8 4.5 + - - -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 3.0 23.4 + - + +
319B GLN* 1.3 79.3 - - + +
321B HIS* 1.3 81.4 + - + +
322B GLY 3.8 0.2 - - - -
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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) + - + + + + + -
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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